[kepler-users] Opal 2.0 and Kepler 1.0
Tirath Ramdas
tramdas at oci.uzh.ch
Tue Jun 16 14:12:58 PDT 2009
(apologies for the previous message - I'm not sure what key combination in
the Live Mail client sent my email off prematurely!)
The following 9 errors were obtained when trying to load the workflow:
1) java.lang.ClassNotFoundException:
ptolemy.actor.parameters.SharedParameter
2) java.lang.ClassNotFoundException: org.kepler.moml.NamedObjIdReferralList
3) ptolemy.kernel.util.IllegalActionException: Cannot find class:
edu.sdsc.nbcr.opal.OpalClient
Because:
-- C:\Users\tramdas\Desktop\edu\sdsc\nbcr\opal\OpalClient.moml (The system
cannot find the path specified)
-- XML file not found relative to classpath.
-- C:\Program Files\Kepler-1.0.0\edu/sdsc/nbcr/opal/OpalClient.moml
C:\Program Files\Kepler-1.0.0\edu\sdsc\nbcr\opal\OpalClient.moml (The system
cannot find the path specified)
4) ptolemy.kernel.util.IllegalActionException: Cannot find class:
edu.sdsc.nbcr.opal.OpalClient
Because:
-- C:\Users\tramdas\Desktop\edu\sdsc\nbcr\opal\OpalClient.moml (The system
cannot find the path specified)
-- XML file not found relative to classpath.
-- C:\Program Files\Kepler-1.0.0\edu/sdsc/nbcr/opal/OpalClient.moml
C:\Program Files\Kepler-1.0.0\edu\sdsc\nbcr\opal\OpalClient.moml (The system
cannot find the path specified)
5) com.microstar.xml.XmlException: No port named "MEME.baseUrl" in
.newOpalActor-meme-mast in
file:/C:/Users/tramdas/Desktop/newOpalActor-meme-mast_3.5.xml at line 534
and column 4
6) com.microstar.xml.XmlException: No port named "MEME.dataSet" in
.newOpalActor-meme-mast in
file:/C:/Users/tramdas/Desktop/newOpalActor-meme-mast_3.5.xml at line 534
and column 4
7) com.microstar.xml.XmlException: No port named "MAST.baseUrl" in
.newOpalActor-meme-mast in
file:/C:/Users/tramdas/Desktop/newOpalActor-meme-mast_3.5.xml at line 534
and column 4
8) com.microstar.xml.XmlException: No port named "MAST.inputFile1Dynamic" in
.newOpalActor-meme-mast in
file:/C:/Users/tramdas/Desktop/newOpalActor-meme-mast_3.5.xml at line 534
and column 4
9) com.microstar.xml.XmlException: No port named "MAST.inputFile2Dynamic" in
.newOpalActor-meme-mast in
file:/C:/Users/tramdas/Desktop/newOpalActor-meme-mast_3.5.xml at line 534
and column 4
Luca, the last time you tested the workflow, what version of Kepler were you
using? Also, do the actors basically just call the generic Opal client? Is
it just as effective to do an external execution call to the client via
command line?
Thanks.
Sincerely,
Tirath Ramdas
--------------------------------------------------
From: "Luca Clementi" <clem at sdsc.edu>
Sent: Monday, June 15, 2009 9:35 PM
To: "Daniel Crawl" <crawl at sdsc.edu>
Cc: "Tirath Ramdas" <tramdas at oci.uzh.ch>; <kepler-users at kepler-project.org>;
"Sriram Krishnan" <sriram at sdsc.edu>
Subject: Re: [kepler-users] Opal 2.0 and Kepler 1.0
>
>
>> Tirath Ramdas wrote:
>>> Hi,
>>>
> Dear Tirath,
> see below...
>
>>> I would like to deploy some apps with Opal 2.0, and to orchestrate
>>> these with Kepler 1.0.0. For what it's worth, the
>>> WebServicesAndDataTransformation example workflow does work for me.
>>>
>>> I've set up opal-ws-2.0 with jakarta-tomcat-5_0_30, with the
>>> "/bin/date" sample service, locally (i.e. on the same system I'm
>>> running Kepler). I get the desired result running the service with the
>>> Opal generic client, with launchJob [1], and subsequently with the
>>> queryStatus/getOutputs methods. Unfortunately, I can't repeat this
>>> with Kepler, pointing to the endpoint
>>> http://localhost:8080/opal2/services/DateServicePort?wsdl.
>>>
>>> [1] java edu.sdsc.nbcr.opal.GenericServiceClient -l
>>> http://localhost:8080/opal2/services/DateServicePort -r launchJob
>>>
>>> I give some arbitrary input to the launchJobInput port which the actor
>>> instantiates the moment I specify the endpoint and method (launchJob),
>>> basically treating this input like a trigger. The result is the same
>>> if it's a constant (1) or an empty string: the workflow returns
>>> "executions finished" almost instantly, with no output on either the
>>> launchJobOutput port or the error port. Looking at the Opal dashboard,
>>> it doesn't look like any of these jobs get started.
>
> If I have understood you are trying to use the generic web service
> actor, and for that actor you need to input a string containing a
> properly formatted SOAP XML request, which is not very easy to make.
>
> For this reason we have developed a OpalClient actor that can be used to
> invoke opal services. You can simply drag and drop the opal actor set
> the URL of your service in the "serviceURL" parameter.
>
> After this you have to type the command line of set the various
> properties of the actor. Input ports are input files, and outputs are
> the URL of the output files.
>
> Attached an example which invoke meme and mast.
>
> Regards,
> Luca
>
>
>
> <?xml version="1.0" standalone="no"?>
> <!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN"
> "http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd">
> <entity name="newOpalActor-meme-mast"
> class="ptolemy.actor.TypedCompositeActor">
> <property name="_createdBy"
> class="ptolemy.kernel.attributes.VersionAttribute" value="8.0.beta">
> </property>
> <property name="PN Director"
> class="ptolemy.domains.pn.kernel.PNDirector">
> <property name="timeResolution"
> class="ptolemy.actor.parameters.SharedParameter" value="1E-10">
> </property>
> <property name="initialQueueCapacity"
> class="ptolemy.data.expr.Parameter" value="1">
> </property>
> <property name="maximumQueueCapacity"
> class="ptolemy.data.expr.Parameter" value="65536">
> </property>
> <property name="KeplerDocumentation"
> class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> <property name="description"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="author"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Mudit Goel,
> Edward A. Lee, Xiaowen Xin</configure></property>
> <property name="version"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="userLevelDocumentation"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
<p>PN
> Directors are natural candidates for managing workflows that require
> parallel processing on distributed computing systems. PN workflows are
> powerful because they have few restrictions. On the other hand, they can
> be very inefficient.</p>
<p>The Process Network (PN)
> Director is similar to the SDF Director in that it does not have a notion
> of time. However, unlike the SDF Director, the PN Director does not
> statically calculate firing schedules. Instead, a PN workflow is driven by
> data availability: tokens are created on output ports whenever input
> tokens are available and the outputs can be calculated. Output tokens are
> passed to connected actors, where they are held in a buffer until that
> next actor collects all required inputs and can fire. The PN Director
> finishes executing a workflow only when there are no new data token
> sources anywhere in the workflow. </p>
<p>The same
> execution process that gives the PN Director its flexibility can also lead
> to some unexpected results: workflows may refuse to automatically
> terminate because tokens are always generated and available to downstream
> actors, for example. If one actor fires at a much higher rate than
> another, a downstream actor's memory buffer may overflow, causing workflow
> execution to fail.</p>
</configure></property>
> <property name="prop:initialQueueCapacity"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The initial
> size of the queues for each communication channel. The value is an integer
> that defaults to 1. This is an advanced parameter that can usually be left
> at its default value.</configure></property>
> <property name="prop:maximumQueueCapacity"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The maximum
> size of the queues for each communication channel. The value is an integer
> that defaults to 65536. To specify unbounded queues, set the value to 0.
> This is an advanced parameter that can usually be left at its default
> value.</configure></property>
> </property> <property name="entityId"
> class="org.kepler.moml.NamedObjId"
> value="urn:lsid:kepler-project.org:director:2:1">
> </property>
> <property name="class" class="ptolemy.kernel.util.StringAttribute"
> value="ptolemy.domains.pn.kernel.PNDirector">
> <property name="id" class="ptolemy.kernel.util.StringAttribute"
> value="urn:lsid:kepler-project.org:directorclass:2:1">
> </property>
> </property>
> <property name="semanticType00" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:1:1#Director">
> </property>
> <property name="semanticType11" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:2:1#Director">
> </property>
> <property name="_location" class="ptolemy.kernel.util.Location"
> value="[55.0, 115.0]">
> </property>
> </property>
> <property name="_windowProperties"
> class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={225,
> 87, 1050, 820}, maximized=false}">
> </property>
> <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute"
> value="[747, 659]">
> </property>
> <property name="_vergilZoomFactor"
> class="ptolemy.data.expr.ExpertParameter" value="1.0">
> </property>
> <property name="_vergilCenter"
> class="ptolemy.data.expr.ExpertParameter" value="{354.5, 329.5}">
> </property>
> <property name="Annotation"
> class="ptolemy.vergil.kernel.attributes.TextAttribute">
> <property name="textColor" class="ptolemy.actor.gui.ColorAttribute"
> value="{0.0,0.4,0.4,1.0}">
> </property>
> <property name="text" class="ptolemy.kernel.util.StringAttribute"
> value="This workflow perform a MEME MAST computation using
NBCR
> remote computation capabilities.
Using Opal this workflow send
> computational intensive tasks
(MEME, MAST) to NBCR cluster
> (ws.nbcr.net).
Modify Input File so that it points to you file
> with DNA or proteins
sequences which you believe share one or more
> motifs.
