git://source.jalview.org / jabaws.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
remove old datamodel javadoc
[jabaws.git] / website / full_javadoc / index-files / index-3.html
diff --git a/website/full_javadoc/index-files/index-3.html b/website/full_javadoc/index-files/index-3.html
index 02682d7..a980810 100644 (file)
--- a/website/full_javadoc/index-files/index-3.html
+++ b/website/full_javadoc/index-files/index-3.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
 C-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
@@ -92,9 +92,9 @@ Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecu
 <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><B>CancelJob</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/CancelJob.html#CancelJob()"><B>CancelJob()</B></A> - \r
 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Stop running job but leave its output untouched\r
+<DT><A HREF="../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
+<DD>Stop running the job <code>jobId</code> but leave its output untouched\r
 <DT><A HREF="../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
 <DD>Stop running job.\r
@@ -119,9 +119,15 @@ Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunne
 <DT><A HREF="../compbio/engine/SyncExecutor.html#cancelJob()"><B>cancelJob()</B></A> - \r
 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 <DD>Stops running job.\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/ClustalWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/GenericMetadataService.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/MafftWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 <DD>&nbsp;\r
@@ -140,13 +146,19 @@ Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.ht
 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><B>CancelJobResponse</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/CancelJobResponse.html#CancelJobResponse()"><B>CancelJobResponse()</B></A> - \r
 Constructor for 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/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.<DT><A HREF="../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)"><B>ChunkHolder(String, long)</B></A> - \r
+<DT><A HREF="../compbio/ws/client/WSTester.html#checkService(compbio.ws.client.Services)"><B>checkService(Services)</B></A> - \r
+Method in class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
+<DD>Test JABA web service\r
+<DT><A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Represents a chunk of a string data together with the position in a file for
+ the next read operation.<DT><A HREF="../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)"><B>ChunkHolder(String, long)</B></A> - \r
 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine"><B>Cleaner</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/Cleaner.html#Cleaner()"><B>Cleaner()</B></A> - \r
+<DT><A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine"><B>Cleaner</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD><B>Deprecated.</B>&nbsp;<DT><A HREF="../compbio/engine/Cleaner.html#Cleaner()"><B>Cleaner()</B></A> - \r
 Constructor for class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#cleanProteinSequence(java.lang.String)"><B>cleanProteinSequence(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>Remove all non AA chars from the sequence\r
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)"><B>cleanSequence(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>Removes all whitespace chars in the sequence string\r
@@ -171,12 +183,27 @@ Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunne
 <DT><A HREF="../compbio/engine/SyncExecutor.html#cleanup()"><B>cleanup()</B></A> - \r
 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 <DD>Clean up after the job\r
+<DT><A HREF="../compbio/data/sequence/FastaReader.html#close()"><B>close()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A>\r
+<DD>Call this method to close the connection to the input file if you want to
+ free up the resources.\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#close()"><B>close()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#closeSilently(java.util.logging.Logger, java.io.Closeable)"><B>closeSilently(Logger, Closeable)</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>Closes the Closable and logs the exception if any\r
 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>ClustalAlignmentUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Tools to read and write clustal formated files<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()"><B>ClustalAlignmentUtil()</B></A> - \r
 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa"><B>ClustalO</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/ClustalO.html#ClustalO()"><B>ClustalO()</B></A> - \r
+Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
+<DD>--threads=<n> Number of processors to use
+ 
+ -l, --log=<file> Log all non-essential output to this file\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server"><B>ClustalOWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/ClustalOWS.html#ClustalOWS()"><B>ClustalOWS()</B></A> - \r
+Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>ClustalW</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/ClustalW.html#ClustalW()"><B>ClustalW()</B></A> - \r
 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 <DD>&nbsp;\r
@@ -195,16 +222,31 @@ Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.
 <DT><A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine"><B>ClusterJobId</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/ClusterJobId.html#ClusterJobId(java.lang.String)"><B>ClusterJobId(String)</B></A> - \r
 Constructor for class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client"><B>ClusterNativeSpecExecutable</B></A>&lt;<A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html" title="type parameter in ClusterNativeSpecExecutable">T</A>&gt; - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterSession</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterUtil</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#ClusterUtil()"><B>ClusterUtil()</B></A> - \r
+<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterSession</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterUtil</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#ClusterUtil()"><B>ClusterUtil()</B></A> - \r
 Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/Disembl.html#COILS_EXPECTATION_THRESHOLD"><B>COILS_EXPECTATION_THRESHOLD</B></A> - \r
+Variable in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
+<DD>For the region to be considered disordered the values must exceed these\r
 <DT><A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>CommandBuilder</B></A>&lt;<A HREF="../compbio/engine/client/CommandBuilder.html" title="type parameter in CommandBuilder">T</A>&gt; - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/CommandBuilder.html#CommandBuilder(java.lang.String)"><B>CommandBuilder(String)</B></A> - \r
 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/pipeline/_jpred/Hit.EvalueComporator.html#compare(compbio.pipeline._jpred.Hit, compbio.pipeline._jpred.Hit)"><B>compare(Hit, Hit)</B></A> - \r
+Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Hit.EvalueComporator.html" title="class in compbio.pipeline._jpred">Hit.EvalueComporator</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/pipeline/_jpred/Hit.NumberComporator.html#compare(compbio.pipeline._jpred.Hit, compbio.pipeline._jpred.Hit)"><B>compare(Hit, Hit)</B></A> - \r
+Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Hit.NumberComporator.html" title="class in compbio.pipeline._jpred">Hit.NumberComporator</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Range.html#compareTo(compbio.data.sequence.Range)"><B>compareTo(Range)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Score.html#compareTo(compbio.data.sequence.Score)"><B>compareTo(Score)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/FilePuller.html#compareTo(java.util.concurrent.Delayed)"><B>compareTo(Delayed)</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/data/_structure/package-summary.html"><B>compbio.data._structure</B></A> - package compbio.data._structure<DD>&nbsp;<DT><A HREF="../compbio/data/msa/package-summary.html"><B>compbio.data.msa</B></A> - package compbio.data.msa<DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/package-summary.html"><B>compbio.data.msa.jaxws</B></A> - package compbio.data.msa.jaxws<DD>&nbsp;<DT><A HREF="../compbio/pipeline/_jpred/package-summary.html"><B>compbio.pipeline._jpred</B></A> - package compbio.pipeline._jpred<DD>&nbsp;<DT><A HREF="../compbio/runner/_jpred/package-summary.html"><B>compbio.runner._jpred</B></A> - package compbio.runner._jpred<DD>&nbsp;<DT><A HREF="../compbio/runner/psiblast/package-summary.html"><B>compbio.runner.psiblast</B></A> - package compbio.runner.psiblast<DD>&nbsp;<DT><A HREF="../compbio/ws/client/package-summary.html"><B>compbio.ws.client</B></A> - package compbio.ws.client<DD>&nbsp;<DT><A HREF="../compbio/ws/server/package-summary.html"><B>compbio.ws.server</B></A> - package compbio.ws.server<DD>&nbsp;<DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#confDir"><B>confDir</B></A> - \r
+<DT><A HREF="../compbio/data/_structure/package-summary.html"><B>compbio.data._structure</B></A> - package compbio.data._structure<DD>&nbsp;<DT><A HREF="../compbio/data/msa/package-summary.html"><B>compbio.data.msa</B></A> - package compbio.data.msa<DD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.<DT><A HREF="../compbio/data/msa/jaxws/package-summary.html"><B>compbio.data.msa.jaxws</B></A> - package compbio.data.msa.jaxws<DD>&nbsp;<DT><A HREF="../compbio/pipeline/_jpred/package-summary.html"><B>compbio.pipeline._jpred</B></A> - package compbio.pipeline._jpred<DD>&nbsp;<DT><A HREF="../compbio/runner/_jpred/package-summary.html"><B>compbio.runner._jpred</B></A> - package compbio.runner._jpred<DD>&nbsp;<DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#confDir"><B>confDir</B></A> - \r
 Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><B>ConfExecutable</B></A>&lt;<A HREF="../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/ConfExecutable.html#ConfExecutable(compbio.engine.client.Executable, java.lang.String)"><B>ConfExecutable(Executable&lt;T&gt;, String)</B></A> - \r
@@ -222,9 +264,28 @@ Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.ht
 <DT><A HREF="../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)"><B>configureExecutable(Executable&lt;T&gt;, Executable.ExecProvider)</B></A> - \r
 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Jws2Client.Services)"><B>connect(String, Jws2Client.Services)</B></A> - \r
+<DT><A HREF="../compbio/ws/client/AAConClient.html#connect()"><B>connect()</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client">AAConClient</A>\r
+<DD>Connects to a AACon web service by the host and the service name\r
+<DT><A HREF="../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)"><B>connect(String, Services)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
+<DD>Connects to a web service by the host and the service name web service
+ type\r
+<DT><A HREF="../compbio/ws/client/Jws2Client.html#connectToRegistry(java.lang.String)"><B>connectToRegistry(String)</B></A> - \r
 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Connects to a web service by the host and the service name\r
+<DD>Get a connection of JABAWS registry\r
+<DT><A HREF="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><B>ConservationMethod</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Enumeration listing of all the supported methods.<DT><A HREF="../compbio/stat/servlet/StatisticCollector.html#contextDestroyed(javax.servlet.ServletContextEvent)"><B>contextDestroyed(ServletContextEvent)</B></A> - \r
+Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ShutdownEngines.html#contextDestroyed(javax.servlet.ServletContextEvent)"><B>contextDestroyed(ServletContextEvent)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server">ShutdownEngines</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/StatisticCollector.html#contextInitialized(javax.servlet.ServletContextEvent)"><B>contextInitialized(ServletContextEvent)</B></A> - \r
+Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ShutdownEngines.html#contextInitialized(javax.servlet.ServletContextEvent)"><B>contextInitialized(ServletContextEvent)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server">ShutdownEngines</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/Util.html#convertToAbsolute(java.lang.String)"><B>convertToAbsolute(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
@@ -240,6 +301,12 @@ Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/
 <DT><A HREF="../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
 <DD>Align a list of sequences with options.\r
+<DT><A HREF="../compbio/ws/server/_MsaService.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_MsaService.html" title="class in compbio.ws.server">_MsaService</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;ClustalO&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;ClustalW&gt;&gt;)</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 <DD>&nbsp;\r
@@ -258,6 +325,25 @@ Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html"
 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>CustomAlignResponse</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/CustomAlignResponse.html#CustomAlignResponse()"><B>CustomAlignResponse()</B></A> - \r
 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws"><B>CustomAnalize</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/CustomAnalize.html#CustomAnalize()"><B>CustomAnalize()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>\r
+<DD>Analyse the sequences according to custom settings defined in options
+ list.\r
+<DT><A HREF="../compbio/ws/server/DisemblWS.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;Disembl&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server">DisemblWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/GlobPlotWS.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;GlobPlot&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/SequenceAnnotationService.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws"><B>CustomAnalizeResponse</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/CustomAnalizeResponse.html#CustomAnalizeResponse()"><B>CustomAnalizeResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</A>\r
+<DD>&nbsp;\r
 </DL>\r
 <HR>\r
 \r