[kepler-users] Opal 2.0 and Kepler 1.0
Tirath Ramdas
tramdas at oci.uzh.ch
Tue Jun 16 14:05:36 PDT 2009
Hi Luca et al.,
Luca, thanks for getting back to me promptly. Unfortunately, I've had
problems trying to load this in Kepler-1.0.0. I get the following exceptions
--------------------------------------------------
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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