[kepler-dev] PIW workflow
Bertram Ludaescher
ludaesch at ucdavis.edu
Mon Nov 6 14:04:42 PST 2006
Thanks Dan for the quick reply!
Anybody else knows of the latest PIW whereabouts? (Maybe a functional
fragment of it?)
Bertram
>>> On Mon, 06 Nov 2006 13:34:40 -0800
>>> Dan Higgins <higgins at nceas.ucsb.edu> wrote:
DH>
DH> Hi Alex,
DH> Attached is the PIW.xml workflow that is still in the
DH> $Kepler/workflows/spa/PIW/ directory of the Kepler checkout from CVS.
DH> However, I think it is now out-of-date and does not function correctly.
DH> Note that the workflows directory was not included in the last installer
DH> version because a number of workflows there no longer operate correctly.
DH>
DH> Dan Higgins
DH> NCEAS
DH>
DH> ----
DH>
DH> Alex Chen wrote:
>> Hi,
>>
>> Does anyone know where or how to obtain a XML copy of the PIW workflow,
>> which were used to exemplified in many presentations. Thanks!
>>
>> Alex Chen
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Kepler-dev mailing list
>> Kepler-dev at ecoinformatics.org
>> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/kepler-dev
>>
DH>
DH>
DH> --
DH> *******************************************************************
DH> Dan Higgins higgins at nceas.ucsb.edu
DH> http://www.nceas.ucsb.edu/ Ph: 805-893-5127
DH> National Center for Ecological Analysis and Synthesis (NCEAS) Marine Science Building - Room 3405
DH> Santa Barbara, CA 93195
DH> *******************************************************************
DH>
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DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> <port name="trueOutput" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="falseOutput" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="BooleanSwitch3" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[730.0, 50.0]">
DH> </property>
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> <port name="trueOutput" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="falseOutput" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Count" class="ptolemy.actor.TypedCompositeActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="660.0, 280.0">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="50.0, 120.0">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="EAST">
DH> </property>
DH> </port>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="425.0, 165.0">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="WEST">
DH> </property>
DH> </port>
DH> <port name="reset" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="50.0, 165.0">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <entity name="Expression" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="reset ? 0 : input + previous">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="255.0, 165.0">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="WEST">
DH> </property>
DH> </port>
DH> <port name="reset" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> </port>
DH> <port name="previous" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> </port>
DH> </entity>
DH> <entity name="SampleDelay" class="ptolemy.domains.sdf.lib.SampleDelay">
DH> <property name="initialOutputs" class="ptolemy.data.expr.Parameter" value="{0}">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="initialOutputs">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="115.0, 120.0">
DH> </property>
DH> </entity>
DH> <entity name="SampleDelay2" class="ptolemy.domains.sdf.lib.SampleDelay">
DH> <property name="initialOutputs" class="ptolemy.data.expr.Parameter" value="{0}">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="initialOutputs">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="295.0, 245.0">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="EAST">
DH> </property>
DH> </port>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="WEST">
DH> </property>
DH> </port>
DH> </entity>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="380.0, 165.0">
DH> </vertex>
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="input" relation="relation3"/>
DH> <link port="output" relation="relation"/>
DH> <link port="reset" relation="relation5"/>
DH> <link port="Expression.output" relation="relation"/>
DH> <link port="Expression.input" relation="relation4"/>
DH> <link port="Expression.reset" relation="relation5"/>
DH> <link port="Expression.previous" relation="relation2"/>
DH> <link port="SampleDelay.input" relation="relation3"/>
DH> <link port="SampleDelay.output" relation="relation4"/>
DH> <link port="SampleDelay2.input" relation="relation"/>
DH> <link port="SampleDelay2.output" relation="relation2"/>
DH> </entity>
DH> <entity name="CheckSegmentLength" class="ptolemy.actor.TypedCompositeActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[595.0, 60.0]">
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={190, 353, 939, 457}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[719, 210]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{359.5, 105.0}">
DH> </property>
DH> <port name="HomologRecord" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="{35.0, 40.0}">
DH> </property>
DH> </port>
DH> <port name="OutRecord" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[632.3341369628906, 52.009765625]">
DH> </property>
DH> </port>
DH> <port name="Pass" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[632.3341369628906, 102.009765625]">
DH> </property>
DH> </port>
DH> <entity name="Length" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.length()">
DH> <property name="style" class="ptolemy.actor.gui.style.LineStyle">
DH> </property>
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[390.99999237060547, 92.0]">
DH> </property>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> </port>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Minimum Length" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="abs(End - Start) + 500">
DH> <property name="style" class="ptolemy.actor.gui.style.LineStyle">
DH> </property>
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[345.99999237060547, 157.0]">
DH> </property>
DH> <port name="Start" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="End" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="RetrieveSequenceSegment" class="ptolemy.actor.TypedCompositeActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[175.0, 90.0]">
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={-113, 333, 1251, 520}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[1031, 413]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{515.5, 206.5}">
DH> </property>
DH> <port name="GeneRecord" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="30.0, 245.0">
DH> </property>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="Sequence" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[960.0, 305.0]">
DH> </property>
DH> </port>
DH> <entity name="subtract" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="positive ? input - 1501 : input - 1">
DH> <property name="style" class="ptolemy.actor.gui.style.LineStyle">
DH> </property>
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[297.0, 205.0]">
DH> </property>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="EAST">
DH> </property>
DH> </port>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="WEST">
DH> </property>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> </port>
DH> <port name="positive" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Remove Noncontigs" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.replaceAll(".*[N,n]{11,}", "")">
DH> <property name="style" class="ptolemy.actor.gui.style.LineStyle">
DH> </property>
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="{825.0, 305.0}">
DH> </property>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="EAST">
DH> </property>
DH> </port>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="WEST">
DH> </property>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="WebService" class="org.sdm.spa.WebService">
DH> <property name="wsdlUrl" class="ptolemy.data.expr.StringParameter" value="http://sdm2.csc.ncsu.edu:8080/axis/services/urn:spa.service.Genbank?wsdl">
DH> </property>
DH> <property name="methodName" class="ptolemy.data.expr.StringParameter" value="service">
DH> </property>
DH> <property name="userName" class="ptolemy.data.expr.StringParameter" value="user1">
DH> </property>
DH> <property name="password" class="ptolemy.data.expr.StringParameter" value="pass1">
DH> </property>
DH> <property name="hasTrigger" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[165.0, 110.0]">
DH> </property>
DH> <port name="in0" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_showName" class="ptolemy.kernel.util.Attribute">
DH> </property>
DH> </port>
DH> <port name="serviceReturn" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_showName" class="ptolemy.kernel.util.Attribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="RecordDisassembler" class="ptolemy.actor.lib.RecordDisassembler">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[102.0, 225.0]">
DH> </property>
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="GeneID" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="Start" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="End" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="QueryStart" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="QueryEnd" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Comparator" class="ptolemy.actor.lib.logic.Comparator">
DH> <property name="comparison" class="ptolemy.kernel.util.StringAttribute" value="<">
DH> <property name="style" class="ptolemy.actor.gui.style.ChoiceStyle">
DH> <property name="gt" class="ptolemy.kernel.util.StringAttribute" value=">">
DH> </property>
DH> <property name="ge" class="ptolemy.kernel.util.StringAttribute" value=">=">
DH> </property>
DH> <property name="lt" class="ptolemy.kernel.util.StringAttribute" value="<">
DH> </property>
DH> <property name="le" class="ptolemy.kernel.util.StringAttribute" value="<=">
DH> </property>
DH> <property name="eq" class="ptolemy.kernel.util.StringAttribute" value="==">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.AttributeValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="comparison">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[172.0, 380.0]">
DH> </property>
DH> </entity>
DH> <entity name="add" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="positive ? input : input + 1500">
DH> <property name="style" class="ptolemy.actor.gui.style.LineStyle">
DH> </property>
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[337.0, 255.0]">
DH> </property>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="EAST">
DH> </property>
DH> </port>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="WEST">
DH> </property>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> </port>