Opal: http://nbcr.net/software/opal/
MEME:
> http://meme.nbcr.net/
Luca Clementi and Sriram Krishnan, 2008,
> NBCR">
> </property>
> <property name="class" class="ptolemy.kernel.util.StringAttribute"
> value="ptolemy.vergil.kernel.attributes.TextAttribute">
> <property name="id" class="ptolemy.kernel.util.StringAttribute"
> value="urn:lsid:kepler-project.org:class:1199:1">
> </property>
> </property>
> <property name="semanticType000"
> class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:1:1#DocumentationActor">
> </property>
> <property name="_location" class="ptolemy.kernel.util.Location"
> value="[210.0, 30.0]">
> </property>
> </property>
> <property name="derivedFrom"
> class="org.kepler.moml.NamedObjIdReferralList"
> value="urn:lsid:kepler-project.org:actor:436:1">
> </property>
> <property name="entityId" class="org.kepler.moml.NamedObjId"
> value="urn:lsid:gamma.msi.ucsb.edu/OpenAuth/:156:18:1">
> </property>
> <entity name="MEME" class="edu.sdsc.nbcr.opal.OpalClient">
> <property name="serviceURL"
> class="ptolemy.data.expr.StringParameter"
> value="http://ws.nbcr.net/opal2/services/MEMEService">
> </property>
> <property name="numberOfExtraInputFiles"
> class="ptolemy.data.expr.StringParameter" value="0">
> </property>
> <property name="KeplerDocumentation"
> class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> <property name="description"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Opal client
> for Kepler</configure></property>
> <property name="author"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Luca
> Clementi</configure></property>
> <property name="version"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.0-alpha</configure></property>
> <property name="userLevelDocumentation"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure><h1>Opal
> Client for Kepler.</h1><p> This actor can be used to access
> Opal based serivce. </p><p>Modify the serviceURL parameter so
> that it points to a valid Opal Service. If you modify the serviceURL in
> the properties editor you have to commit and reopen the properties
> editor.</p><p>Below there is the documentation of the service
> pointed by the current URL.</p> <p>MEME is a tool for
> discovering motifs in a group of related DNA or protein sequences. Version
> 3.5.7</p><pre>
meme
> <dataset> [optional arguments]
> <dataset> file containing sequences in FASTA
> format
[-h] print this message
> [-dna] sequences use DNA alphabet
[-protein]
> sequences use protein alphabet
[-mod oops|zoops|anr]
> distribution of motifs
[-nmotifs <nmotifs>]
> maximum number of motifs to find
[-evt <ev>]
> stop if motif E-value greater than <evt>
> [-nsites <sites>] number of sites for each motif
> [-minsites <minsites>] minimum number of sites for each
> motif
[-maxsites <maxsites>] maximum number of
> sites for each motif
[-wnsites <wnsites>]
> weight on expected number of sites
[-w <w>]
> motif width
[-minw <minw>] minumum
> motif width
[-maxw <maxw>] maximum
> motif width
[-nomatrim] do not adjust motif width
> using multiple
alignment
> [-wg <wg>] gap opening cost for multiple
> alignments
[-ws <ws>] gap extension
> cost for multiple alignments
[-noendgaps] do not
> count end gaps in multiple alignments
[-bfile
> <bfile>] name of background Markov model file
> [-revcomp] allow sites on + or - DNA strands
> [-pal] force palindromes (requires -dna)
> [-maxiter <maxiter>] maximum EM iterations to run
> [-distance <distance>] EM convergence criterion
> [-prior dirichlet|dmix|mega|megap|addone]
> type of prior to use
[-b <b>]
> strength of the prior
[-plib <plib>]
> name of Dirichlet prior file
[-spfuzz <spfuzz>]
> fuzziness of sequence to theta mapping
[-spmap uni|pam]
> starting point seq to theta mapping type
[-cons
> <cons>] consensus sequence to start EM from
> [-text] output in text format (default is HTML)
> [-maxsize <maxsize>] maximum dataset size in
> characters
[-nostatus] do not print progress
> reports to terminal
[-p <np>] use
> parallel version with <np> processors
[-time
> <t>] quit before <t> CPU seconds
> consumed
[-sf <sf>] print
> <sf> as name of sequence file
> </pre></configure></property>
> <property name="port:output"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>It returns a
> list of Strings, containing the URL of the output
> files</configure></property>
> <property name="port:baseUrl"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The base URL
> containing the working directory of the running
> jobs</configure></property>
> <property name="prop:revcomp"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>MEME searches
> for motifs on both the given DNA strand and the reverse complement strand
> by default. Checking this box will cause MEME to search the given DNA
> strand only.</configure></property>
> <property name="prop:numberOfExtraInputFiles"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The number of
> extra input files that are needed to execture the
> application</configure></property>
> <property name="prop:dataSet"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>File
> containing sequences in FASTA format. You can get a sample from here
> <a
> href="http://meme.nbcr.net/meme/examples/At.fa">At.fa</a>
> </configure></property>
> <property name="prop:nmotifs"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The number
> of different motifs to search for.</configure></property>
> <property name="prop:serviceURL"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The URL of
> the Opal service that you want to execute</configure></property>
> <property name="prop:maxsites"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Maximum
> number of sites for each motif (<=300).</configure></property>
> <property name="prop:maxw"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The maximu
> width of the motif(s) to search for.</configure></property>
> <property name="prop:mod"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Distribution
> of motifs. <UL> <LI>oops: MEME assumes that
> each sequence in the dataset contains exactly one occurrence of each
> motif.</LI><LI>zoops: MEME assumes that each
> sequence may contain at most one occurrence of each
> motif.</LI><LI> anr: MEME assumes each
> sequence may contain any number of non-overlapping occurrences of each
> motif.</LI></UL></configure></property>
> <property name="prop:minsites"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Minimum
> number of sites for each motif (>=2).</configure></property>
> <property name="prop:pal"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Checking this
> box causes MEME to search only for DNA palindromes</configure></property>
> <property name="prop:text"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Output in
> text format (default is html).</configure></property>
> <property name="prop:minw"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The minum
> width of the motif(s) to search for.</configure></property>
> </property> <property name="entityId"
> class="org.kepler.moml.NamedObjId"
> value="urn:lsid:kepler-project.org:actor:842:1">
> </property>
> <property name="class" class="ptolemy.kernel.util.StringAttribute"
> value="edu.sdsc.nbcr.opal.OpalClient">
> <property name="id" class="ptolemy.kernel.util.StringAttribute"
> value="urn:lsid:kepler-project.org:class:842:1">
> </property>
> </property>
> <property name="semanticType00" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:1:1#WebServiceActor">
> </property>
> <property name="semanticType11" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:2:1#WebService">
> </property>
> <property name="_location" class="ptolemy.kernel.util.Location"
> value="[120.0, 275.0]">
> </property>
> <property name="dataSet"
> class="ptolemy.actor.parameters.FilePortParameter" value="At.fa">
> </property>
> <property name="nmotifs" class="ptolemy.data.expr.StringParameter"
> value="3">
> </property>
> <property name="minw" class="ptolemy.data.expr.StringParameter"
> value="6">
> </property>
> <property name="maxw" class="ptolemy.data.expr.StringParameter"
> value="50">
> </property>
> <property name="mod" class="ptolemy.data.expr.StringParameter"
> value="zoops">
> </property>
> <property name="minsites" class="ptolemy.data.expr.StringParameter"
> value="">
> </property>
> <property name="maxsites" class="ptolemy.data.expr.StringParameter"
> value="">
> </property>
> <property name="text" class="ptolemy.data.expr.Parameter"
> value="false">
> </property>
> <property name="revcomp" class="ptolemy.data.expr.Parameter"
> value="false">
> </property>
> <property name="pal" class="ptolemy.data.expr.Parameter"
> value="false">
> </property>
> <port name="output" class="ptolemy.actor.TypedIOPort">
> <property name="output"/>
> <property name="_showName" class="ptolemy.data.expr.Parameter"
> value="false">
> </property>
> </port>
> <port name="baseUrl" class="ptolemy.actor.TypedIOPort">
> <property name="output"/>
> <property name="_showName" class="ptolemy.data.expr.Parameter"
> value="false">
> </property>
> </port>
> <port name="dataSet"
> class="ptolemy.actor.parameters.ParameterPort">
> <property name="input"/>
> </port>
> </entity>
> <entity name="Input File" class="ptolemy.actor.lib.StringConst">
> <property name="firingCountLimit"
> class="ptolemy.data.expr.Parameter" value="1">
> </property>
> <property name="NONE" class="ptolemy.data.expr.Parameter"
> value="0">
> </property>
> <property name="value" class="ptolemy.data.expr.Parameter"
> value="At.fa">
> </property>
> <property name="KeplerDocumentation"
> class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> <property name="description"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="author"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Edward
> Lee</configure></property>
> <property name="version"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="userLevelDocumentation"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The
> StringConstant actor outputs a string specified via the actor's value
> parameter.</p>
<p>Specifying strings with the
> StringConstant actor is convenient, as the actor does not require that
> strings be surrounded by quotes. The actor is often used to specify file
> paths, which can be selected using the Browse button available in the
> actor's parameters.</p>
<p>Specified string values
> can include references to parameters within scope (i.e., parameters
> defined at the same level of the hierarchy or higher).
> </p>
<p>NOTE: If using a PN Director, the
> 'firingCountLimit' parameter is often set to a finite integer (e.g. '1')
> so that the workflow will terminate.
> </p>
</configure></property>
> <property name="port:output"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output
> port that broadcasts a string constant specified by the value parameter.
> </configure></property>
> <property name="port:trigger"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>A multiport
> that has no declared type (in other words, the port can accept any data
> type: double, int, array, etc.) If the port is connected, the actor will
> not fire until the trigger port receives an input token. Connecting the
> port is optional, but useful when scheduling the actor to perform at a
> certain time. </configure></property>
> <property name="prop:firingCountLimit"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The limit on
> the number of times the actor will fire. The default value is 'NONE',
> meaning there is no limit on the number of time the constant will be
> provided to the output port. Any integer can be provided as a value for
> this parameter.</configure></property>
> <property name="prop:value"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The value
> produced by the actor. Specified strings do not require enclosing quotes.
