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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / dm_javadoc / index-files / index-16.html
diff --git a/website/dm_javadoc/index-files/index-16.html b/website/dm_javadoc/index-files/index-16.html
new file mode 100644 (file)
index 0000000..87f5b0b
--- /dev/null
+++ b/website/dm_javadoc/index-files/index-16.html
@@ -0,0 +1,408 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:08:25 GMT 2011 -->\r
+<TITLE>\r
+S-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2011-12-07">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+    if (location.href.indexOf('is-external=true') == -1) {\r
+        parent.document.title="S-Index";\r
+    }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+  <TR ALIGN="center" VALIGN="top">\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
+  </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+&nbsp;<A HREF="index-15.html"><B>PREV LETTER</B></A>&nbsp;\r
+&nbsp;<A HREF="index-17.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+  <A HREF="../index.html?index-filesindex-16.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="index-16.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
+&nbsp;<SCRIPT type="text/javascript">\r
+  <!--\r
+  if(window==top) {\r
+    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+  }\r
+  //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_S_"><!-- --></A><H2>\r
+<B>S</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>Score</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>A value class for AACon annotation results storage.<DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList)"><B>Score(Enum&lt;?&gt;, ArrayList&lt;Float&gt;)</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD>Instantiate the Score\r
+<DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList, java.util.TreeSet)"><B>Score(Enum&lt;?&gt;, ArrayList&lt;Float&gt;, TreeSet&lt;Range&gt;)</B></A> - \r
+Constructor for 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/data/sequence/Score.html#Score(java.lang.Enum, java.util.TreeSet)"><B>Score(Enum&lt;?&gt;, TreeSet&lt;Range&gt;)</B></A> - \r
+Constructor for 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/data/sequence/Score.html#Score(java.lang.Enum, float[])"><B>Score(Enum&lt;?&gt;, float[])</B></A> - \r
+Constructor for 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/data/sequence/ScoreManager.html" title="class in compbio.data.sequence"><B>ScoreManager</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>&nbsp;<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence"><B>ScoreManager.ScoreHolder</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>&nbsp;<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#scores"><B>scores</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/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa"><B>SequenceAnnotation</B></A>&lt;<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>&gt; - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Interface for tools that results to one or more annotation to sequence(s)
+ 
+ Single, multiple sequences their groups or alignments can be annotated<DT><A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>SequenceUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Utility class for operations on sequences<DT><A HREF="../compbio/data/msa/JABAService.html#SERVICE_NAMESPACE"><B>SERVICE_NAMESPACE</B></A> - \r
+Static variable in interface compbio.data.msa.<A HREF="../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>Services</B></A> - Enum in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>List of web services currently supported by JABAWS version 2<DT><A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client"><B>ServicesUtil</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>&nbsp;<DT><A HREF="../compbio/ws/client/ServicesUtil.html#ServicesUtil()"><B>ServicesUtil()</B></A> - \r
+Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setActualNumberofSequences(int)"><B>setActualNumberofSequences(int)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws">GetServiceDescription</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> - \r
+Method in 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/jaxws/TestService.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Option.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>Sets one of the values defined in optionList as default.\r
+<DT><A HREF="../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Option.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Preset.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/Align.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/Analize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
+Method in 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/jaxws/CustomAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
+Method in 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/jaxws/PresetAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List&lt;FastaSequence&gt;)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)"><B>setFurtherDetails(URL)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
+Method in 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/jaxws/GetAnnotation.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#setMax(java.lang.String)"><B>setMax(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)"><B>setMin(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Option.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Preset.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setNumberOfSequencesAllowed(int)"><B>setNumberOfSequencesAllowed(int)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Parameter.html#setOptionName(java.lang.String)"><B>setOptionName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Option.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set&lt;String&gt;)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set&lt;String&gt;)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)"><B>setOptions(List&lt;Option&gt;)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#setOptions(java.util.List)"><B>setOptions(List&lt;Option&gt;)</B></A> - \r
+Method in 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/metadata/Preset.html#setOptions(java.util.List)"><B>setOptions(List&lt;String&gt;)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)"><B>setOptions(List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Adds the list of options or parameters to the internal list of options\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)"><B>setParameters(List&lt;Parameter&lt;T&gt;&gt;)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Sets the list of parameters as internal list\r
+<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setPosition(long)"><B>setPosition(long)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)"><B>setPossibleValues(Set&lt;String&gt;)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setPreset(compbio.metadata.Preset)"><B>setPreset(Preset)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#setPreset(compbio.metadata.Preset)"><B>setPreset(Preset)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#setPresetName(java.lang.String)"><B>setPresetName(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/PresetManager.html#setPresets(java.util.List)"><B>setPresets(List&lt;Preset&lt;T&gt;&gt;)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)"><B>setPrmSeparator(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Sets name value separator character\r
+<DT><A HREF="../compbio/data/sequence/Score.html#setRanges(java.util.TreeSet)"><B>setRanges(TreeSet&lt;Range&gt;)</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/metadata/Option.html#setRequired(boolean)"><B>setRequired(boolean)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
+Method in 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/data/msa/jaxws/CancelJobResponse.html#setReturn(boolean)"><B>setReturn(boolean)</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/data/msa/jaxws/CustomAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
+Method in 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/CustomAnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
+Method in 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
+<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#setReturn(compbio.data.sequence.ScoreManager)"><B>setReturn(ScoreManager)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#setReturn(compbio.metadata.JobStatus)"><B>setReturn(JobStatus)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#setReturn(java.util.Date)"><B>setReturn(Date)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#setReturn(int)"><B>setReturn(int)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#setReturn(compbio.metadata.Limit)"><B>setReturn(Limit)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#setReturn(compbio.metadata.LimitsManager)"><B>setReturn(LimitsManager)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#setReturn(compbio.metadata.PresetManager)"><B>setReturn(PresetManager)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#setReturn(compbio.data.sequence.Alignment)"><B>setReturn(Alignment)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#setReturn(compbio.metadata.RunnerConfig)"><B>setReturn(RunnerConfig)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html#setReturn(java.util.Set)"><B>setReturn(Set&lt;Category&gt;)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws">GetServiceCategoriesResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws">GetServiceDescriptionResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#setReturn(java.util.Set)"><B>setReturn(Set&lt;Services&gt;)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#setReturn(boolean)"><B>setReturn(boolean)</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/msa/jaxws/PresetAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#setReturn(compbio.metadata.ChunkHolder)"><B>setReturn(ChunkHolder)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Set the name of a runner class\r
+<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtActual(int)"><B>setSequenceLenghtActual(int)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtAllowed(int)"><B>setSequenceLenghtAllowed(int)</B></A> - \r
+Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)"><B>setType(ValueConstrain.Type)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)"><B>setValidValue(ValueConstrain)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Argument.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
+Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
+<DD>Set default values for the parameter or an option\r
+<DT><A HREF="../compbio/metadata/Option.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY"><B>SINGLE_ENTRY_KEY</B></A> - \r
+Static variable 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/SMERFSConstraints.html" title="enum in compbio.data.sequence"><B>SMERFSConstraints</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Enumeration defining two constraints for SMERFS columns score calculation.</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
+  </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
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+  //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
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+\r
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+</HTML>\r