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remove old datamodel javadoc
[jabaws.git] / website / full_javadoc / index-files / index-1.html
diff --git a/website/full_javadoc/index-files/index-1.html b/website/full_javadoc/index-files/index-1.html
index 03324d7..a94a21b 100644 (file)
--- a/website/full_javadoc/index-files/index-1.html
+++ b/website/full_javadoc/index-files/index-1.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
 A-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
@@ -85,9 +85,17 @@ function windowTitle()
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AA"><B>AA</B></A> - \r
 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 <DD>Valid Amino acids\r
+<DT><A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation"><B>AACon</B></A> - Class in <A HREF="../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A><DD>Command line
+ 
+ java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out<DT><A HREF="../compbio/runner/conservation/AACon.html#AACon()"><B>AACon()</B></A> - \r
+Constructor for class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client"><B>AAConClient</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>A command line client for AACon web service<DT><A HREF="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server"><B>AAConWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/AAConWS.html#AAConWS()"><B>AAConWS()</B></A> - \r
+Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)"><B>addOption(Option&lt;T&gt;)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
+<DD>Adds Option to the internal list of options\r
 <DT><A HREF="../compbio/metadata/Option.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 <DD>Adds an option to the optionName list\r
@@ -96,10 +104,10 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" ti
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)"><B>addParameter(Parameter&lt;T&gt;)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>&nbsp;\r
+<DD>Adds parameter to the internal parameter list\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)"><B>addParameter(String)</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 <DD>&nbsp;\r
@@ -114,10 +122,10 @@ Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.h
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])"><B>addParameters(String[])</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/runner/msa/Mafft.html#addParameters(java.util.List)"><B>addParameters(List&lt;String&gt;)</B></A> - \r
 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
 <DD>Mafft input must always be the last parameter!\r
@@ -136,6 +144,12 @@ Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/
 <DT><A HREF="../compbio/data/msa/MsaWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&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 default settings.\r
+<DT><A HREF="../compbio/ws/server/_MsaService.html#align(java.util.List)"><B>align(List&lt;FastaSequence&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#align(java.util.List)"><B>align(List&lt;FastaSequence&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#align(java.util.List)"><B>align(List&lt;FastaSequence&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
@@ -151,7 +165,7 @@ Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html"
 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&gt;)</B></A> - \r
 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)"><B>align(List&lt;FastaSequence&gt;, ConfiguredExecutable&lt;T&gt;, Logger, WebServiceContext, String, Limit&lt;T&gt;)</B></A> - \r
+<DT><A HREF="../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)"><B>align(List&lt;FastaSequence&gt;, ConfiguredExecutable&lt;T&gt;, Logger, String, Limit&lt;T&gt;)</B></A> - \r
 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>Alignment</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Multiple sequence alignment.<DT><A HREF="../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)"><B>Alignment(List&lt;FastaSequence&gt;, Program, char)</B></A> - \r
@@ -172,6 +186,27 @@ Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE"><B>AMBIGUOUS_NUCLEOTIDE</B></A> - \r
 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 <DD>Ambiguous nucleotide\r
+<DT><A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws"><B>Analize</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/Analize.html#Analize()"><B>Analize()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#analize(java.util.List)"><B>analize(List&lt;FastaSequence&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.\r
+<DT><A HREF="../compbio/ws/server/AAConWS.html#analize(java.util.List)"><B>analize(List&lt;FastaSequence&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/SequenceAnnotationService.html#analize(java.util.List)"><B>analize(List&lt;FastaSequence&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/ws/server/WSUtil.html#analize(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)"><B>analize(List&lt;FastaSequence&gt;, ConfiguredExecutable&lt;T&gt;, Logger, String, Limit&lt;T&gt;)</B></A> - \r
+Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws"><B>AnalizeResponse</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/AnalizeResponse.html#AnalizeResponse()"><B>AnalizeResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet"><B>AnnualStat</B></A> - Class in <A HREF="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</A><DD>&nbsp;<DT><A HREF="../compbio/stat/servlet/AnnualStat.html#AnnualStat()"><B>AnnualStat()</B></A> - \r
+Constructor for class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet">AnnualStat</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A>&lt;<A HREF="../compbio/metadata/Argument.html" title="type parameter in Argument">T</A>&gt; - Interface in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>An unmodifiable view for the options and parameters, with one exception - it
  allows to set a value<DT><A HREF="../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)"><B>argumentsToCommandString(List&lt;? extends Option&lt;?&gt;&gt;)</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
@@ -179,6 +214,12 @@ Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html"
 <DT><A HREF="../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)"><B>argumentsToCommandString(List&lt;? extends Option&lt;?&gt;&gt;, RunnerConfig&lt;? extends Executable&lt;?&gt;&gt;)</B></A> - \r
 Static method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#asMap()"><B>asMap()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#asSet()"><B>asSet()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine"><B>AsyncExecutor</B></A> - Interface in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>An asynchronous executor engine, capable of running, cancelling, 
  obtaining results calculated by a native executable wrapper in Executable interface.<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>AsyncJobRunner</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>Single cluster job runner class<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#AsyncJobRunner()"><B>AsyncJobRunner()</B></A> - \r
 Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
@@ -186,9 +227,6 @@ Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cl
 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local"><B>AsyncLocalRunner</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#AsyncLocalRunner()"><B>AsyncLocalRunner()</B></A> - \r
 Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#awaitTermination(long, java.util.concurrent.TimeUnit)"><B>awaitTermination(long, TimeUnit)</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
 </DL>\r
 <HR>\r
 \r