DH> <port name="positive" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="ReverseComplement" class="ptolemy.actor.TypedCompositeActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[650.0, 305.0]">
DH> </property>
DH> <property name="Annotation" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="Reverse the sequence and complement it. A <-> T G <-> C">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[15.0, 20.0]">
DH> </property>
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={286, 317, 940, 515}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[726, 407]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{363.0, 203.5}">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[30.0, 135.0]">
DH> </property>
DH> </port>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[645.0, 125.0]">
DH> </property>
DH> </port>
DH> <port name="positive" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[30.0, 195.0]">
DH> </property>
DH> </port>
DH> <entity name="StringReverse" class="org.sdm.spa.StringReverse">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[220.0, 190.0]">
DH> </property>
DH> </entity>
DH> <entity name="BooleanSwitch" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[130.0, 135.0]">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.replaceAll("A", "B")">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[132.33467864990234, 274.0272979736328]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression2" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.replaceAll("T", "A")">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[312.33467864990234, 274.0272979736328]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression3" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.replaceAll("B", "T")">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[492.33467864990234, 274.0272979736328]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression4" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.replaceAll("B", "C")">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[492.33467864990234, 349.0272979736328]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression5" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.replaceAll("G", "B")">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[135.0837631225586, 349.2769775390625]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression6" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.replaceAll("C", "G")">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[315.0837631225586, 349.2769775390625]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[600.0, 125.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation6" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation8" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation9" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation10" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="input" relation="relation"/>
DH> <link port="output" relation="relation5"/>
DH> <link port="positive" relation="relation2"/>
DH> <link port="StringReverse.input" relation="relation4"/>
DH> <link port="StringReverse.output" relation="relation3"/>
DH> <link port="BooleanSwitch.input" relation="relation"/>
DH> <link port="BooleanSwitch.control" relation="relation2"/>
DH> <link port="BooleanSwitch.trueOutput" relation="relation5"/>
DH> <link port="BooleanSwitch.falseOutput" relation="relation4"/>
DH> <link port="Expression.output" relation="relation6"/>
DH> <link port="Expression.input" relation="relation3"/>
DH> <link port="Expression2.output" relation="relation7"/>
DH> <link port="Expression2.input" relation="relation6"/>
DH> <link port="Expression3.output" relation="relation10"/>
DH> <link port="Expression3.input" relation="relation7"/>
DH> <link port="Expression4.output" relation="relation5"/>
DH> <link port="Expression4.input" relation="relation8"/>
DH> <link port="Expression5.output" relation="relation9"/>
DH> <link port="Expression5.input" relation="relation10"/>
DH> <link port="Expression6.output" relation="relation8"/>
DH> <link port="Expression6.input" relation="relation9"/>
DH> </entity>
DH> <entity name="Expression" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.substring(max(0, start), min(input.length(), end))">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[575.0, 145.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="start" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> <port name="end" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation8" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation9" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation10" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation12" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[365.0, 315.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation6" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation11" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation13" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="GeneRecord" relation="relation"/>
DH> <link port="Sequence" relation="relation8"/>
DH> <link port="subtract.output" relation="relation5"/>
DH> <link port="subtract.input" relation="relation3"/>
DH> <link port="subtract.positive" relation="relation2"/>
DH> <link port="Remove Noncontigs.output" relation="relation8"/>
DH> <link port="Remove Noncontigs.input" relation="relation6"/>
DH> <link port="WebService.in0" relation="relation4"/>
DH> <link port="WebService.serviceReturn" relation="relation7"/>
DH> <link port="RecordDisassembler.input" relation="relation"/>
DH> <link port="RecordDisassembler.GeneID" relation="relation4"/>
DH> <link port="RecordDisassembler.Start" relation="relation3"/>
DH> <link port="RecordDisassembler.End" relation="relation12"/>
DH> <link port="RecordDisassembler.QueryStart" relation="relation9"/>
DH> <link port="RecordDisassembler.QueryEnd" relation="relation10"/>
DH> <link port="Comparator.left" relation="relation9"/>
DH> <link port="Comparator.right" relation="relation10"/>
DH> <link port="Comparator.output" relation="relation2"/>
DH> <link port="add.output" relation="relation11"/>
DH> <link port="add.input" relation="relation12"/>
DH> <link port="add.positive" relation="relation2"/>
DH> <link port="ReverseComplement.input" relation="relation13"/>
DH> <link port="ReverseComplement.output" relation="relation6"/>
DH> <link port="ReverseComplement.positive" relation="relation2"/>
DH> <link port="Expression.output" relation="relation13"/>
DH> <link port="Expression.input" relation="relation7"/>
DH> <link port="Expression.start" relation="relation5"/>
DH> <link port="Expression.end" relation="relation11"/>
DH> </entity>
DH> <entity name="Compare Length" class="ptolemy.actor.lib.logic.Comparator">
DH> <property name="comparison" class="ptolemy.kernel.util.StringAttribute" value=">">
DH> <property name="style" class="ptolemy.actor.gui.style.ChoiceStyle">
DH> <property name="gt" class="ptolemy.kernel.util.StringAttribute" value=">">
DH> </property>
DH> <property name="ge" class="ptolemy.kernel.util.StringAttribute" value=">=">
DH> </property>
DH> <property name="lt" class="ptolemy.kernel.util.StringAttribute" value="<">
DH> </property>
DH> <property name="le" class="ptolemy.kernel.util.StringAttribute" value="<=">
DH> </property>
DH> <property name="eq" class="ptolemy.kernel.util.StringAttribute" value="==">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="tolerance" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.AttributeValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="comparison">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="6">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[500.99999237060547, 102.0]">
DH> </property>
DH> <port name="left" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="right" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="RecordDisassembler" class="ptolemy.actor.lib.RecordDisassembler">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[150.99999237060547, 137.0]">
DH> </property>
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="{Start=int,End=int}">
DH> </property>
DH> </port>
DH> <port name="Start" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="End" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="RecordUpdater" class="ptolemy.actor.lib.RecordUpdater">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[330.99999237060547, 32.0]">
DH> </property>
DH> <port name="Sequence" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> </port>
DH> </entity>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[235.99999237060547, 92.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation6" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[120.99999237060547, 42.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation8" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="HomologRecord" relation="relation6"/>
DH> <link port="OutRecord" relation="relation8"/>
DH> <link port="Pass" relation="relation7"/>
DH> <link port="Length.output" relation="relation4"/>
DH> <link port="Length.input" relation="relation5"/>
DH> <link port="Minimum Length.output" relation="relation3"/>
DH> <link port="Minimum Length.Start" relation="relation"/>
DH> <link port="Minimum Length.End" relation="relation2"/>
DH> <link port="RetrieveSequenceSegment.GeneRecord" relation="relation6"/>
DH> <link port="RetrieveSequenceSegment.Sequence" relation="relation5"/>
DH> <link port="Compare Length.left" relation="relation4"/>
DH> <link port="Compare Length.right" relation="relation3"/>
DH> <link port="Compare Length.output" relation="relation7"/>
DH> <link port="RecordDisassembler.input" relation="relation6"/>
DH> <link port="RecordDisassembler.Start" relation="relation"/>
DH> <link port="RecordDisassembler.End" relation="relation2"/>
DH> <link port="RecordUpdater.output" relation="relation8"/>
DH> <link port="RecordUpdater.input" relation="relation6"/>
DH> <link port="RecordUpdater.Sequence" relation="relation5"/>
DH> </entity>
DH> <entity name="BooleanSwitch" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[455.0, 60.0]">
DH> </property>
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> <port name="trueOutput" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="falseOutput" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="CheckStartIndex" class="ptolemy.actor.TypedCompositeActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[350.0, 70.0]">
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={140, 413, 905, 457}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[685, 348]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{342.5, 174.0}">
DH> </property>
DH> <port name="HomologRecord" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[40.0, 185.0]">
DH> </property>
DH> </port>
