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updated javadoc
[jabaws.git] / website / full_javadoc / index-files / index-9.html
diff --git a/website/full_javadoc/index-files/index-9.html b/website/full_javadoc/index-files/index-9.html
index 43d75c9..c51fba0 100644 (file)
--- a/website/full_javadoc/index-files/index-9.html
+++ b/website/full_javadoc/index-files/index-9.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
 <TITLE>\r
 I-Index\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-08-12">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -82,9 +82,18 @@ function windowTitle()
 <A NAME="_I_"><!-- --></A><H2>\r
 <B>I</B></H2>\r
 <DL>\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#id"><B>id</B></A> - \r
+Variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/FilePuller.html#initPull()"><B>initPull()</B></A> - \r
 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#INPUT"><B>INPUT</B></A> - \r
+Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><B>IOHelper</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>&nbsp;<DT><A HREF="../compbio/ws/client/IOHelper.html#IOHelper()"><B>IOHelper()</B></A> - \r
+Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/Configurator.html#IS_CLUSTER_ENGINE_ENABLED"><B>IS_CLUSTER_ENGINE_ENABLED</B></A> - \r
 Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 <DD>&nbsp;\r
@@ -97,16 +106,23 @@ Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/P
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)"><B>isAmbiguosProtein(String)</B></A> - \r
 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 <DD>Check whether the sequence confirms to amboguous protein sequence\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#isClusterJob()"><B>isClusterJob()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/Limit.html#isDefault()"><B>isDefault()</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/Limit.html#isExceeded(java.util.List)"><B>isExceeded(List&lt;FastaSequence&gt;)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 <DD>Checks if the number of sequences or their average length in the dataset
- exceeds limits the values defined by this Limit\r
+ exceeds this limit.\r
 <DT><A HREF="../compbio/engine/FilePuller.html#isFileCreated()"><B>isFileCreated()</B></A> - \r
 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/Util.html#isJavaLibrary(java.lang.Class)"><B>isJavaLibrary(Class&lt;?&gt;)</B></A> - \r
+Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
+<DD>Returns true of executableName.jar.file property has some value in the
+ Executable.properties file, false otherwise.\r
 <DT><A HREF="../compbio/engine/client/Util.html#isMarked(java.lang.String, compbio.metadata.JobStatus)"><B>isMarked(String, JobStatus)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 <DD>&nbsp;\r
@@ -117,6 +133,18 @@ Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/S
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)"><B>isNucleotideSequence(FastaSequence)</B></A> - \r
 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws"><B>IsOperating</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#IsOperating()"><B>IsOperating()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html#isOperating(compbio.ws.client.Services)"><B>isOperating(Services)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
+<DD>Check whether a particular web service is working on this server\r
+<DT><A HREF="../compbio/ws/server/RegistryWS.html#isOperating(compbio.ws.client.Services)"><B>isOperating(Services)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws"><B>IsOperatingResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#IsOperatingResponse()"><B>IsOperatingResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)"><B>isProteinSequence(String)</B></A> - \r
 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 <DD>&nbsp;\r
@@ -127,15 +155,12 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title
 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#isReturn()"><B>isReturn()</B></A> - \r
 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#isShutdown()"><B>isShutdown()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#isTerminated()"><B>isTerminated()</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
+<DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#isReturn()"><B>isReturn()</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</B></A> - \r
 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD>&nbsp;\r
+<DD>Please note this method closes the input stream provided as a parameter\r
 <DT><A HREF="../compbio/engine/client/PathValidator.html#isValidDirectory(java.lang.String)"><B>isValidDirectory(String)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
 <DD>&nbsp;\r
@@ -145,6 +170,14 @@ Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/P
 <DT><A HREF="../compbio/engine/client/Util.html#isValidJobId(java.lang.String)"><B>isValidJobId(String)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder"><B>IUPred</B></A> - Class in <A HREF="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A><DD>iupred sequenceFile <short long glob >
+ 
+ Maximum sequence length is 40000 chars.<DT><A HREF="../compbio/runner/disorder/IUPred.html#IUPred()"><B>IUPred()</B></A> - \r
+Constructor for class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server"><B>IUPredWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/IUPredWS.html#IUPredWS()"><B>IUPredWS()</B></A> - \r
+Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server">IUPredWS</A>\r
+<DD>&nbsp;\r
 </DL>\r
 <HR>\r
 \r