> (To include a '$' sign in the string, enter '$$'.)</configure></property>
> </property> <property name="entityId"
> class="org.kepler.moml.NamedObjId"
> value="urn:lsid:kepler-project.org:actor:204:1">
> </property>
> <property name="class" class="ptolemy.kernel.util.StringAttribute"
> value="ptolemy.actor.lib.StringConst">
> <property name="id" class="ptolemy.kernel.util.StringAttribute"
> value="urn:lsid:kepler-project.org:class:1052:1">
> </property>
> </property>
> <property name="semanticType00" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
> </property>
> <property name="semanticType11" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:2:1#Constant">
> </property>
> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> <property name="attributeName"
> class="ptolemy.kernel.util.StringAttribute" value="value">
> </property>
> <property name="displayWidth"
> class="ptolemy.data.expr.Parameter" value="60">
> </property>
> </property>
> <property name="_location" class="ptolemy.kernel.util.Location"
> value="[25.0, 535.0]">
> </property>
> </entity>
> <entity name="MEME Output Directory"
> class="ptolemy.actor.lib.gui.Display">
> <property name="_windowProperties"
> class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={627,
> 417, 426, 216}, maximized=false}">
> </property>
> <property name="_paneSize" class="ptolemy.actor.gui.SizeAttribute"
> value="[418, 158]">
> </property>
> <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter"
> value="10">
> </property>
> <property name="columnsDisplayed"
> class="ptolemy.data.expr.Parameter" value="40">
> </property>
> <property name="suppressBlankLines"
> class="ptolemy.data.expr.Parameter" value="false">
> </property>
> <property name="KeplerDocumentation"
> class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> <property name="description"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="author"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Yuhong Xiong,
> Edward A. Lee</configure></property>
> <property name="version"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="userLevelDocumentation"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The
> Display actor reads tokens of any type via its input multiport, and
> displays each token on a separate line in a text display
> window.</p>
<p>Specify the size of the text display
> window with the rowsDisplayed and columnsDisplayed parameters. Simply
> resizing the window onscreen does not persistently change the size when
> the workflow is saved, closed, and then re-opened.
> </p>
<p>If the input is a string token, then the
> actor strips the surrounding quotation marks before displaying the
> value.</p>
<p>Select the suppressBlankLines
> parameter to specify that the actor not add blank lines to the display. By
> default, the actor will add blank lines.</p>
<p>Note:
> this actor can consume large amounts of memory. It is not advisable to use
> it to display large output streams.</p></configure></property>
> <property name="port:input"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>A multiport
> that accepts tokens of any type.</configure></property>
> <property name="prop:suppressBlankLines"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify
> whether the actor should display blank lines (the default) or suppress
> them.</configure></property>
> <property name="prop:rowsDisplayed"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The vertical
> size of the display, in rows. The value is an integer that defaults to
> 10.</configure></property>
> <property name="prop:columnsDisplayed"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The
> horizontal size of the display, in columns. The value is an integer that
> defaults to 40.</configure></property>
> <property name="prop:title"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The title of
> the text display window. If specified, the value will appear in the title
> bar of the text display window.</configure></property>
> </property> <property name="entityId"
> class="org.kepler.moml.NamedObjId"
> value="urn:lsid:kepler-project.org:actor:7:1">
> </property>
> <property name="class" class="ptolemy.kernel.util.StringAttribute"
> value="ptolemy.actor.lib.gui.Display">
> <property name="id" class="ptolemy.kernel.util.StringAttribute"
> value="urn:lsid:kepler-project.org:class:883:1">
> </property>
> </property>
> <property name="semanticType00" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:1:1#TextualOutputActor">
> </property>
> <property name="semanticType11" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:2:1#TextualOutput">
> </property>
> <property name="_location" class="ptolemy.kernel.util.Location"
> value="[404.15625, 285.875]">
> </property>
> </entity>
> <entity name="URL To Local File" class="util.URLToLocalFile">
> <property name="fileOrURL" class="ptolemy.data.expr.FileParameter"
> value="http://ws.nbcr.net/app1242864332657/stdout.txt">
> </property>
> <property name="outputFile" class="ptolemy.data.expr.FileParameter"
> value="memeoutput.html">
> </property>
> <property name="overwrite" class="ptolemy.data.expr.Parameter"
> value="true">
> </property>
> <property name="KeplerDocumentation"
> class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> <property name="description"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="author"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Dan
> Higgins</configure></property>
> <property name="version"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="userLevelDocumentation"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The
> URLToLocalFile actor reads a URL and copies it to the local file system.
> The actor can also be used to read a local file and then write it to
> another location in the file system.</p>
<p>Use the
> optional outputFilePort to provide a name for the copied file. Specify an
> output file name with either the outputFilePort or the outputFile
> parameter. When the actor is done reading and saving the file, the output
> port will produce a true value.</p></configure></property>
> <property name="port:fileOrURLPort"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An optional
> input port that accepts the file name or URL of a file to be read. When
> the port is connected, the actor reads the file sent by the previous
> workflow step. The file name or URL can also be specified using the
> fileOrURL parameter.</configure></property>
> <property name="port:output"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output
> port that indicates whether or not the end of the file has been reached.
> If the end of the file has been reached, the port will produce a true
> value. Otherwise, the value is false.</configure></property>
> <property name="port:trigger"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>A multiport
> that has no declared type (in other words, the port can accept any data
> type: double, int, array, etc.) If the port is connected, the actor will
> not fire until the trigger port receives an input token. Connecting the
> port is optional, but useful when scheduling the actor to perform at a
> certain time.</configure></property>
> <property name="port:outputFilePort"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An optional
> input port that accepts the name of the output file. The output file name
> can also be specified using the outputFile
> parameter.</configure></property>
> <property name="prop:overwrite"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Select
> overwrite to replace the content of an existing destination file with the
> new content.</configure></property>
> <property name="prop:Parameters @UserLevelDescription"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure></configure></property>
> <property name="prop:outputFile"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The path of
> an output file to which to write.</configure></property>
> <property name="prop:fileOrURL"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The file name
> or URL from which to read. See FileParameter for more information about
> specifying file names.</configure></property>
> </property> <property name="entityId"
> class="org.kepler.moml.NamedObjId"
> value="urn:lsid:kepler-project.org:actor:252:1">
> </property>
> <property name="class" class="ptolemy.kernel.util.StringAttribute"
> value="util.URLToLocalFile">
> <property name="id" class="ptolemy.kernel.util.StringAttribute"
> value="urn:lsid:kepler-project.org:class:1078:1">
> </property>
> </property>
> <property name="semanticType00" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:1:1#ExternalInputActor">
> </property>
> <property name="semanticType11" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:2:1#RemoteInput">
> </property>
> <property name="_location" class="ptolemy.kernel.util.Location"
> value="[330.0, 370.0]">
> </property>
> <property name="" class="ptolemy.vergil.basic.DocAttribute">
> <property name="description"
> class="ptolemy.data.expr.StringParameter" value="<p>The
> URLToLocalFile actor reads a URL and copies it to the local file system.
> The actor can also be used to read a local file and then write it to
> another location in the file system.</p>
<p>Use the
> optional outputFilePort to provide a name for the copied file. Specify an
> output file name with either the outputFilePort or the outputFile
> parameter. When the actor is done reading and saving the file, the output
> port will produce a true value.</p>">
> </property>
> <property name="author"
> class="ptolemy.kernel.util.StringAttribute" value="Dan Higgins">
> </property>
> <property name="version"
> class="ptolemy.kernel.util.StringAttribute" value="null">
> </property>
> <property name="fileOrURL (parameter)"
> class="ptolemy.data.expr.StringParameter" value="The file name or URL from
> which to read. See FileParameter for more information about specifying
> file names.">
> </property>
> <property name="outputFile (parameter)"
> class="ptolemy.data.expr.StringParameter" value="The path of an output
> file to which to write.">
> </property>
> <property name="overwrite (parameter)"
> class="ptolemy.data.expr.StringParameter" value="Select overwrite to
> replace the content of an existing destination file with the new
> content.">
> </property>
> <property name="output (port)"
> class="ptolemy.kernel.util.StringAttribute" value="An output port that
> indicates whether or not the end of the file has been reached. If the end
> of the file has been reached, the port will produce a true value.
> Otherwise, the value is false.">
> </property>
> <property name="trigger (port)"
> class="ptolemy.kernel.util.StringAttribute" value="A multiport that has no
> declared type (in other words, the port can accept any data type: double,
> int, array, etc.) If the port is connected, the actor will not fire until
> the trigger port receives an input token. Connecting the port is optional,
> but useful when scheduling the actor to perform at a certain time.">
> </property>
> <property name="fileOrURLPort (port)"
> class="ptolemy.kernel.util.StringAttribute" value="An optional input port
> that accepts the file name or URL of a file to be read. When the port is
> connected, the actor reads the file sent by the previous workflow step.
> The file name or URL can also be specified using the fileOrURL
> parameter.">
> </property>
> <property name="outputFilePort (port)"
> class="ptolemy.kernel.util.StringAttribute" value="An optional input port
> that accepts the name of the output file. The output file name can also be
> specified using the outputFile parameter.">
> </property>
> <property name="Parameters @UserLevelDescription (parameter)"
> class="ptolemy.data.expr.StringParameter" value="">
> </property>
> </property>
> </entity>
> <entity name="String Constant3" class="ptolemy.actor.lib.StringConst">
> <property name="firingCountLimit"
> class="ptolemy.data.expr.Parameter" value="1">
> </property>
> <property name="NONE" class="ptolemy.data.expr.Parameter"
> value="0">
> </property>
> <property name="value" class="ptolemy.data.expr.Parameter"
> value="memeoutput.html">
> </property>
> <property name="KeplerDocumentation"
> class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> <property name="description"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="author"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Edward
> Lee</configure></property>
> <property name="version"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="userLevelDocumentation"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The
> StringConstant actor outputs a string specified via the actor's value
> parameter.</p>
<p>Specifying strings with the
> StringConstant actor is convenient, as the actor does not require that
> strings be surrounded by quotes. The actor is often used to specify file
> paths, which can be selected using the Browse button available in the
> actor's parameters.</p>
<p>Specified string values
> can include references to parameters within scope (i.e., parameters
> defined at the same level of the hierarchy or higher).