DH> <port name="OutRecord" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[570.0, 185.0]">
DH> </property>
DH> </port>
DH> <port name="Pass" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[570.0, 240.0]">
DH> </property>
DH> </port>
DH> <entity name="RecordDisassembler" class="ptolemy.actor.lib.RecordDisassembler">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[110.0, 220.0]">
DH> </property>
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="QueryStart" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="QueryEnd" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="QueryStart < QueryEnd ? QueryStart == 1 : QueryEnd == 1">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[370.0, 240.0]">
DH> </property>
DH> <port name="QueryStart" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="QueryEnd" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[85.0, 185.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="HomologRecord" relation="relation2"/>
DH> <link port="OutRecord" relation="relation2"/>
DH> <link port="Pass" relation="relation4"/>
DH> <link port="RecordDisassembler.input" relation="relation2"/>
DH> <link port="RecordDisassembler.QueryStart" relation="relation"/>
DH> <link port="RecordDisassembler.QueryEnd" relation="relation3"/>
DH> <link port="Expression.output" relation="relation4"/>
DH> <link port="Expression.QueryStart" relation="relation"/>
DH> <link port="Expression.QueryEnd" relation="relation3"/>
DH> </entity>
DH> <entity name="RecordUpdater" class="ptolemy.actor.lib.RecordUpdater">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[925.0, 140.0]">
DH> </property>
DH> <port name="Sequence" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression2" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="""">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[870.0, 170.0]">
DH> </property>
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="2" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="1">
DH> <property name="style" class="ptolemy.actor.gui.style.LineStyle">
DH> </property>
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[825.0, 225.0]">
DH> </property>
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="4" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="0">
DH> <property name="style" class="ptolemy.actor.gui.style.LineStyle">
DH> </property>
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[740.0, 210.0]">
DH> </property>
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
DH> </property>
DH> </port>
DH> </entity>
DH> <relation name="relation8" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[825.0, 50.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="205.0, 365.0">
DH> </vertex>
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[740.0, 150.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation6" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[740.0, 280.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation14" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation15" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="405.0, 270.0">
DH> </vertex>
DH> </relation>
DH> <relation name="relation16" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[120.0, 70.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation22" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation9" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation10" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation11" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation12" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation13" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation17" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="HomologRecord" relation="relation16"/>
DH> <link port="PassRecord" relation="relation8"/>
DH> <link port="FailRecord" relation="relation17"/>
DH> <link port="Expression.output" relation="relation7"/>
DH> <link port="Expression.input" relation="relation"/>
DH> <link port="RecordDisassembler.input" relation="relation16"/>
DH> <link port="RecordDisassembler.index" relation="relation"/>
DH> <link port=".output" relation="relation14"/>
DH> <link port=".input" relation="relation15"/>
DH> <link port="Seen two.left" relation="relation15"/>
DH> <link port="Seen two.right" relation="relation14"/>
DH> <link port="Seen two.output" relation="relation22"/>
DH> <link port="Comparator.left" relation="relation"/>
DH> <link port="Comparator.right" relation="relation7"/>
DH> <link port="Comparator.output" relation="relation2"/>
DH> <link port="BooleanSwitch2.input" relation="relation16"/>
DH> <link port="BooleanSwitch2.control" relation="relation22"/>
DH> <link port="BooleanSwitch2.trueOutput" relation="relation12"/>
DH> <link port="BooleanSwitch2.falseOutput" relation="relation5"/>
DH> <link port="BooleanSwitch3.input" relation="relation10"/>
DH> <link port="BooleanSwitch3.control" relation="relation11"/>
DH> <link port="BooleanSwitch3.trueOutput" relation="relation8"/>
DH> <link port="BooleanSwitch3.falseOutput" relation="relation5"/>
DH> <link port="Count.input" relation="relation6"/>
DH> <link port="Count.output" relation="relation15"/>
DH> <link port="Count.reset" relation="relation2"/>
DH> <link port="CheckSegmentLength.HomologRecord" relation="relation3"/>
DH> <link port="CheckSegmentLength.OutRecord" relation="relation10"/>
DH> <link port="CheckSegmentLength.Pass" relation="relation11"/>
DH> <link port="BooleanSwitch.input" relation="relation4"/>
DH> <link port="BooleanSwitch.control" relation="relation9"/>
DH> <link port="BooleanSwitch.trueOutput" relation="relation3"/>
DH> <link port="BooleanSwitch.falseOutput" relation="relation5"/>
DH> <link port="CheckStartIndex.HomologRecord" relation="relation12"/>
DH> <link port="CheckStartIndex.OutRecord" relation="relation4"/>
DH> <link port="CheckStartIndex.Pass" relation="relation9"/>
DH> <link port="RecordUpdater.output" relation="relation17"/>
DH> <link port="RecordUpdater.input" relation="relation5"/>
DH> <link port="RecordUpdater.Sequence" relation="relation13"/>
DH> <link port="Expression2.output" relation="relation13"/>
DH> <link port="Expression2.input" relation="relation5"/>
DH> <link port="2.output" relation="relation6"/>
DH> <link port="2.input" relation="relation8"/>
DH> <link port="4.output" relation="relation6"/>
DH> <link port="4.input" relation="relation5"/>
DH> </entity>
DH> <entity name="SequenceToArray" class="ptolemy.domains.sdf.lib.SequenceToArray">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[645.0, 240.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Run Transfac" class="ptolemy.actor.TypedCompositeActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[515.0, 435.0]">
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={88, 71, 1154, 679}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[934, 572]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{467.0, 286.0}">
DH> </property>
DH> <port name="GeneRecord" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[60.0, 310.0]">
DH> </property>
DH> </port>
DH> <port name="Record" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[855.0, 330.0]">
DH> </property>
DH> </port>
DH> <port name="log" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[550.0, 205.0]">
DH> </property>
DH> </port>
DH> <entity name="RecordDisassembler2" class="ptolemy.actor.lib.RecordDisassembler">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="178.5, 45.0">
DH> </property>
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <port name="Start" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="End" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="AccessionNumber" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="GeneID" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="Sequence" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="BLAST Output" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="">" + GeneID+"_"+AccessionNumber + "_" + Start + "_" + End + "\n" + Sequence + "\n"">
DH> <property name="style" class="ptolemy.actor.gui.style.LineStyle">
DH> </property>
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[520.0, 120.0]">
DH> </property>
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="EAST">
DH> </property>
DH> </port>
DH> <port name="Sequence" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
DH> </property>
DH> </port>
DH> <port name="GeneID" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
DH> </property>
DH> </port>
DH> <port name="AccessionNumber" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
DH> </property>
DH> </port>
DH> <port name="End" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
DH> </property>
DH> </port>
DH> <port name="Start" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="int">
DH> </property>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="MatchDisplay" class="org.sdm.spa.MatchDisplay">
DH> <doc>To display Match result</doc>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[255.0, 200.0]">
DH> </property>
DH> <port name="GI" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="EAST">
DH> </property>
DH> </port>
DH> <port name="Context" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="WEST">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Match" class="org.sdm.spa.WebServiceActor">
DH> <property name="nameSpace" class="ptolemy.kernel.util.StringAttribute" value="urn:spa.service.Match">
DH> </property>
DH> <property name="locationUrl" class="ptolemy.kernel.util.StringAttribute" value="http://sdm2.csc.ncsu.edu:8080/axis/servlet/AxisServlet">
DH> </property>
DH> <property name="userName" class="ptolemy.kernel.util.StringAttribute" value="user1">
DH> </property>
DH> <property name="password" class="ptolemy.kernel.util.StringAttribute" value="pass1">
DH> </property>
DH> <property name="method" class="ptolemy.kernel.util.StringAttribute" value="service">
DH> </property>
DH> <property name="paramName" class="ptolemy.kernel.util.StringAttribute" value="input">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[640.0, 265.0]">
DH> </property>
DH> <port name="result" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="WEST">
DH> </property>
DH> </port>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="EAST">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="RecordDisassembler" class="ptolemy.actor.lib.RecordDisassembler">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[165.0, 180.0]">
DH> </property>
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <port name="GeneID" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="RecordUpdater" class="ptolemy.actor.lib.RecordUpdater">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[795.0, 310.0]">
DH> </property>
