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" <[email protected]> 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 > &lt;dataset&gt; [optional arguments] > &lt;dataset&gt; 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 &lt;nmotifs&gt;] > maximum number of motifs to find [-evt &lt;ev&gt;] > stop if motif E-value greater than &lt;evt&gt; > [-nsites &lt;sites&gt;] number of sites for each motif > [-minsites &lt;minsites&gt;] minimum number of sites for each > motif [-maxsites &lt;maxsites&gt;] maximum number of > sites for each motif [-wnsites &lt;wnsites&gt;] > weight on expected number of sites [-w &lt;w&gt;] > motif width [-minw &lt;minw&gt;] minumum > motif width [-maxw &lt;maxw&gt;] maximum > motif width [-nomatrim] do not adjust motif width > using multiple alignment > [-wg &lt;wg&gt;] gap opening cost for multiple > alignments [-ws &lt;ws&gt;] gap extension > cost for multiple alignments [-noendgaps] do not > count end gaps in multiple alignments [-bfile > &lt;bfile&gt;] name of background Markov model file > [-revcomp] allow sites on + or - DNA strands > [-pal] force palindromes (requires -dna) > [-maxiter &lt;maxiter&gt;] maximum EM iterations to run > [-distance &lt;distance&gt;] EM convergence criterion > [-prior dirichlet|dmix|mega|megap|addone] > type of prior to use [-b &lt;b&gt;] > strength of the prior [-plib &lt;plib&gt;] > name of Dirichlet prior file [-spfuzz &lt;spfuzz&gt;] > fuzziness of sequence to theta mapping [-spmap uni|pam] > starting point seq to theta mapping type [-cons > &lt;cons&gt;] consensus sequence to start EM from > [-text] output in text format (default is HTML) > [-maxsize &lt;maxsize&gt;] maximum dataset size in > characters [-nostatus] do not print progress > reports to terminal [-p &lt;np&gt;] use > parallel version with &lt;np&gt; processors [-time > &lt;t&gt;] quit before &lt;t&gt; CPU seconds > consumed [-sf &lt;sf&gt;] print > &lt;sf&gt; 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 > &lt;a > href=&quot;http://meme.nbcr.net/meme/examples/At.fa&quot;&gt;At.fa&lt;/a&gt; > > </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 (&lt;=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. &lt;UL&gt; &lt;LI&gt;oops: MEME assumes that > each sequence in the dataset contains exactly one occurrence of each > motif.&lt;/LI&gt;&lt;LI&gt;zoops: MEME assumes that each > sequence may contain at most one occurrence of each > motif.&lt;/LI&gt;&lt;LI&gt; anr: MEME assumes each > sequence may contain any number of non-overlapping occurrences of each > motif.&lt;/LI&gt;&lt;/UL&gt;</configure></property> > <property name="prop:minsites" > class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Minimum > number of sites for each motif (&gt;=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 &lt;mfile&gt; > [optional arguments ...] &lt;mfile&gt; > file containing motifs to use; may be a MEME output > file or a file with the format given below > [&lt;database&gt;] or [-d &lt;database&gt;] > database to search with motifs or [-stdin] read > database from standard input; Default: reads > database specified inside &lt;mfile&gt; [-c > &lt;count&gt;] only use the first &lt;count&gt; > motifs [-a &lt;alphabet&gt;] &lt;mfile&gt; is > assumed to contain motifs in the format output > by bin/make_logodds and > &lt;alphabet&gt; is their alphabet; -d > &lt;database&gt; 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 &lt;rank&gt;] print results starting with > &lt;rank&gt; best (default: 1) [-smax > &lt;smax&gt;] print results for no more than &lt;smax&gt; > sequences (default: all) [-ev > &lt;ev&gt;] print results for sequences with E-value &lt; > &lt;ev&gt; (default: 10) > [-mt &lt;mt&gt;] show motif matches with p-value &lt; mt > (default: 0.0001) [-w] show weak matches > (mt&lt;p-value&lt;mt*10) in angle brackets [-bfile > &lt;bfile&gt;] read background frequencies from > &lt;bfile&gt; [-seqp] use SEQUENCE p-values > for motif thresholds (default: use POSITION > p-values) [-mf &lt;mf&gt;] print > &lt;mf&gt; as motif file name [-df &lt;df&gt;] > print &lt;df&gt; as database name [-minseqs > &lt;minseqs&gt;] lower bound on number of sequences in db > [-mev &lt;mev&gt;]+ use only motifs with E-values less than > &lt;mev&gt; [-m &lt;m&gt;]+ use only > motif(s) number &lt;m&gt; (overrides -mev) [-diag > &lt;diag&gt;] 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 > >