> </p>
<p>NOTE: If using a PN Director, the
> 'firingCountLimit' parameter is often set to a finite integer (e.g. '1')
> so that the workflow will terminate.
> </p>
</configure></property>
> <property name="port:output"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output
> port that broadcasts a string constant specified by the value parameter.
> </configure></property>
> <property name="port:trigger"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>A multiport
> that has no declared type (in other words, the port can accept any data
> type: double, int, array, etc.) If the port is connected, the actor will
> not fire until the trigger port receives an input token. Connecting the
> port is optional, but useful when scheduling the actor to perform at a
> certain time. </configure></property>
> <property name="prop:firingCountLimit"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The limit on
> the number of times the actor will fire. The default value is 'NONE',
> meaning there is no limit on the number of time the constant will be
> provided to the output port. Any integer can be provided as a value for
> this parameter.</configure></property>
> <property name="prop:value"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The value
> produced by the actor. Specified strings do not require enclosing quotes.
> (To include a '$' sign in the string, enter '$$'.)</configure></property>
> </property> <property name="entityId"
> class="org.kepler.moml.NamedObjId"
> value="urn:lsid:kepler-project.org:actor:204:1">
> </property>
> <property name="class" class="ptolemy.kernel.util.StringAttribute"
> value="ptolemy.actor.lib.StringConst">
> <property name="id" class="ptolemy.kernel.util.StringAttribute"
> value="urn:lsid:kepler-project.org:class:1052:1">
> </property>
> </property>
> <property name="semanticType00" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:1:1#StringFunctionActor">
> </property>
> <property name="semanticType11" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:2:1#Constant">
> </property>
> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> <property name="attributeName"
> class="ptolemy.kernel.util.StringAttribute" value="value">
> </property>
> <property name="displayWidth"
> class="ptolemy.data.expr.Parameter" value="60">
> </property>
> </property>
> <property name="_location" class="ptolemy.kernel.util.Location"
> value="[180.0, 455.0]">
> </property>
> </entity>
> <entity name="Boolean Switch" class="ptolemy.actor.lib.BooleanSwitch">
> <property name="KeplerDocumentation"
> class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> <property name="description"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="author"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Steve
> Neuendorffer</configure></property>
> <property name="version"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="userLevelDocumentation"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The
> BooleanSwitch actor reads a value of any type, as well as a Boolean token
> that is used as a control. If the Boolean token is true, the actor outputs
> the received value to the trueOutput port; if the Boolean token is false,
> the actor outputs the received value to the falseOutput port.
If the
> actor has never received a value on the control port, then the actor will
> output to the falseOutput port.</p>
<p>The actor only
> works under certain directors. It will not work under an SDF Director, but
> it will under a PN Director, for example.</p></configure></property>
> <property name="port:input"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An input port
> that accepts tokens of any type.</configure></property>
> <property name="port:falseOutput"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output
> port that broadcasts the input token when the control is
> false.</configure></property>
> <property name="port:trueOutput"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output
> port that broadcasts the input token when the control is
> true.</configure></property>
> <property name="port:control"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An input port
> that accepts a Boolean token used to select which output port (trueOutput
> or falseOutput) to broadcast.</configure></property>
> </property> <property name="entityId"
> class="org.kepler.moml.NamedObjId"
> value="urn:lsid:kepler-project.org:actor:54:1">
> </property>
> <property name="class" class="ptolemy.kernel.util.StringAttribute"
> value="ptolemy.actor.lib.BooleanSwitch">
> <property name="id" class="ptolemy.kernel.util.StringAttribute"
> value="urn:lsid:kepler-project.org:class:930:1">
> </property>
> </property>
> <property name="semanticType00" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:1:1#BooleanControlActor">
> </property>
> <property name="semanticType11" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:2:1#BooleanControl">
> </property>
> <property name="_location" class="ptolemy.kernel.util.Location"
> value="[430.0, 435.0]">
> </property>
> <property name="" class="ptolemy.vergil.basic.DocAttribute">
> <property name="description"
> class="ptolemy.data.expr.StringParameter" value="<p>The
> BooleanSwitch actor reads a value of any type, as well as a Boolean token
> that is used as a control. If the Boolean token is true, the actor outputs
> the received value to the trueOutput port; if the Boolean token is false,
> the actor outputs the received value to the falseOutput port.
If the
> actor has never received a value on the control port, then the actor will
> output to the falseOutput port.</p>
<p>The actor only
> works under certain directors. It will not work under an SDF Director, but
> it will under a PN Director, for example.</p>">
> </property>
> <property name="author"
> class="ptolemy.kernel.util.StringAttribute" value="Steve Neuendorffer">
> </property>
> <property name="version"
> class="ptolemy.kernel.util.StringAttribute" value="null">
> </property>
> <property name="input (port)"
> class="ptolemy.kernel.util.StringAttribute" value="An input port that
> accepts tokens of any type.">
> </property>
> <property name="control (port)"
> class="ptolemy.kernel.util.StringAttribute" value="An input port that
> accepts a Boolean token used to select which output port (trueOutput or
> falseOutput) to broadcast.">
> </property>
> <property name="trueOutput (port)"
> class="ptolemy.kernel.util.StringAttribute" value="An output port that
> broadcasts the input token when the control is true.">
> </property>
> <property name="falseOutput (port)"
> class="ptolemy.kernel.util.StringAttribute" value="An output port that
> broadcasts the input token when the control is false.">
> </property>
> </property>
> <port name="control" class="ptolemy.actor.TypedIOPort">
> <property name="input"/>
> <property name="_cardinal"
> class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> </property>
> </port>
> </entity>
> <entity name="MAST" class="edu.sdsc.nbcr.opal.OpalClient">
> <property name="serviceURL"
> class="ptolemy.data.expr.StringParameter"
> value="http://ws.nbcr.net/opal2/services/MASTService">
> </property>
> <property name="numberOfExtraInputFiles"
> class="ptolemy.data.expr.StringParameter" value="2">
> </property>
> <property name="KeplerDocumentation"
> class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> <property name="description"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Opal client
> for Kepler</configure></property>
> <property name="author"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Luca
> Clementi</configure></property>
> <property name="version"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.0-alpha</configure></property>
> <property name="userLevelDocumentation"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure><h1>Opal
> Client for Kepler.</h1><p> This actor can be used to access
> Opal based serivce. </p><p>Modify the serviceURL parameter so
> that it points to a valid Opal Service. If you modify the serviceURL in
> the properties editor you have to commit and reopen the properties
> editor.</p><p>Below there is the documentation of the service
> pointed by the current URL.</p> <p>MAST is a tool for
> searching sequence databases using motifs. Version
> 3.5.7</p><pre>
mast <mfile>
> [optional arguments ...]