DH> <port name="Fasta" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="Transfac" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="TransfacNames" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="TransfacSites" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.trim()">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[217.06365203857422, 377.11305236816406]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression2" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.split("\n")">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[352.0636520385742, 377.11305236816406]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression3" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="map( function(str:string) str.split("\t+") , input)">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[597.0636520385742, 377.11305236816406]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Get Index of Binding Site" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="map( function(arr:{string}) arr.length() > 3 ? arr(2).split(" ") : {"", ""}, input)">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[260.0, 510.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Get Transcription Factor Name" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="map( function(arr:{string}) arr.length() > 3 ? arr(1) : "", input)">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[575.0, 460.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Parse Out the Integer Part" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="map( function(arr:{string}) parseInt(arr(0)) * ("(+)" == arr(1) ? 1 : -1), input)">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[650.0, 510.0]">
DH> </property>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="{int}">
DH> </property>
DH> </port>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression4" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="""">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[605.0, 330.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation6" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[765.0, 255.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation10" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[120.0, 310.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation9" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[325.0, 265.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation8" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation11" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation12" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation13" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[60.0, 425.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation14" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation15" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation16" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation17" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="GeneRecord" relation="relation10"/>
DH> <link port="Record" relation="relation8"/>
DH> <link port="log" relation="relation7"/>
DH> <link port="RecordDisassembler2.input" relation="relation10"/>
DH> <link port="RecordDisassembler2.Start" relation="relation2"/>
DH> <link port="RecordDisassembler2.End" relation="relation"/>
DH> <link port="RecordDisassembler2.AccessionNumber" relation="relation4"/>
DH> <link port="RecordDisassembler2.GeneID" relation="relation3"/>
DH> <link port="RecordDisassembler2.Sequence" relation="relation5"/>
DH> <link port="BLAST Output.output" relation="relation6"/>
DH> <link port="BLAST Output.Sequence" relation="relation5"/>
DH> <link port="BLAST Output.GeneID" relation="relation3"/>
DH> <link port="BLAST Output.AccessionNumber" relation="relation4"/>
DH> <link port="BLAST Output.End" relation="relation"/>
DH> <link port="BLAST Output.Start" relation="relation2"/>
DH> <link port="MatchDisplay.GI" relation="relation7"/>
DH> <link port="MatchDisplay.Context" relation="relation9"/>
DH> <link port="Match.result" relation="relation7"/>
DH> <link port="Match.input" relation="relation6"/>
DH> <link port="RecordDisassembler.input" relation="relation10"/>
DH> <link port="RecordDisassembler.GeneID" relation="relation9"/>
DH> <link port="RecordUpdater.output" relation="relation8"/>
DH> <link port="RecordUpdater.input" relation="relation10"/>
DH> <link port="RecordUpdater.Fasta" relation="relation6"/>
DH> <link port="RecordUpdater.Transfac" relation="relation17"/>
DH> <link port="RecordUpdater.TransfacNames" relation="relation15"/>
DH> <link port="RecordUpdater.TransfacSites" relation="relation16"/>
DH> <link port="Expression.output" relation="relation11"/>
DH> <link port="Expression.input" relation="relation7"/>
DH> <link port="Expression2.output" relation="relation12"/>
DH> <link port="Expression2.input" relation="relation11"/>
DH> <link port="Expression3.output" relation="relation13"/>
DH> <link port="Expression3.input" relation="relation12"/>
DH> <link port="Get Index of Binding Site.output" relation="relation14"/>
DH> <link port="Get Index of Binding Site.input" relation="relation13"/>
DH> <link port="Get Transcription Factor Name.output" relation="relation15"/>
DH> <link port="Get Transcription Factor Name.input" relation="relation13"/>
DH> <link port="Parse Out the Integer Part.output" relation="relation16"/>
DH> <link port="Parse Out the Integer Part.input" relation="relation14"/>
DH> <link port="Expression4.output" relation="relation17"/>
DH> <link port="Expression4.input" relation="relation7"/>
DH> </entity>
DH> <entity name="Synchronizer" class="org.sdm.spa.Synchronizer">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[540.25, 346.25]">
DH> </property>
DH> <port name="FunctionInput" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="WEST">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="FunctionOutput" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="EAST">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Fasta" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="""">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[465.91138458251953, 516.7907867431641]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="RecordUpdater" class="ptolemy.actor.lib.RecordUpdater">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[565.9113845825195, 506.79078674316406]">
DH> </property>
DH> <port name="Fasta" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="Transfac" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="TransfacNames" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> <port name="TransfacSites" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Transfac" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="""">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[465.91138458251953, 551.7907867431641]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="TransfacSites" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="{0}">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[465.91138458251953, 631.7907867431641]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="TransfacNames" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="{""}">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[465.91138458251953, 591.7907867431641]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Blast Web Service" class="org.sdm.spa.WebServiceActor">
DH> <property name="nameSpace" class="ptolemy.kernel.util.StringAttribute" value="urn:spa.service.Blast">
DH> </property>
DH> <property name="locationUrl" class="ptolemy.kernel.util.StringAttribute" value="http://sdm2.csc.ncsu.edu:8080/axis/servlet/AxisServlet">
DH> </property>
DH> <property name="userName" class="ptolemy.kernel.util.StringAttribute" value="user1">
DH> </property>
DH> <property name="password" class="ptolemy.kernel.util.StringAttribute" value="pass1">
DH> </property>
DH> <property name="method" class="ptolemy.kernel.util.StringAttribute" value="service">
DH> </property>
DH> <property name="paramName" class="ptolemy.kernel.util.StringAttribute" value="input">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[305.0, 165.0]">
DH> </property>
DH> <property name="_imagePath" class="ptolemy.kernel.util.StringAttribute" value="C:\SDM-SSDBM03\blast1.gif">
DH> </property>
DH> </entity>
DH> <entity name="Debug" class="org.sdm.spa.Debug">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[305.0, 70.0]">
DH> </property>
DH> <property name="debug" class="ptolemy.data.expr.Parameter" value="debug_blast">
DH> </property>
DH> <property name="filename" class="ptolemy.data.expr.Parameter" value="CWD + "/workflows/spa/PIW/debug/PIW-BLAST.txt"">
DH> </property>
DH> </entity>
DH> <relation name="relation6" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[115.0, 230.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[245.0, 280.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation11" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation12" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[590.0, 425.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation10" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[430.75000762939453, 478.75001525878906]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation13" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation15" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation16" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation8" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation14" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation17" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation18" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation19" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation9" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="Gene Accession Number" relation="relation6"/>
DH> <link port="Fasta Output" relation="relation8"/>
DH> <link port="log_blast" relation="relation2"/>
DH> <link port="log_transfac" relation="relation14"/>
DH> <link port="Display.input" relation="relation6"/>
DH> <link port="Display.input" relation="relation"/>
DH> <link port="Process Blast.Log" relation="relation2"/>
DH> <link port="Process Blast.Blast" relation="relation19"/>
DH> <link port="Process Blast.AccessionNumber" relation="relation6"/>
DH> <link port="Process Blast.Sequence" relation="relation"/>
DH> <link port="Process Blast.HomologRecords" relation="relation3"/>
DH> <link port="Process Blast.Length" relation="relation9"/>
DH> <link port="Get Sequence.AccessionNumber" relation="relation6"/>
DH> <link port="Get Sequence.Sequence" relation="relation"/>
DH> <link port="Filter.HomologRecord" relation="relation4"/>
DH> <link port="Filter.PassRecord" relation="relation5"/>
DH> <link port="Filter.FailRecord" relation="relation10"/>
DH> <link port="SequenceToArray.input" relation="relation11"/>
DH> <link port="SequenceToArray.output" relation="relation8"/>
DH> <link port="SequenceToArray.arrayLength" relation="relation9"/>
DH> <link port="Run Transfac.GeneRecord" relation="relation5"/>
