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remove old project javadoc
[jabaws.git] / website / full_javadoc / compbio / ws / server / DisemblWS.html
diff --git a/website/full_javadoc/compbio/ws/server/DisemblWS.html b/website/full_javadoc/compbio/ws/server/DisemblWS.html
deleted file mode 100644 (file)
index 5ea4721..0000000
--- a/website/full_javadoc/compbio/ws/server/DisemblWS.html
+++ /dev/null
@@ -1,414 +0,0 @@
-<!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 Fri Aug 12 14:32:34 BST 2011 -->\r
-<TITLE>\r
-DisemblWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2011-08-12">\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="DisemblWS";\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">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/DisemblWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-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="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&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="../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../../../index.html?compbio/ws/server/DisemblWS.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="DisemblWS.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
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.server</FONT>\r
-<BR>\r
-Class DisemblWS</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
-  <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">compbio.ws.server.GenericMetadataService</A>\r
-      <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">compbio.ws.server.SequenceAnnotationService</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;\r
-          <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.DisemblWS</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;, <A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>DisemblWS</B><DT>extends <A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;<DT>implements <A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="fields_inherited_from_class_compbio.data.msa.JABAService"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Fields inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</A>, <A HREF="../../../compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/DisemblWS.html#DisemblWS()">DisemblWS</A></B>()</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/DisemblWS.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-              <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;&gt;&nbsp;options)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to custom settings defined in options
- list.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/DisemblWS.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-              <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;&nbsp;preset)</CODE>\r
-\r
-<BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to the preset settings.</TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.ws.server.SequenceAnnotationService"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.ws.server.<A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#analize(java.util.List)">analize</A>, <A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#getAnnotation(java.lang.String)">getAnnotation</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.ws.server.GenericMetadataService"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class compbio.ws.server.<A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/ws/server/GenericMetadataService.html#cancelJob(java.lang.String)">cancelJob</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#getJobStatus(java.lang.String)">getJobStatus</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#getPresets()">getPresets</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#getRunnerOptions()">getRunnerOptions</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.data.msa.SequenceAnnotation"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#analize(java.util.List)">analize</A>, <A HREF="../../../compbio/data/msa/SequenceAnnotation.html#getAnnotation(java.lang.String)">getAnnotation</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.data.msa.JManagement"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)">cancelJob</A>, <A HREF="../../../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)">getJobStatus</A>, <A HREF="../../../compbio/data/msa/JManagement.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;<A NAME="methods_inherited_from_class_compbio.data.msa.Metadata"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/data/msa/Metadata.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getPresets()">getPresets</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">getRunnerOptions</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
-&nbsp;\r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="DisemblWS()"><!-- --></A><H3>\r
-DisemblWS</H3>\r
-<PRE>\r
-public <B>DisemblWS</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="customAnalize(java.util.List, java.util.List)"><!-- --></A><H3>\r
-customAnalize</H3>\r
-<PRE>\r
-public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>customAnalize</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                            <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;&gt;&nbsp;options)\r
-                     throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
-                            <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
-                            <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                            <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#customAnalize(java.util.List, java.util.List)">SequenceAnnotation</A></CODE></B></DD>\r
-<DD>Analyse the sequences according to custom settings defined in options
- list. The actual analysis algorithm is defined by the type T. Default
- Limit is used to decide whether the calculation will be permitted or
- denied\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></CODE> in class <CODE><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>options</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JABAWS is deployed on Windows and
-             Mafft service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
-             following reasons: 1) The number of sequences in the
-             submission or their average length is greater then defined by
-             the default Limit. 2) Any problems on the server side e.g. it
-             is misconfigured or malfunction, is reported via this
-             exception. In the first case the information on the limit
-             could be obtained from an exception.\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="presetAnalize(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
-presetAnalize</H3>\r
-<PRE>\r
-public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>presetAnalize</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;&nbsp;preset)\r
-                     throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
-                            <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
-                            <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
-                            <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">SequenceAnnotation</A></CODE></B></DD>\r
-<DD>Analyse the sequences according to the preset settings. The actual
- analysis algorithm is defined by the type T.
- 
- Limit for a presetName is used whether the calculation will be permitted
- or denied. If no Limit was defined for a presetName, than default limit
- is used.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></CODE> in class <CODE><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
-            any sequence validity checks. Nor does it checks whether the
-            sequences names are unique. It is responsibility of the caller
-            to validate this information<DD><CODE>preset</CODE> - A list of Options\r
-<DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
-             given web service, e.g. JABAWS is deployed on Windows and
-             Mafft service is called\r
-<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
-             exceeds what is defined by the limit\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
-             following reasons: 1) The number of sequences in the
-             submission or their average length is greater then defined by
-             the default Limit. 2) Any problems on the server side e.g. it
-             is misconfigured or malfunction, is reported via this
-             exception. In the first case the information on the limit
-             could be obtained from an exception.\r
-<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
-             supported, 2) The value of the option is defined outside the
-             boundaries. In both cases exception object contain the
-             information on the violating Option.</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
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-&nbsp;<A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
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