<mfile>
> file containing motifs to use; may be a MEME output
> file or a file with the format given below
> [<database>] or
[-d <database>]
> database to search with motifs or
[-stdin] read
> database from standard input;
Default: reads
> database specified inside <mfile>
[-c
> <count>] only use the first <count>
> motifs
[-a <alphabet>] <mfile> is
> assumed to contain motifs in the
format output
> by bin/make_logodds
and
> <alphabet> is their alphabet; -d
> <database>
or -stdin must be
> specified when this option is used
[-stdout] print
> output to standard output instead of file
[-text]
> output in text (ASCII) format;
(default:
> hypertext (HTML) format)
[-sep] score reverse
> complement DNA strand as a separate
> sequence
[-norc] do not score reverse complement DNA
> strand
[-dna] translate DNA sequences to protein
> [-comp] adjust p-values and E-values for sequence composition
> [-rank <rank>] print results starting with
> <rank> best (default: 1)
[-smax
> <smax>] print results for no more than <smax>
> sequences
(default: all)
[-ev
> <ev>] print results for sequences with E-value <
> <ev>
(default: 10)
> [-mt <mt>] show motif matches with p-value < mt
> (default: 0.0001)
[-w] show weak matches
> (mt<p-value<mt*10) in angle brackets
[-bfile
> <bfile>] read background frequencies from
> <bfile>
[-seqp] use SEQUENCE p-values
> for motif thresholds
(default: use POSITION
> p-values)
[-mf <mf>] print
> <mf> as motif file name
[-df <df>]
> print <df> as database name
[-minseqs
> <minseqs>] lower bound on number of sequences in db
> [-mev <mev>]+ use only motifs with E-values less than
> <mev>
[-m <m>]+ use only
> motif(s) number <m> (overrides -mev)
[-diag
> <diag>] nominal order and spacing of motifs
> [-best] include only the best motif in diagrams
> [-remcorr] remove highly correlated motifs from query
> [-brief] brief output--do not print documentation
[-b]
> print only sections I and II
[-nostatus] do not print
> progress report
[-hit_list] print hit_list instead of
> diagram; implies -text
> </pre></configure></property>
> <property name="port:output"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>It returns a
> list of Strings, containing the URL of the output
> files</configure></property>
> <property name="port:baseUrl"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The base URL
> containing the working directory of the running
> jobs</configure></property>
> <property name="prop:commandLine"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Insert the
> command line you want to execute (without the application
> name)</configure></property>
> <property name="prop:inputFile"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Select an
> input file</configure></property>
> <property name="prop:cpuNumber"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>If it is a
> parallel application insert the CPU number</configure></property>
> <property name="prop:numberOfExtraInputFiles"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The number of
> extra input files that are needed to execture the
> application</configure></property>
> <property name="prop:serviceURL"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The URL of
> the Opal service that you want to execute</configure></property>
> </property> <property name="entityId"
> class="org.kepler.moml.NamedObjId"
> value="urn:lsid:kepler-project.org:actor:842:1">
> </property>
> <property name="class" class="ptolemy.kernel.util.StringAttribute"
> value="edu.sdsc.nbcr.opal.OpalClient">
> <property name="id" class="ptolemy.kernel.util.StringAttribute"
> value="urn:lsid:kepler-project.org:class:842:1">
> </property>
> </property>
> <property name="semanticType00" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:1:1#WebServiceActor">
> </property>
> <property name="semanticType11" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:2:1#WebService">
> </property>
> <property name="_location" class="ptolemy.kernel.util.Location"
> value="[520.0, 505.0]">
> </property>
> <property name="commandLine"
> class="ptolemy.data.expr.StringParameter" value="memeoutput.html">
> </property>
> <property name="cpuNumber"
> class="ptolemy.data.expr.StringParameter" value="">
> </property>
> <property name="inputFile1Dynamic"
> class="ptolemy.actor.parameters.FilePortParameter"
> value="memeoutput.html">
> </property>
> <property name="inputFile2Dynamic"
> class="ptolemy.actor.parameters.FilePortParameter" value="At.fa">
> </property>
> <port name="output" class="ptolemy.actor.TypedIOPort">
> <property name="output"/>
> <property name="_showName" class="ptolemy.data.expr.Parameter"
> value="false">
> </property>
> </port>
> <port name="baseUrl" class="ptolemy.actor.TypedIOPort">
> <property name="output"/>
> <property name="_showName" class="ptolemy.data.expr.Parameter"
> value="false">
> </property>
> </port>
> <port name="inputFile1Dynamic"
> class="ptolemy.actor.parameters.ParameterPort">
> <property name="input"/>
> </port>
> <port name="inputFile2Dynamic"
> class="ptolemy.actor.parameters.ParameterPort">
> <property name="input"/>
> </port>
> </entity>
> <entity name="BrowserUI" class="org.sdm.spa.BrowserUI">
> <property name="fileOrURL" class="ptolemy.data.expr.FileParameter"
> value="http://ws.nbcr.net/app1242864427939">
> </property>
> <property name="file extension"
> class="ptolemy.data.expr.StringParameter" value="">
> </property>
> <property name="portConfiguration"
> class="ptolemy.data.expr.StringParameter" value="">
> <property name="portConfiguration"
> class="ptolemy.actor.gui.style.TextStyle">
> <property name="height" class="ptolemy.data.expr.Parameter"
> value="10">
> </property>
> <property name="width" class="ptolemy.data.expr.Parameter"
> value="30">
> </property>
> </property>
> </property>
> <property name="use for display"
> class="ptolemy.data.expr.Parameter" value="false">
> </property>
> <property name="hasTrigger" class="ptolemy.data.expr.Parameter"
> value="false">
> </property>
> <property name="KeplerDocumentation"
> class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> <property name="description"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="author"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Ilkay
> Altintas, Efrat Jaeger and Kai Lin</configure></property>
> <property name="version"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="userLevelDocumentation"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The
> BrowserUI actor displays text/HTML in the system's default browser,
> allowing users to interact with the content during workflow execution. The
> actor outputs arrays of user-selected "(name, value)" pairs in
> XML format.</p>
<p>The actor can also be used to
> simply display a file in a Web browser, which is useful for displaying the
> output of legacy applications. Select the useForDisplay parameter to use
> the BrowserUI actor as a browser viewer with no output
> port.</p>
<p>The actor accepts either a URL/file path
> or a string of HTML/text. If content is input as a string, select a file
> type (e.g., html or xml) with the
> fileExtensionParameter.</p>
<p>The BrowserUI actor is
> often used in conjunction with the SRBCreateQueryConditions and
> SRBCreateQueryInterface actors to create a set of user-specified query
> conditions.</p></configure></property>
> <property name="port:trigger"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The port to
> trigger the actor in case there are no other input ports. By default, this
> port is hidden.</configure></property>
> <property name="port:connected"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>This port is
> used only for scheduling the actor. Activate the hasTrigger parameter to
> display the trigger port.</configure></property>
> <property name="port:xmlOutput"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output
> port that broadcasts an array of user-selected xml "(name,
> value)" pairs.</configure></property>
> <property name="port:fileContent"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An input port
> that accepts a string of content to display. Select a file extension that
> matches the content (e.g., .html,.xml or .svg) with the file extension
> parameter.</configure></property>
> <property name="port:fileOrURL"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An input port
> that accepts the file name or URL of a file to be read. The value can also
> be specified with the fileOrURL parameter.</configure></property>
> <property name="prop:file extension"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The extension
> of the input content: .html, .xml, .txt, .xsl, or .svg. Specify this
> parameter when content is input via the fileContent input
> port.</configure></property>
> <property name="prop:use for display"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Select this
> setting to use the actor solely for display. The output port will be
> turned off. By default, the setting is off.</configure></property>
> <property name="prop:portConfiguration"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The output
> port configuration. The actor will create the described ports. Each port
> should be represented on a separate line as portName portType (e.g.,
> height int).</configure></property>
> <property name="prop:fileOrURL"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The file name
> or URL of a file to be read. The value can also be specified via the
> fileOrURL port.</configure></property>
> <property name="prop:hasTrigger"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify
> whether to activate a trigger port or not. The default is
> off.</configure></property>
> </property> <property name="entityId"
> class="org.kepler.moml.NamedObjId"
> value="urn:lsid:kepler-project.org:actor:240:1">
> </property>
> <property name="class" class="ptolemy.kernel.util.StringAttribute"
> value="org.sdm.spa.BrowserUI">
> <property name="id" class="ptolemy.kernel.util.StringAttribute"
> value="urn:lsid:kepler-project.org:class:1066:1">
> </property>
> </property>
> <property name="semanticType00" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:1:1#ExternalGraphicalOutputActor">
> </property>
> <property name="semanticType11" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:2:1#TextualOutput">
> </property>
> <property name="_location" class="ptolemy.kernel.util.Location"
> value="[665.0, 525.0]">
> </property>
> <port name="trigger" class="ptolemy.actor.TypedIOPort">
> <property name="input"/>
> <property name="_hide"
> class="ptolemy.data.expr.SingletonParameter" value="true">
> </property>
> </port>
> </entity>
> <entity name="Output file from meme"
> class="ptolemy.actor.lib.Expression">
> <property name="expression"
> class="ptolemy.kernel.util.StringAttribute" value="baseURL +
> "/stdout.txt"">
> <property name="_hide" class="ptolemy.data.expr.Parameter"
> value="true">
> </property>
> </property>
> <property name="KeplerDocumentation"
> class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> <property name="description"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="author"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu,
> Edward A. Lee, Steve Neuendorffer</configure></property>
> <property name="version"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> <property name="userLevelDocumentation"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The
> Expression actor evaluates a specified expression (e.g., an addition or
> multiplication operation), which may reference the values of
> user-specified input ports, the current time, or the actor's iteration
> count. The actor outputs the value of the evaluated expression.
> </p>
<p>Expressions are specified in the Ptolemy
> expression language via the expression parameter. For more information
> about the expression language, see
> http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf.
> </p>
<p>By default, the expression parameter is
> empty, and attempting to execute the actor without first specifying an
> expression generates an error. Expressions can refer to the values of
> inputs by the port name; to the current time by the identifier
> "time"; and to the current iteration count by the identifier
> "iteration." </p>
<p>Input ports are
> created by the user and correspond to variables used in the specified
> expression. Currently, the Expression actor does not support input
> multiports. The actor requires all of its inputs to be present. If inputs
> are not all present, then the actor will generate an error.
> </p>
<p>Note: the Expression actor can be used
> instead of many of the arithmetic actors, such as AddSubtract,
> MultiplyDivide, and TrigFunction. However, those actors will be usually be
> more efficient, and sometimes more convenient to
> use.</p></configure></property>
> <property name="port:output"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output
> port that broadcasts the value of the evaluated expression. The actor
> automatically determines the type based on the type of the
> input.</configure></property>
> <property name="prop:expression"
> class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression
> to evaluate. Expressions are specified in the Ptolemy expression language.
> For more information about the expression language, see
> http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf.
> By default, the parameter is empty, and attempting to execute the actor
> without first specifying an expression generates an error. Expressions can
> refer to the values of inputs by the port name; to the current time by the
> identifier "time"; and to the current iteration count by the
> identifier "iteration."</configure></property>
> </property> <property name="entityId"
> class="org.kepler.moml.NamedObjId"
> value="urn:lsid:kepler-project.org:actor:75:1">
> </property>
> <property name="class" class="ptolemy.kernel.util.StringAttribute"
> value="ptolemy.actor.lib.Expression">
> <property name="id" class="ptolemy.kernel.util.StringAttribute"
> value="urn:lsid:kepler-project.org:class:950:1">
> </property>
> </property>
> <property name="semanticType00" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> </property>
> <property name="semanticType11" class="org.kepler.sms.SemanticType"
> value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> </property>
> <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> <property name="attributeName"
> class="ptolemy.kernel.util.StringAttribute" value="expression">
> </property>
> <property name="displayWidth"
> class="ptolemy.data.expr.Parameter" value="60">
> </property>
> </property>
> <property name="_location" class="ptolemy.kernel.util.Location"
> value="[220.0, 390.0]">
> </property>
> <property name="" class="ptolemy.vergil.basic.DocAttribute">
> <property name="description"
> class="ptolemy.data.expr.StringParameter" value="<p>The Expression
> actor evaluates a specified expression (e.g., an addition or
> multiplication operation), which may reference the values of
> user-specified input ports, the current time, or the actor's iteration
> count. The actor outputs the value of the evaluated expression.
> </p>
<p>Expressions are specified in the Ptolemy
> expression language via the expression parameter. For more information
> about the expression language, see
> http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf.