DH> <link port="Run Transfac.Record" relation="relation12"/>
DH> <link port="Run Transfac.log" relation="relation14"/>
DH> <link port="Synchronizer.Input" relation="relation3"/>
DH> <link port="Synchronizer.Output" relation="relation11"/>
DH> <link port="Synchronizer.FunctionInput" relation="relation4"/>
DH> <link port="Synchronizer.FunctionOutput" relation="relation12"/>
DH> <link port="Fasta.output" relation="relation7"/>
DH> <link port="Fasta.input" relation="relation10"/>
DH> <link port="RecordUpdater.output" relation="relation12"/>
DH> <link port="RecordUpdater.input" relation="relation10"/>
DH> <link port="RecordUpdater.Fasta" relation="relation7"/>
DH> <link port="RecordUpdater.Transfac" relation="relation13"/>
DH> <link port="RecordUpdater.TransfacNames" relation="relation15"/>
DH> <link port="RecordUpdater.TransfacSites" relation="relation16"/>
DH> <link port="Transfac.output" relation="relation13"/>
DH> <link port="Transfac.input" relation="relation10"/>
DH> <link port="TransfacSites.output" relation="relation16"/>
DH> <link port="TransfacSites.input" relation="relation10"/>
DH> <link port="TransfacNames.output" relation="relation15"/>
DH> <link port="TransfacNames.input" relation="relation10"/>
DH> <link port="Blast Web Service.result" relation="relation18"/>
DH> <link port="Blast Web Service.input" relation="relation17"/>
DH> <link port="Debug.input" relation="relation"/>
DH> <link port="Debug.output" relation="relation19"/>
DH> <link port="Debug.FunctionInput" relation="relation17"/>
DH> <link port="Debug.FunctionOutput" relation="relation18"/>
DH> </entity>
DH> <entity name="GeneAccessionNumberList" class="ptolemy.actor.lib.Ramp">
DH> <property name="firingCountLimit" class="ptolemy.data.expr.Parameter" value="1">
DH> </property>
DH> <property name="init" class="ptolemy.data.expr.Parameter" value="1">
DH> </property>
DH> <property name="step" class="ptolemy.actor.parameters.PortParameter" value="0">
DH> </property>
DH> <doc>Create a sequence of tokens with increasing value</doc>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[50.0, 195.0]">
DH> </property>
DH> </entity>
DH> <entity name="Expression" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.length()">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[245.0, 315.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="ArrayToSequence" class="ptolemy.domains.sdf.lib.ArrayToSequence">
DH> <property name="enforceArrayLength" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[165.0, 395.0]">
DH> </property>
DH> </entity>
DH> <entity name="SequenceToArray" class="ptolemy.domains.sdf.lib.SequenceToArray">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[360.0, 315.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression4" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="AccessNumbers">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[400.0, 235.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Merge and Discard" class="ptolemy.actor.TypedCompositeActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[150.0, 635.0]">
DH> </property>
DH> <property name="Annotation" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="Given an array of arrays, figure out how many total elements there are with non-empty Fasta fields.">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[290.0, 230.0]">
DH> </property>
DH> </property>
DH> <property name="Annotation2" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="Merge the array of arrays into a single array.">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[20.0, 225.0]">
DH> </property>
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={52, 10, 1161, 466}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[947, 292]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{473.5, 146.0}">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[35.0, 200.0]">
DH> </property>
DH> </port>
DH> <port name="port" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[895.0, 190.0]">
DH> </property>
DH> </port>
DH> <entity name="ArrayMerge" class="org.sdm.spa.ArrayMerge">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[110.0, 200.0]">
DH> </property>
DH> </entity>
DH> <entity name="Expression" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="map(function(rec:{Fasta = string}) rec.Fasta == "" ? 0 : 1, input)">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[365.0, 200.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression2" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="sum(input)">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[630.0, 200.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="BooleanSwitch" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[660.0, 100.0]">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression4" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.Fasta == """>
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[475.0, 150.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Discard" class="ptolemy.actor.lib.Discard">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[795.0, 90.0]">
DH> </property>
DH> </entity>
DH> <entity name="ArrayToSequence" class="ptolemy.domains.sdf.lib.ArrayToSequence">
DH> <property name="enforceArrayLength" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[230.0, 100.0]">
DH> </property>
DH> </entity>
DH> <entity name="SequenceToArray" class="ptolemy.domains.sdf.lib.SequenceToArray">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[775.0, 190.0]">
DH> </property>
DH> </entity>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation6" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation8" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation9" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[160.0, 200.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[385.0, 100.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="input" relation="relation"/>
DH> <link port="port" relation="relation7"/>
DH> <link port="ArrayMerge.input" relation="relation"/>
DH> <link port="ArrayMerge.output" relation="relation9"/>
DH> <link port="Expression.output" relation="relation3"/>
DH> <link port="Expression.input" relation="relation9"/>
DH> <link port="Expression2.output" relation="relation2"/>
DH> <link port="Expression2.input" relation="relation3"/>
DH> <link port="BooleanSwitch.input" relation="relation5"/>
DH> <link port="BooleanSwitch.control" relation="relation6"/>
DH> <link port="BooleanSwitch.trueOutput" relation="relation8"/>
DH> <link port="BooleanSwitch.falseOutput" relation="relation4"/>
DH> <link port="Expression4.output" relation="relation6"/>
DH> <link port="Expression4.input" relation="relation5"/>
DH> <link port="Discard.input" relation="relation8"/>
DH> <link port="ArrayToSequence.input" relation="relation9"/>
DH> <link port="ArrayToSequence.output" relation="relation5"/>
DH> <link port="SequenceToArray.input" relation="relation4"/>
DH> <link port="SequenceToArray.output" relation="relation7"/>
DH> <link port="SequenceToArray.arrayLength" relation="relation2"/>
DH> </entity>
DH> <entity name="Parse Clustal" class="workflows.spa.PIW.PIW-ParseClustalW">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[460.0, 695.0]">
DH> </property>
DH> </entity>
DH> <entity name="Viz" class="org.sdm.spa.actors.piw.viz.VizActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[625.0, 705.0]">
DH> </property>
DH> </entity>
DH> <entity name="Setup" class="ptolemy.actor.TypedCompositeActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[255.0, 195.0]">
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={217, 306, 984, 519}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[764, 412]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{382.0, 206.0}">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="{20.0, 200.0}">
DH> </property>
DH> </port>
DH> <port name="log" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[515.0, 285.0]">
DH> </property>
DH> </port>
DH> <port name="output" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[505.0, 105.0]">
DH> </property>
DH> </port>
DH> <entity name="DirectoryCreate" class="org.sdm.spa.actors.io.DirectoryCreate">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[190.0, 200.0]">
DH> </property>
DH> </entity>
DH> <entity name="Expression" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="dir_log">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[100.0, 200.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="BooleanSwitch" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[360.0, 200.0]">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression2" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""" == input">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[305.0, 285.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression3" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""Logs will be placed in " + dir_log + "."">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[610.0, 190.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[250.0, 200.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[455.0, 190.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[455.0, 210.0]">
DH> </vertex>
DH> </relation>
DH> <link port="input" relation="relation"/>
DH> <link port="log" relation="relation5"/>
DH> <link port="output" relation="relation7"/>
DH> <link port="DirectoryCreate.name" relation="relation2"/>
DH> <link port="DirectoryCreate.errors" relation="relation3"/>
DH> <link port="Expression.output" relation="relation2"/>
DH> <link port="Expression.input" relation="relation"/>
DH> <link port="BooleanSwitch.input" relation="relation3"/>
DH> <link port="BooleanSwitch.control" relation="relation4"/>
DH> <link port="BooleanSwitch.trueOutput" relation="relation7"/>
DH> <link port="BooleanSwitch.falseOutput" relation="relation5"/>
DH> <link port="Expression2.output" relation="relation4"/>
DH> <link port="Expression2.input" relation="relation3"/>
DH> <link port="Expression3.output" relation="relation5"/>
DH> <link port="Expression3.input" relation="relation7"/>
DH> </entity>
DH> <entity name="Run ClustalW" class="ptolemy.actor.TypedCompositeActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[285.0, 545.0]">
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={23, 69, 1236, 459}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[1016, 352]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{508.0, 176.0}">
DH> </property>
DH> <property name="annotation" class="ptolemy.kernel.util.Attribute">
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <property name="_iconDescription" class="ptolemy.kernel.util.SingletonConfigurableAttribute">
DH> <configure><svg><text x="20" y="20" style="font-size:10; font-family:SansSerif; fill:blue">Shows the physical alignment
DH> of multiple gene sequences.
DH> Uses DDBL-ClustalW Multiple
DH> Alignment Tool.
DH> </text></svg></configure>
DH> </property>
DH> <property name="_smallIconDescription" class="ptolemy.kernel.util.SingletonConfigurableAttribute">
DH> <configure>
DH> <svg>
DH> <text x="20" style="font-size:14; font-family:SansSerif; fill:blue" y="20">-A-</text>
DH> </svg>
DH> </configure>
DH> </property>
DH> <property name="_controllerFactory" class="ptolemy.vergil.basic.NodeControllerFactory">
DH> </property>
DH> <property name="_editorFactory" class="ptolemy.vergil.toolbox.AnnotationEditorFactory">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[575.0, 250.0]">
DH> </property>
DH> </property>
DH> <port name="port" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[45.0, 160.0]">
DH> </property>
DH> </port>
DH> <port name="port2" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[950.0, 220.0]">
DH> </property>
DH> </port>
DH> <entity name="Display" class="ptolemy.actor.lib.gui.Display">
DH> <property name="title" class="ptolemy.kernel.util.StringAttribute" value="Fasta">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[605.0, 90.0]">
DH> </property>
DH> </entity>
DH> <entity name="Expression" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="map(function(rec:{Fasta=string}) rec.Fasta, input)">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[245.0, 160.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="ClustalW Results Display" class="ptolemy.actor.lib.gui.Display">
DH> <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="100">
DH> </property>
DH> <property name="title" class="ptolemy.kernel.util.StringAttribute" value="ClustalW Results Display">
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={267, 87, 1111, 205}, maximized=false}">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[855.0, 155.0]">
DH> </property>
DH> </entity>
DH> <entity name="Expression2" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="sum(input)">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[465.0, 160.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="WebService" class="org.sdm.spa.WebService">
DH> <property name="wsdlUrl" class="ptolemy.data.expr.StringParameter" value="http://xml.nig.ac.jp/wsdl/ClustalW.wsdl">
DH> </property>
DH> <property name="methodName" class="ptolemy.data.expr.StringParameter" value="analyzeParam">
DH> </property>
DH> <property name="userName" class="ptolemy.data.expr.StringParameter" value="user1">
DH> </property>
DH> <property name="password" class="ptolemy.data.expr.StringParameter" value="pass1">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[590.0, 185.0]">
DH> </property>
DH> <port name="query" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_showName" class="ptolemy.kernel.util.Attribute">
DH> </property>
DH> </port>
DH> <port name="param" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_showName" class="ptolemy.kernel.util.Attribute">
DH> </property>
DH> </port>
DH> <port name="Result" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_showName" class="ptolemy.kernel.util.Attribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression3" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""-quicktree -type=dna -output=gde"">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[400.0, 245.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[810.0, 220.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[530.0, 200.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="port" relation="relation5"/>
DH> <link port="port2" relation="relation3"/>
DH> <link port="Display.input" relation="relation4"/>
DH> <link port="Expression.output" relation="relation"/>
DH> <link port="Expression.input" relation="relation5"/>
DH> <link port="ClustalW Results Display.input" relation="relation3"/>
DH> <link port="Expression2.output" relation="relation4"/>
DH> <link port="Expression2.input" relation="relation"/>
DH> <link port="WebService.query" relation="relation4"/>
DH> <link port="WebService.param" relation="relation2"/>
DH> <link port="WebService.Result" relation="relation3"/>
DH> <link port="Expression3.output" relation="relation2"/>
DH> <link port="Expression3.input" relation="relation4"/>
DH> </entity>
DH> <entity name="log" class="ptolemy.actor.TypedCompositeActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[625.0, 415.0]">
DH> </property>
DH> <property name="dir_log" class="ptolemy.data.expr.Parameter" value="dir_log">
DH> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.ValueIcon">
DH> <property name="_color" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> </property>
DH> <property name="_smallIconDescription" class="ptolemy.kernel.util.SingletonConfigurableAttribute">
DH> <configure>
DH> <svg>
DH> <text x="20" style="font-size:14; font-family:SansSerif; fill:blue" y="20">-P-</text>
DH> </svg>
DH> </configure>
DH> </property>
DH> <property name="_editorFactory" class="ptolemy.vergil.toolbox.VisibleParameterEditorFactory">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[650.0, 275.0]">
DH> </property>
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={129, 34, 1082, 677}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[862, 570]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{431.0, 285.0}">
DH> </property>
DH> <port name="setup" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[45.0, 75.0]">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="blast" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[45.0, 160.0]">
DH> </property>
DH> </port>
DH> <port name="transfac" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[45.0, 250.0]">
DH> </property>
DH> </port>
DH> <port name="align" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[45.0, 415.0]">
DH> </property>
DH> </port>
DH> <port name="tfbs" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[45.0, 330.0]">
DH> </property>
DH> </port>
DH> <port name="viz" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[45.0, 505.0]">
DH> </property>
DH> </port>
DH> <class name="output" extends="ptolemy.actor.TypedCompositeActor">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[695.0, 175.0]">
DH> </property>
DH> <property name="filename" class="ptolemy.data.expr.Parameter" value="HOME">
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={83, 10, 998, 464}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[776, 350]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{388.0, 175.0}">
DH> </property>
DH> <property name="timestamp_enable" class="ptolemy.data.expr.Parameter" value="true">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[50.0, 160.0]">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="duplicate" class="ptolemy.actor.TypedIOPort">
DH> <property name="output"/>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[345.0, 90.0]">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <entity name="LineWriter" class="ptolemy.actor.lib.io.LineWriter">
DH> <property name="fileName" class="ptolemy.data.expr.FileParameter" value="$filename">
DH> </property>
DH> <property name="confirmOverwrite" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <doc>Write the value of a string token, one per line, to a text file.</doc>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[695.0, 170.0]">
DH> </property>
DH> </entity>
DH> <entity name="No Op" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[210.0, 90.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Timestamp" class="org.sdm.spa.Timestamp">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[375.0, 270.0]">
DH> </property>
DH> </entity>
DH> <entity name="Add" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="timestamp +input">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[560.0, 170.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> <port name="timestamp" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> <property name="_showName" class="ptolemy.kernel.util.SingletonAttribute">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="BooleanSwitch" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="{315.0, 240.0}">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Not enable" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="! timestamp_enable">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[226.27783203125, 287.00341796875]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Add colon" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input + " : "">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[525.0, 280.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Empty" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="""">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[410.0, 230.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[140.0, 160.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation6" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[455.0, 230.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation8" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="input" relation="relation"/>
DH> <link port="duplicate" relation="relation2"/>
DH> <link port="LineWriter.input" relation="relation4"/>
DH> <link port="No Op.output" relation="relation2"/>
DH> <link port="No Op.input" relation="relation"/>
DH> <link port="Timestamp.output" relation="relation7"/>
DH> <link port="Timestamp.trigger" relation="relation3"/>
DH> <link port="Add.output" relation="relation4"/>
DH> <link port="Add.input" relation="relation"/>
DH> <link port="Add.timestamp" relation="relation6"/>
DH> <link port="BooleanSwitch.input" relation="relation"/>
DH> <link port="BooleanSwitch.control" relation="relation5"/>
DH> <link port="BooleanSwitch.trueOutput" relation="relation8"/>
DH> <link port="BooleanSwitch.falseOutput" relation="relation3"/>
DH> <link port="Not enable.output" relation="relation5"/>
DH> <link port="Not enable.input" relation="relation"/>
DH> <link port="Add colon.output" relation="relation6"/>
DH> <link port="Add colon.input" relation="relation7"/>
DH> <link port="Empty.output" relation="relation6"/>
DH> <link port="Empty.input" relation="relation8"/>
DH> </class>
DH> <entity name="Display" class="ptolemy.actor.lib.gui.Display">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[695.0, 75.0]">
DH> </property>
DH> </entity>
DH> <entity name="InstanceOfoutput" class="output">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[530.0, 75.0]">
DH> </property>
DH> <property name="filename" class="ptolemy.data.expr.Parameter" value="dir_log + "/log-all.txt"">
DH> </property>
DH> <entity name="BooleanSwitch" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_icon" class="ptolemy.vergil.icon.EditorIcon">
DH> <property name="rectangle" class="ptolemy.vergil.kernel.attributes.RectangleAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="33.0">
DH> </property>
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="40.0">
DH> </property>
DH> <property name="centered" class="ptolemy.data.expr.Parameter" value="true">
DH> </property>
DH> <property name="fillColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="rounding" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line2" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 20.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0,0.6,1.0,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-30.0">