> </p>
<p>By default, the expression parameter is
> empty, and attempting to execute the actor without first specifying an
> expression generates an error. Expressions can refer to the values of
> inputs by the port name; to the current time by the identifier
> "time"; and to the current iteration count by the identifier
> "iteration." </p>
<p>Input ports are
> created by the user and correspond to variables used in the specified
> expression. Currently, the Expression actor does not support input
> multiports. The actor requires all of its inputs to be present. If inputs
> are not all present, then the actor will generate an error.
> </p>
<p>Note: the Expression actor can be used
> instead of many of the arithmetic actors, such as AddSubtract,
> MultiplyDivide, and TrigFunction. However, those actors will be usually be
> more efficient, and sometimes more convenient to use.</p>">
> </property>
> <property name="author"
> class="ptolemy.kernel.util.StringAttribute" value="Xiaojun Liu, Edward A.
> Lee, Steve Neuendorffer">
> </property>
> <property name="version"
> class="ptolemy.kernel.util.StringAttribute" value="null">
> </property>
> <property name="expression (parameter)"
> class="ptolemy.data.expr.StringParameter" value="An expression to
> evaluate. Expressions are specified in the Ptolemy expression language.
> For more information about the expression language, see
> http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf.
> By default, the parameter is empty, and attempting to execute the actor
> without first specifying an expression generates an error. Expressions can
> refer to the values of inputs by the port name; to the current time by the
> identifier "time"; and to the current iteration count by the
> identifier "iteration."">
> </property>
> <property name="output (port)"
> class="ptolemy.kernel.util.StringAttribute" value="An output port that
> broadcasts the value of the evaluated expression. The actor automatically
> determines the type based on the type of the input.">
> </property>
> </property>
> <port name="baseURL" class="ptolemy.actor.TypedIOPort">
> <property name="input"/>
> </port>
> </entity>
> <relation name="relation2" class="ptolemy.actor.TypedIORelation">
> <property name="width" class="ptolemy.data.expr.Parameter"
> value="1">
> </property>
> <vertex name="vertex1" value="[100.0, 535.0]">
> </vertex>
> </relation>
> <relation name="relation" class="ptolemy.actor.TypedIORelation">
> <property name="width" class="ptolemy.data.expr.Parameter"
> value="1">
> </property>
> <vertex name="vertex1" value="[210.0, 305.0]">
> </vertex>
> </relation>
> <relation name="relation4" class="ptolemy.actor.TypedIORelation">
> <property name="width" class="ptolemy.data.expr.Parameter"
> value="1">
> </property>
> <vertex name="vertex1" value="[300.0, 455.0]">
> </vertex>
> </relation>
> <relation name="relation5" class="ptolemy.actor.TypedIORelation">
> <property name="width" class="ptolemy.data.expr.Parameter"
> value="1">
> </property>
> </relation>
> <relation name="relation7" class="ptolemy.actor.TypedIORelation">
> <property name="width" class="ptolemy.data.expr.Parameter"
> value="1">
> </property>
> </relation>
> <relation name="relation3" class="ptolemy.actor.TypedIORelation">
> <property name="width" class="ptolemy.data.expr.Parameter"
> value="1">
> </property>
> </relation>
> <relation name="relation6" class="ptolemy.actor.TypedIORelation">
> </relation>
> <link port="MEME.baseUrl" relation="relation"/>
> <link port="MEME.dataSet" relation="relation2"/>
> <link port="Input File.output" relation="relation2"/>
> <link port="MEME Output Directory.input" relation="relation"/>
> <link port="URL To Local File.output" relation="relation5"/>
> <link port="URL To Local File.fileOrURLPort" relation="relation3"/>
> <link port="URL To Local File.outputFilePort" relation="relation4"/>
> <link port="String Constant3.output" relation="relation4"/>
> <link port="Boolean Switch.input" relation="relation4"/>
> <link port="Boolean Switch.control" relation="relation5"/>
> <link port="Boolean Switch.trueOutput" relation="relation6"/>
> <link port="MAST.baseUrl" relation="relation7"/>
> <link port="MAST.inputFile1Dynamic" relation="relation6"/>
> <link port="MAST.inputFile2Dynamic" relation="relation2"/>
> <link port="BrowserUI.fileOrURL" relation="relation7"/>
> <link port="Output file from meme.output" relation="relation3"/>
> <link port="Output file from meme.baseURL" relation="relation"/>
> </entity>
>
>>At1g01140.1_4-2-4_SnRK3.12 SNF1-related Protein Kinase, subfamily 3
> MSGSRRKATPASRTRVGNYEMGRTLGEGSFAKVKYAKNTVTGDQAAIKILDREKVFRHKM
> VEQLKREISTMKLIKHPNVVEIIEVMASKTKIYIVLELVNGGELFDKIAQQGRLKEDEAR
> RYFQQLINAVDYCHSRGVYHRDLKPENLILDANGVLKVSDFGLSAFSRQVREDGLLHTAC
> GTPNYVAPEVLSDKGYDGAAADVWSCGVILFVLMAGYLPFDEPNLMTLYKRICKAEFSCP
> PWFSQGAKRVIKRILEPNPITRISIAELLEDEWFKKGYKPPSFDQDDEDITIDDVDAAFS
> NSKECLVTEKKEKPVSMNAFELISSSSEFSLENLFEKQAQLVKKETRFTSQRSASEIMSK
> MEETAKPLGFNVRKDNYKIKMKGDKSGRKGQLSVATEVFEVAPSLHVVELRKTGGDTLEF
> HKFYKNFSSGLKDVVWNTDAAAEEQKQ
>>At1g01140.2_SnRK3.12 SNF1-related Protein Kinase, subfamily 3
> MSGSRRKATPASRTRVGNYEMGRTLGEGSFAKVKYAKNTVTGDQAAIKILDREKVFRHKM
> VEQLKREISTMKLIKHPNVVEIIEVMASKTKIYIVLELVNGGELFDKIAQQGRLKEDEAR
> RYFQQLINAVDYCHSRGVYHRDLKPENLILDANGVLKVSDFGLSAFSRQVREDGLLHTAC
> GTPNYVAPEVLSDKGYDGAAADVWSCGVILFVLMAGYLPFDEPNLMTLYKRVRICKAEFS
> CPPWFSQGAKRVIKRILEPNPITRISIAELLEDEWFKKGYKPPSFDQDDEDITIDDVDAA