DH> </property>
DH> </property>
DH> <property name="line3" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line4" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line5" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line6" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-10.0">
DH> </property>
DH> </property>
DH> <property name="line7" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="14.14">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line8" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> </property>
DH> <property name="line9" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="5.41">
DH> </property>
DH> </property>
DH> <property name="line10" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-5.41">
DH> </property>
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={5, 136, 815, 516}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 400]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="4.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{28.5151515151515, -18.8181818181818}">
DH> </property>
DH> <property name="annotation" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="T">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -25.0">
DH> </property>
DH> </property>
DH> <property name="annotation2" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="F">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[75.0, 235.0]">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> </entity>
DH> <entity name="InstanceOfoutput2" class="output">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[365.0, 160.0]">
DH> </property>
DH> <property name="filename" class="ptolemy.data.expr.Parameter" value="dir_log + "/log-blast.txt"">
DH> </property>
DH> <property name="timestamp_enable" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <entity name="BooleanSwitch" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_icon" class="ptolemy.vergil.icon.EditorIcon">
DH> <property name="rectangle" class="ptolemy.vergil.kernel.attributes.RectangleAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="33.0">
DH> </property>
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="40.0">
DH> </property>
DH> <property name="centered" class="ptolemy.data.expr.Parameter" value="true">
DH> </property>
DH> <property name="fillColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="rounding" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line2" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 20.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0,0.6,1.0,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-30.0">
DH> </property>
DH> </property>
DH> <property name="line3" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line4" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line5" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line6" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-10.0">
DH> </property>
DH> </property>
DH> <property name="line7" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="14.14">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line8" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> </property>
DH> <property name="line9" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="5.41">
DH> </property>
DH> </property>
DH> <property name="line10" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-5.41">
DH> </property>
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={5, 136, 815, 516}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 400]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="4.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{28.5151515151515, -18.8181818181818}">
DH> </property>
DH> <property name="annotation" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="T">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -25.0">
DH> </property>
DH> </property>
DH> <property name="annotation2" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="F">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[75.0, 235.0]">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> </entity>
DH> <entity name="InstanceOfoutput3" class="output">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[365.0, 250.0]">
DH> </property>
DH> <property name="filename" class="ptolemy.data.expr.Parameter" value="dir_log + "/log-transfac.txt"">
DH> </property>
DH> <property name="timestamp_enable" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <entity name="BooleanSwitch" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_icon" class="ptolemy.vergil.icon.EditorIcon">
DH> <property name="rectangle" class="ptolemy.vergil.kernel.attributes.RectangleAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="33.0">
DH> </property>
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="40.0">
DH> </property>
DH> <property name="centered" class="ptolemy.data.expr.Parameter" value="true">
DH> </property>
DH> <property name="fillColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="rounding" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line2" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 20.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0,0.6,1.0,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-30.0">
DH> </property>
DH> </property>
DH> <property name="line3" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line4" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line5" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line6" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-10.0">
DH> </property>
DH> </property>
DH> <property name="line7" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="14.14">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line8" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> </property>
DH> <property name="line9" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="5.41">
DH> </property>
DH> </property>
DH> <property name="line10" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-5.41">
DH> </property>
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={5, 136, 815, 516}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 400]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="4.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{28.5151515151515, -18.8181818181818}">
DH> </property>
DH> <property name="annotation" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="T">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -25.0">
DH> </property>
DH> </property>
DH> <property name="annotation2" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="F">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[75.0, 235.0]">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> </entity>
DH> <entity name="Expression" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input + "\n\n\n-----\n\n\n"">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[190.0, 160.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression2" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input + "\n\n\n-----\n\n\n"">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[190.0, 250.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="InstanceOfoutput5" class="output">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[410.0, 415.0]">
DH> </property>
DH> <property name="filename" class="ptolemy.data.expr.Parameter" value="dir_log + "/log-align.txt"">
DH> </property>
DH> <property name="timestamp_enable" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <entity name="BooleanSwitch" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_icon" class="ptolemy.vergil.icon.EditorIcon">
DH> <property name="rectangle" class="ptolemy.vergil.kernel.attributes.RectangleAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="33.0">
DH> </property>
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="40.0">
DH> </property>
DH> <property name="centered" class="ptolemy.data.expr.Parameter" value="true">
DH> </property>
DH> <property name="fillColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="rounding" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line2" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 20.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0,0.6,1.0,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-30.0">
DH> </property>
DH> </property>
DH> <property name="line3" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line4" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line5" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line6" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-10.0">
DH> </property>
DH> </property>
DH> <property name="line7" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="14.14">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line8" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> </property>
DH> <property name="line9" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="5.41">
DH> </property>
DH> </property>
DH> <property name="line10" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-5.41">
DH> </property>
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={5, 136, 815, 516}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 400]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="4.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{28.5151515151515, -18.8181818181818}">
DH> </property>
DH> <property name="annotation" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="T">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -25.0">
DH> </property>
DH> </property>
DH> <property name="annotation2" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="F">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[75.0, 235.0]">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> </entity>
DH> <entity name="Expression4" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.toString() + "\n\n\n-----\n\n\n"">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[205.0, 415.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="InstanceOfoutput4" class="output">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[410.0, 330.0]">
DH> </property>
DH> <property name="filename" class="ptolemy.data.expr.Parameter" value="dir_log + "/log-tfbs.txt"">
DH> </property>
DH> <property name="timestamp_enable" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <entity name="BooleanSwitch" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_icon" class="ptolemy.vergil.icon.EditorIcon">
DH> <property name="rectangle" class="ptolemy.vergil.kernel.attributes.RectangleAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="33.0">
DH> </property>
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="40.0">
DH> </property>
DH> <property name="centered" class="ptolemy.data.expr.Parameter" value="true">
DH> </property>
DH> <property name="fillColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="rounding" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line2" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 20.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0,0.6,1.0,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-30.0">
DH> </property>
DH> </property>
DH> <property name="line3" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line4" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line5" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line6" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-10.0">