> FSNSKECLVTEKKEKPVSMNAFELISSSSEFSLENLFEKQAQLVKKETRFTSQRSASEIM
> SKMEETAKPLGFNVRKDNYKIKMKGDKSGRKGQLSVATEVFEVAPSLHVVELRKTGGDTL
> EFHKFYKNFSSGLKDVVWNTDAAAEEQKQ
>>At1g01140.3_SnRK3.12 SNF1-related Protein Kinase, subfamily 3
> MSGSRRKATPASRTRVGNYEMGRTLGEGSFAKVKYAKNTVTGDQAAIKILDREKVFRHKM
> VEQLKREISTMKLIKHPNVVEIIEVMASKTKIYIVLELVNGGELFDKIAQQGRLKEDEAR
> RYFQQLINAVDYCHSRGVYHRDLKPENLILDANGVLKVSDFGLSAFSRQVREDGLLHTAC
> GTPNYVAPEVLSDKGYDGAAADVWSCGVILFVLMAGYLPFDEPNLMTLYKRICKAEFSCP
> PWFSQGAKRVIKRILEPNPITRISIAELLEDEWFKKGYKPPSFDQDDEDITIDDVDAAFS
> NSKECLVTEKKEKPVSMNAFELISSSSEFSLENLFEKQAQLVKKETRFTSQRSASEIMSK
> MEETAKPLGFNVRKDNYKIKMKGDKSGRKGQLSVATEVFEVAPSLHVVELRKTGGDTLEF
> HKVCDSFYKNFSSGLKDVVWNTDAAAEEQKQ
>>At1g01450.1_2-1-1 putative protein kinase
> MADFLLKHLGDGNESPKLFPSSLLDNTKDYQVKKRLGNGSQYKEITWLGESFALRHFFGD
> IDALLPQITPLLSLSHPNIVYYLCGFTDEEKKECFLVMELMRKTLGMHIKEVCGPRKKNT
> LSLPVAVDLMLQIALGMEYLHSKRIYHGELNPSNILVKPRSNQSGDGYLLGKIFGFGLNS
> VKGFSSKSASLTSQNENFPFIWYSPEVLEEQEQSGTAGSLKYSDKSDVYSFGMVSFELLT
> GKVPFEDSHLQGDKMSRNIRAGERPLFPFNSPKFITNLTKRCWHADPNQRPTFSSISRIL
> RYIKRFLALNPECYSSSQQDPSIAPTVDYCEIETKLLQKLSWESTELTKVSQVPFQMFAY
> RVVERAKTCEKDNLREPSESGSEWASCSEDEGGAGSDEQLSYAKERRLSCSSNDVGMSKK
> QVSNLLKRASSLKPIQKPGEIIISQYIYIYIGSLTNMNLVTCTNFFVLCH
>>At1g01540.1_1-6-3 Putative protein kinase
> MSVYDAAFLNTELSKPTSIFGLRLWVVIGILLGSLIVIALFLLSLCLTSRRKNRKPRADF
> ASAAIATPPISKEIKEIVPAQNQSVPAEIQVDIGKIEHRVVFSDRVSSGESRGTASASET
> ASYSGSGNCGPEVSHLGWGRWYTLRELEAATNGLCEENVIGEGGYGIVYRGILTDGTKVA
> VKNLLNNRGQAEKEFKVEVEVIGRVRHKNLVRLLGYCVEGAYRMLVYDFVDNGNLEQWIH
> GDVGDVSPLTWDIRMNIILGMAKGLAYLHEGLEPKVVHRDIKSSNILLDRQWNAKVSDFG
> LAKLLGSESSYVTTRVMGTFGYVAPEYACTGMLNEKSDIYSFGILIMEIITGRNPVDYSR
> PQGEVFDKHIQSSLCFCKWSYYVSWL
>>At1g01540.2_Putative protein kinase
> MSVYDAAFLNTELSKPTSIFGLRLWVVIGILLGSLIVIALFLLSLCLTSRRKNRKPRADF
> ASAAIATPPISKEIKEIVPAQNQSVPAEIQVDIGKIEHRVVFSDRVSSGESRGTASASET
> ASYSGSGNCGPEVSHLGWGRWYTLRELEAATNGLCEENVIGEGGYGIVYRGILTDGTKVA
> VKNLLNNRGQAEKEFKVEVEVIGRVRHKNLVRLLGYCVEGAYRMLVYDFVDNGNLEQWIH
> GDVGDVSPLTWDIRMNIILGMAKGLAYLHEGLEPKVVHRDIKSSNILLDRQWNAKVSDFG
> LAKLLGSESSYVTTRVMGTFGYVAPEYACTGMLNEKSDIYSFGILIMEIITGRNPVDYSR
> PQGETNLVDWLKSMVGNRRSEEVVDPKIPEPPSSKALKRVLLVALRCVDPDANKRPKMGH
> IIHMLEAEDLLYRDERRTTRDHGSRERQETAVVAAGSESGESGSRHHQQKQR
>>At1g01560.1_4-5-1_MPK11 MAP kinase 11
> MSIEKPFFGDDSNRGVSINGGRYVQYNVYGNLFEVSKKYVPPLRPIGRGASGIVCAAWNS
> ETGEEVAIKKIGNAFGNIIDAKRTLREIKLLKHMDHDNVIAIIDIIRPPQPDNFNDVHIV
> YELMDTDLHHIIRSNQPLTDDHSRFFLYQLLRGLKYVHSANVLHRDLKPSNLLLNANCDL
> KIGDFGLARTKSETDFMTEYVVTRWYRAPELLLNCSEYTAAIDIWSVGCILGEIMTREPL
> FPGRDYVQQLRLITEVNFSLFHLTILFRFNLKKEH
>>At1g01740.1_1-16-1 putative protein kinase
> MGGQSSKIGTCCSHKTTALEAPDVENKENGEVNGVHSFREYSLEQLKIATSCFALENVVS
> EHGETAPNVVYQGKLENHMKIAIKRFSGTAWPDPRQFLEEARLVGQLRSKRMANLLGYCC
> EGGERLLVAEFMPNETLAKHLFHWDTEPMKWAMRLRVALYISEALEYCSNNGHTLYHDLN
> AYRVLFDEECNPRLSTFGLMKNSRDGKSYSTNLAFTPPEYLRTGRITAESVIYSFGTLLL
> DLLTGKHIPPSHALDLIRDRNLQTLTDSCLEGQFSDSDGTELVRLTSCCLQYEARERPNI
> KSLVTALISLQKDTEVLSHVLMGLPQSGTFASPPSPFAEACSGKDLTSMVEILEKIGYKD
> DEDLSFMWTEQMQEAINSKKKGDIAFRRKDFSEAIEFYTQFLDLGMISATVLVRRSQSYL
> MSNMAKEALDDAMKAQGISPVWYVALYLQSAALSVLGMEKESQIALTEGSILEARKISAS
> TQN
>>At1g02970.1_4-3-1 putative protein kinase
> MFEKNGRTLLAKRKTQGTIKTRASKKIRKMEGTLERHSLLQFGQLSKISFENRPSSNVAS
> SAFQGLLDSDSSELRNQLGSADSDANCGEKDFILSQDFFCTPDYITPDNQNLMSGLDISK
> DHSPCPRSPVKLNTVKSKRCRQESFTGNHSNSTWSSKHRVDEQENDDIDTDEVMGDKLQA
> NQTERTGYVSQAAVALRCRAMPPPCLKNPYVLNQSETATDPFGHQRSKCASFLPVSTSGD
> GLSRYLTDFHEIRQIGAGHFSRVFKVLKRMDGCLYAVKHSTRKLYLDSERRKAMMEVQAL
> AALGFHENIVGYYSSWFENEQLYIQLELCDHSLSALPKKSSLKVSEREILVIMHQIAKAL
> HFVHEKGIAHLDVKPDNIYIKNGVCKLGDFGCATRLDKSLPVEEGDARYMPQEILNEDYE
> HLDKVDIFSLGVTVYELIKGSPLTESRNQSLNIKEGKLPLLPGHSLQLQQLLKTMMDRDP
> KRRPSARELLDHPMFDRIRG
>>At1g03740.1_4-5-2 putative protein kinase
> MGCVNSRHRPFRRKSTTLKESSEEKRSSRIDSSRRIDDWIQPEDGFDRLSNSGDAKVRLI
> ESEMFSTSRCHDHQIGKILENPATVAHMDRVVHDQELRRASSAVVDSDLDIDPKVVKAKL
> DRWNSKDSKVRLIESEKLSSSMFSEHHQIEKGVEKPEVEASVRVVHRELKRGSSIVSPKD
> AERKQVAAGWPSWLVSVAGESLVDWAPRRANTFEKLEKIGQGTYSSVYRARDLLHNKIVA
> LKKVRFDLNDMESVKFMAREIIVMRRLDHPNVLKLEGLITAPVSSSLYLVFEYMDHDLLG
> LSSLPGVKFTEPQVKCYMRQLLSGLEHCHSRGVLHRDIKGSNLLIDSKGVLKIADFGLAT
> FFDPAKSVSLTSHVVTLWYRPPELLLGASHYGVGVDLWSTGCILGELYAGKPILPGKTEV
> EQLHKIFKLCGSPTENYWRKQKLPSSAGFKTAIPYRRKVSEMFKDFPASVLSLLETLLSI
> DPDHRSSADRALESEYFKTKPFACDPSNLPKYPPSKEIDAKMRDEAKRQQPMRAEKQEDK
> TL
>>At1g03920.1_4-2-6 putative protein kinase
> MDSARSWFHKFQPRDKPRKKDMFSGSTYGGGVTETTVPDGGNDTETATKLPPLGGDGEAL
> SNSTKQKVAAAKQYIENHYKEQMKNLNERKERRTTLEKKLADADVCEEDQTNLMKFLEKK
> ETEYMRLQRHKMGADDFELLTMIGKGAFGEVRVVREINTGHVFAMKKLKKSEMLRRGQVE
> HVRAERNLLAEVDSNCIVKLYCSFQDNEYLYLIMEYLPGGDMMTLLMRKDTLSEDEAKFY
> IAESVLAIESIHNRNYIHRDIKPDNLLLDRYGHLRLSDFGLCKPLDCSVIDGEDFTVGNA
> GSGGGSESVSTTPKRSQQEQLEHWQKNRRMLAYSTVGTPDYIAPEVLLKKGYGMECDWWS
> LGAIMYEMLVGYPPFYADDPMSTCRKIVNWKTHLKFPEESRLSRGARDLIGKLLCSVNQR
> LGSTGASQIKAHPWFEGVQWEKIYQMEAAFIPEVNDDLDTQNFEKFDEEDNQTQAPSRTG
> PWRKMLSSKDINFVGYTYKNFEIVNDYQVPGIAELKKKESKSKRPSVKSLFESESDSSSS
> GSEQQTINRSYSNPTPRGMEPNLRRLDSE
>>At1g03930.1_3-1-1-1_ADK1 protein kinase ADK1
> MDLVIGGKFKLGRKIGSGSFGELYLGINVQTGEEVAVKLESVKTKHPQLHYESKLYMLLQ
> GGTGVPNLKWYGVEGDYNVMVIDLLGPSLEDLFNYCNRKLSLKTVLMLADQLINRVEFMH
> TRGFLHRDIKPDNFLMGLGRKANQVYIIDFGLGKKYRDLQTHRHIPYRENKNLTGTARYA
> SVNTHLGVEQSRRDDLEALGYVLMYFLKGSLPWQGLKAGTKKQKYDRISEKKVATPIEVL
> CKNQPSEFVSYFRYCRSLRFDDKPDYSYLKRLFRDLFIREGYQFDYVFDWTVLKYPQIGS
> SSGSSSRTRNHTTANPGLTAGASLEKQERIAGKETRENRFSGAVEAFSRRHPATSTTRDR