DH> </property>
DH> </property>
DH> <property name="line7" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="14.14">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line8" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> </property>
DH> <property name="line9" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="5.41">
DH> </property>
DH> </property>
DH> <property name="line10" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-5.41">
DH> </property>
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={5, 136, 815, 516}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 400]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="4.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{28.5151515151515, -18.8181818181818}">
DH> </property>
DH> <property name="annotation" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="T">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -25.0">
DH> </property>
DH> </property>
DH> <property name="annotation2" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="F">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[75.0, 235.0]">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> </entity>
DH> <entity name="Expression3" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.toString() + "\n\n\n-----\n\n\n"">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[205.0, 330.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="Expression5" class="ptolemy.actor.lib.Expression">
DH> <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="input.toString() + "\n\n\n-----\n\n\n"">
DH> </property>
DH> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
DH> <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
DH> </property>
DH> <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[210.0, 505.0]">
DH> </property>
DH> <port name="input" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_type" class="ptolemy.actor.TypeAttribute" value="unknown">
DH> </property>
DH> </port>
DH> </entity>
DH> <entity name="InstanceOfoutput6" class="output">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[415.0, 505.0]">
DH> </property>
DH> <property name="filename" class="ptolemy.data.expr.Parameter" value="dir_log + "/log-viz.txt"">
DH> </property>
DH> <property name="timestamp_enable" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <entity name="BooleanSwitch" class="ptolemy.actor.lib.BooleanSwitch">
DH> <property name="_icon" class="ptolemy.vergil.icon.EditorIcon">
DH> <property name="rectangle" class="ptolemy.vergil.kernel.attributes.RectangleAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="33.0">
DH> </property>
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="40.0">
DH> </property>
DH> <property name="centered" class="ptolemy.data.expr.Parameter" value="true">
DH> </property>
DH> <property name="fillColor" class="ptolemy.actor.gui.ColorAttribute" value="none">
DH> </property>
DH> <property name="rounding" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line2" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-15.0, 20.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0,0.6,1.0,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-30.0">
DH> </property>
DH> </property>
DH> <property name="line3" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line4" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line5" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-30.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line6" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 0.0, 1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-10.0">
DH> </property>
DH> </property>
DH> <property name="line7" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="14.14">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="0.0">
DH> </property>
DH> </property>
DH> <property name="line8" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="10.0">
DH> </property>
DH> </property>
DH> <property name="line9" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="5.41">
DH> </property>
DH> </property>
DH> <property name="line10" class="ptolemy.vergil.kernel.attributes.LineAttribute">
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-20.0, 0.0">
DH> </property>
DH> <property name="lineWidth" class="ptolemy.data.expr.Parameter" value="1.0">
DH> </property>
DH> <property name="lineColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.6,0.6,0.6,1.0}">
DH> </property>
DH> <property name="x" class="ptolemy.data.expr.Parameter" value="13.07">
DH> </property>
DH> <property name="y" class="ptolemy.data.expr.Parameter" value="-5.41">
DH> </property>
DH> </property>
DH> <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={5, 136, 815, 516}, maximized=false}">
DH> </property>
DH> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 400]">
DH> </property>
DH> <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="4.0">
DH> </property>
DH> <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{28.5151515151515, -18.8181818181818}">
DH> </property>
DH> <property name="annotation" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="T">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, -25.0">
DH> </property>
DH> </property>
DH> <property name="annotation2" class="ptolemy.vergil.kernel.attributes.TextAttribute">
DH> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="F">
DH> <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
DH> <property name="height" class="ptolemy.data.expr.Parameter" value="20">
DH> </property>
DH> <property name="width" class="ptolemy.data.expr.Parameter" value="80">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="textSize" class="ptolemy.data.expr.Parameter" value="10">
DH> </property>
DH> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
DH> </property>
DH> <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
DH> </property>
DH> <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="-10.0, 10.0">
DH> </property>
DH> </property>
DH> </property>
DH> <property name="_location" class="ptolemy.kernel.util.Location" value="[75.0, 235.0]">
DH> </property>
DH> <port name="control" class="ptolemy.actor.TypedIOPort">
DH> <property name="input"/>
DH> <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
DH> </property>
DH> </port>
DH> </entity>
DH> </entity>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[435.0, 75.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation6" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation8" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation9" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation10" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation11" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation12" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <link port="setup" relation="relation2"/>
DH> <link port="blast" relation="relation5"/>
DH> <link port="transfac" relation="relation6"/>
DH> <link port="align" relation="relation8"/>
DH> <link port="tfbs" relation="relation10"/>
DH> <link port="viz" relation="relation11"/>
DH> <link port="Display.input" relation="relation"/>
DH> <link port="InstanceOfoutput.input" relation="relation2"/>
DH> <link port="InstanceOfoutput.duplicate" relation="relation"/>
DH> <link port="InstanceOfoutput2.input" relation="relation3"/>
DH> <link port="InstanceOfoutput3.input" relation="relation4"/>
DH> <link port="Expression.output" relation="relation3"/>
DH> <link port="Expression.input" relation="relation5"/>
DH> <link port="Expression2.output" relation="relation4"/>
DH> <link port="Expression2.input" relation="relation6"/>
DH> <link port="InstanceOfoutput5.input" relation="relation7"/>
DH> <link port="Expression4.output" relation="relation7"/>
DH> <link port="Expression4.input" relation="relation8"/>
DH> <link port="InstanceOfoutput4.input" relation="relation9"/>
DH> <link port="Expression3.output" relation="relation9"/>
DH> <link port="Expression3.input" relation="relation10"/>
DH> <link port="Expression5.output" relation="relation12"/>
DH> <link port="Expression5.input" relation="relation11"/>
DH> <link port="InstanceOfoutput6.input" relation="relation12"/>
DH> </entity>
DH> <relation name="relation" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[120.0, 270.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation6" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation8" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[445.7786102294922, 502.076171875]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation13" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[515.0, 635.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation9" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation11" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation12" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation10" class="ptolemy.actor.TypedIORelation">
DH> </relation>
DH> <relation name="relation14" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[515.0, 185.0]">
DH> </vertex>
DH> </relation>
DH> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="{385.0, 545.0}">
DH> </vertex>
DH> </relation>
DH> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
DH> <vertex name="vertex1" value="[555.0, 705.0]">
DH> </vertex>
DH> </relation>
DH> <link port="Gene Sequence Processing.Gene Accession Number" relation="relation4"/>
DH> <link port="Gene Sequence Processing.Fasta Output" relation="relation3"/>
DH> <link port="Gene Sequence Processing.log_blast" relation="relation12"/>
DH> <link port="Gene Sequence Processing.log_transfac" relation="relation11"/>
DH> <link port="GeneAccessionNumberList.output" relation="relation9"/>
DH> <link port="Expression.output" relation="relation6"/>
DH> <link port="Expression.input" relation="relation"/>
DH> <link port="ArrayToSequence.input" relation="relation"/>
DH> <link port="ArrayToSequence.output" relation="relation4"/>
DH> <link port="SequenceToArray.input" relation="relation3"/>
DH> <link port="SequenceToArray.output" relation="relation8"/>
DH> <link port="SequenceToArray.arrayLength" relation="relation6"/>
DH> <link port="Expression4.output" relation="relation"/>
DH> <link port="Expression4.input" relation="relation10"/>
DH> <link port="Merge and Discard.input" relation="relation8"/>
DH> <link port="Merge and Discard.port" relation="relation13"/>
DH> <link port="Parse Clustal.output" relation="relation2"/>
DH> <link port="Parse Clustal.blast" relation="relation13"/>
DH> <link port="Parse Clustal.input" relation="relation7"/>
DH> <link port="Viz.Sequences" relation="relation2"/>
DH> <link port="Setup.input" relation="relation9"/>
DH> <link port="Setup.log" relation="relation14"/>
DH> <link port="Setup.output" relation="relation10"/>
DH> <link port="Run ClustalW.port" relation="relation13"/>
DH> <link port="Run ClustalW.port2" relation="relation7"/>
DH> <link port="log.setup" relation="relation14"/>
DH> <link port="log.blast" relation="relation12"/>
DH> <link port="log.transfac" relation="relation11"/>
DH> <link port="log.align" relation="relation7"/>
DH> <link port="log.tfbs" relation="relation13"/>
DH> <link port="log.viz" relation="relation2"/>
DH> </entity>
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