> SASRNSVDGPLSKHPPGDSERPRSSSRYGSSSRRAIPSSSRPSSAGGPSDSRSSSRLVTS
> TGGVGTVSNRASTSQRIQAGNESRTSSFSRAARNTREDPLRRSLELLTLRK
>>At1g04210.1_protein kinase ADK1
> MDSKIKKPANLIEDADIDGGSESDSTISSVLSLEDDSVVDVSGQNLEFSLLDNVDDSVKG
> LYFFRNVFNLIPKSIGGLGRLRKLKFFSNEIDLFPPELGNLVNLEYLQVKISSPGFGDGL
> SWDKLKGLKELELTKVPKRSSALTLLSEISGLKCLTRLSVCHFSIRYLPPEIGCLKSLEY
> LDLSFNKIKSLPNEIGYLSSLTFLKVAHNRLMELSPVLALLQNLESLDVSNNRLTTLHPL
> DLNLMPRLQILNLRYNKLPSYCWIPTWIQCNFEGNYEEMGVDTCSSSMVEMDVFETPYEN
> NVITVPHKGSHRNPLNMSTGISSISRCFSARKSSKRWKRRQYYFQQRARQERLNNSRKWK
> GEVPPEGLSLKMEVEETGKQGMKVPQNTDRGSVDNSCSDENDKLFEEASVITSEEEESSL
> KADVVSDNSQCVETQLTSERDNYESCEIKTSSPSSGDAPGTVDYNSSSERKKPNNKSKRC
> SEKYLDNPKGSKCHKLSTDITNLSRKYSSNSFCSTEDSLPDGFFDAGRDRPFMTLSKYEK
> VLPLDSREVILLDRAKDEVLDAITLSARALVARLKKLNCLTPDVDQVSIDNLQVASFLAL
> FVSDHFGGSDRTAIIERTRKAVSGTNYQKPFICTCLTGNQDDLAALNKQVSTTAEDAILS
> DVCEKSLRSIKSKRNSIVVPLGKLQFGICRHRALLMKYLCDRMEPPVPCELVRGYLDFMP
> HAWNIVPVKQGSSWVRMVVDACRPHDIREDTDQEYFCRYIPLNRLNESIRIKEKLEPGCS
> VSSLSTGKGVERANSSLIRCKLGSTEAVVKMRTLEVSGASLDDIRTFEYTCLGEVRILGA
> LKHDCIVELYGHEISSKWITSENGNEHRVLQSSILMEHIKGGSLKGHIEKLSEAGKHHVP
> MDLALSIARDISGALMELHSKDIIHRDIKSENVLIDLDNQSANGEPIVKLCDFDRAVPLR
> SHLHGCCIAHVGIPPPNICVGTPRWMSPEVFRAMHEQNFYGLEVDIWSFGCLIFELLTLQ
> NPYFDLSELQIHESLQNGKRPKLPKKLETLISETEEEESTNKLSEVFDLTESDLDTMRFL
> IDVFHQCTEESPSDRLNAGDLHEMILSRKKRE
>>At1g04440.1_3-1-1-1 putative casein kinase I
> MDRVVGGKFKLGRKLGSGSFGEIFLGVNVQTGEEVAVKLEPLRARHPQLHYESKLYMLLQ
> GGTGIPHLKWFGVEGEFNCMVIDLLGPSMEEFFNYCSRSFSLKTVLMLADQMINRVEYMH
> VKGFLHRDIKPDNFLMGLGRKANQVYIIDYGLAKKYRDLQTHKHIPYRENKNLTGTARYA
> SVNTHLGIEQSRRDDLESLGYLLMYFLRGSLPWQGLRAGTKKQKYDKISEKKRLTPVEVL
> CKNFPPEFTSYFLYVRSLRFEDKPDYSYLKRLFRDLFIREGYQFDYVFDWTILRYPQFGS
> SSSSNSKPRPTLRPAMNIPVPSADKAEKPPIGQDSRERFSGVFEAYTRRNGSGTGVQADQ
> SSRPRTSENVLASKDTQNQERPNSLSRNLSSSRKAIAGSSVRATSSADFTENRLSRLIPN
> NDRSSTTLRTQFAPSSSSVATKAAPTRAARDITLQSLELLSIGNSKRK
>>At1g04700.1_2-1-4-1_Raf16 MAP kinase kinase kinase Raf16
> MRMEFPGSSNQHLGRDRFNGEVGCGNNCSQTGEEFSNEFLRDFGAQRRLQHGGVNRNVEG
> NYNNRHLVYEDFNRILGLQRVDSNMSEGINSSNGYFAESNVADSPRKMFQTAISDVYLPE
> VLKLLCSFGGRILQRPGDGKLRYIGGETRIISIRKHVGLNELMHKTYALCNHPHTIKYQL
> PGEDLDALISVCSDEDLLHMIEEYQEAETKAGSQRIRVFLVPSTESSESPKIFHERNMNI
> NRNTNQQTDIDHYQYVSALNGIVDVSPQKSSSGQSGTSQTTQFGNASEFSPTFHLRDSPT
> SVHTWEHKDSNSPTFMKPYGNTNAVHFMPKMQIPRNSFGQQSPPTSPFSVHKRANTDVPY
> FADQNGFFDPYLAAPNFPQQNRFFFETTTQKQKHPEVNLHDRRPSDDIYPHGQAYIGAEK
> MTLKKNALSDPQLHDESQINNGLEAFTKQPWKILRKNLRVVATSKWEDSDDIYFNNPEGK
> RCKELELTKEVPNSWINRDNNPDSFDQATKKQDGSNSNSSFSPNYFSPNHQPAAQITSSD
> SQDSGSSVFSLSVNTNENYLDCSREKFNGFQHDMSLDILIRSHTSATDQLCSTTKSSDKA
> DYSSPNTNFPVVFLRQEPMIPRHDLETNSDDSDTQKSLPREESIHYSGLPLRKVGSRETT
> FMHTQGSDDFFKSKLLGPQLIVEDVTNEVISDNLLSATIVPQVNRESDDDHKSYTREKEI
> TNADHESEMEEKYKKSRNTDDSFSEAAMVEIEAGIYGLQIIKNTDLEDLHELGSGTFGTV
> YYGKWRGTDVAIKRIKNSCFSGGSSEQARQTKDFWREARILANLHHPNVVAFYGVVPDGP
> GGTMATVTEYMVNGSLRHVLQRKDRLLDRRKKLMITLDSAFGMEYLHMKNIVHFDLKCDN
> LLVNLRDPQRPICKVGDFGLSRIKRNTLVSGGVRGTLPWMAPELLNGSSNRVSEKVDVFS
> FGIVMWEILTGEEPYANLHCGAIIGGIVNNTLRPPVPERCEAEWRKLMEQCWSFDPGVRP
> SFTEIVERLRSMTVALQPKRRT
>>At1g05100.1_4-4-1_MAPKKK18 MAP kinase kinase kinase 18
> MNWTRGKTLGRGSTATVSAATCHESGETLAVKSAEFHRSEFLQREAKILSSLNSPYVIGY
> RGCEITREPFHNNGEATTYSLLMEYAPYGTLTDVATKNGGFIDEARVVKYTRQILLGLEY
> IHNSKGIAHCDIKGSNVLVGENGEAKIADFGCAKWVEPEITEPVRGTPAFMAPEAARGER
> QGKESDIWAVGCTVIEMVTGSQPWIGADFTDPVSVLYRVGYLGELPELPCSLTEQAKDFL
> GKCLKKEATERWTASQLLNHPFLVNKEPELVTGLVTNSPTSVTDQMFWRSVEEEVSEDRS
> SWWECHEDERIGVLSWIGHVVVESTWDLDGEDWITVRRN
>>At1g05700.1_1-8-1 putative light repressible receptor protein
> MEEFRFLYLIYSAAFALCLVVSVLAQDQSGFISIDCGIPSGSSYKDDTTGINYVSDSSFV
> ETGVSKSIPFTAQRQLQNLRSFPEGSRNCYTLIPIQGKGKKYLIRASFMYGNYDGENGSP
> EFDLFLGGNIWDTVLLSNGSSIVSKEVVYLSQSENIFVCLGNKGKGTPFISTLELRFLGN
> DNTTYDSPNGALFFSRRWDLRSLMGSPVRYDDDVYDRIWIPRNFGYCREINTSLPVTSDN
> NSYSLSSLVMSTAMTPINTTRPITMTLENSDPNVRYFVYMHFAEVEDLSLKPNQTREFDI
> SINGVTVAAGFSPKYLQTNTFFLNPESQSKIAFSLVRTPKSTLPPIVNALEIYVANSFSQ
> SLTNQEDGDAVTSLKTSYKVKKNWHGDPCLPNDYIWEGLNCSYDSLTPPRITSLNLSSSG
> LTGHISSSFSNLTMIQELDLSNNGLTGDIPEFLSKLKFLRVLNLENNTLTGSVPSELLER
> SNTGSFSLRLGENPGLCTEISCRKSNSKKLVIPLVASFAALFILLLLSGVFWRIRNRRNN
> PMAKSENKLLFTFADVIKMTNNFGQVLGKGGFGTVYHGFYDNLQVAVKLLSETSAQGFKE
> FRSEVEVLVRVHHVNLTALIGYFHEGDQMGLIYEFMANGNMADHLAGKYQHTLSWRQRLQ
> IALDAAQGLEYLHCGCKPPIVHRDVKTSNILLNEKNRAKLADFGLSRSFHTESRSHVSTL
> VAGTPGYLDPLCFETNGLNEKSDIYSFGVVLLEMITGKTVIKESQTKRVHVSDWVISILR
> STNDVNNVIDSKMAKDFDVNSVWKVVELALSSVSQNVSDRPNMPHIVRGLNECLQREESN
> KNY
>>At1g06390.1_4-5-4_ASK-iota GSK3/shaggy-like protein kinase iota
> MASLPLGPQPHALAPPLQLHDGDALKRRPELDSDKEMSAAVIEGNDAVTGHIISTTIGGK
> NGEPKQTISYMAERVVGTGSFGIVFQAKCLETGESVAIKKVLQDRRYKNRELQLMRPMDH
> PNVISLKHCFFSTTSRDELFLNLVMEYVPETLYRVLRHYTSSNQRMPIFYVKLYTYQIFR
> GLAYIHTVPGVCHRDVKPQNLLVDPLTHQVKLCDFGSAKVLVKGEPNISYICSRYYRAPE
> LIFGATEYTASIDIWSAGCVLAELLLGQPLFPGENSVDQLVEIIKVLGTPTREEIRCMNP
> NYTDFRFPQIKAHPWHKVFHKRMPPEAIDLASRLLQYSPSLRCTALEACAHPFFNELREP
> NARLPNGRPLPPLFNFKQELGGASMELINRLIPEHVRRQMSTGLQNS
>>At1g06390.2_ASK-iota GSK3/shaggy-like protein kinase iota
> MASLPLGPQPHALAPPLQLHDGDALKRRPELDSDKEMSAAVIEGNDAVTGHIISTTIGGK
> NGEPKQTISYMAERVVGTGSFGIVFQAKCLETGESVAIKKVLQDRRYKNRELQLMRPMDH
> PNVISLKHCFFSTTSRDELFLNLVMEYVPETLYRVLRHYTSSNQRMPIFYVKLYTYQIFR
> GLAYIHTVPGVCHRDVKPQNLLVDPLTHQVKLCDFGSAKVLVKGEPNISYICSRYYRAPE
> LIFGATEYTASIDIWSAGCVLAELLLGQPLFPGENSVDQLVEIIKVLGTPTREEIRCMNP
> NYTDFRFPQIKAHPWHKVFHKRMPPEAIDLASRLLQYSPSLRCTALEACAHPFFNELREP
> NARLPNGRPLPPLFNFKQELGGASMELINRLIPEHVRRQMSTGLQNS
>
>
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