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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / full_javadoc / compbio / metadata / class-use / RunnerConfig.html
diff --git a/website/full_javadoc/compbio/metadata/class-use/RunnerConfig.html b/website/full_javadoc/compbio/metadata/class-use/RunnerConfig.html
index 26548ba..21645ab 100644 (file)
--- a/website/full_javadoc/compbio/metadata/class-use/RunnerConfig.html
+++ b/website/full_javadoc/compbio/metadata/class-use/RunnerConfig.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 Wed Dec 07 12:30:42 GMT 2011 -->\r
 <TITLE>\r
 Uses of Class compbio.metadata.RunnerConfig\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-12-07">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
 \r
@@ -91,7 +91,7 @@ Packages that use <A HREF="../../../compbio/metadata/RunnerConfig.html" title="c
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
@@ -99,7 +99,7 @@ Packages that use <A HREF="../../../compbio/metadata/RunnerConfig.html" title="c
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
+<TD>&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
@@ -133,8 +133,8 @@ Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in co
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
+<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>Metadata.</B><B><A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get options supported by a web service</TD>\r
@@ -207,7 +207,7 @@ Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in co
 </TR>\r
 </TABLE>\r
 </CODE></FONT></TD>\r
-<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
+<TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -255,7 +255,7 @@ Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in co
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&gt;</CODE></FONT></TD>\r
+<CODE>&nbsp;<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/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&gt;</CODE></FONT></TD>\r
 <TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&nbsp;rconfig)</CODE>\r
 \r
 <BR>\r
@@ -297,7 +297,7 @@ Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in co
 </TR>\r
 </TABLE>\r
 </CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
+<TD><CODE><B>Util.</B><B><A HREF="../../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -312,8 +312,8 @@ Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in co
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</A></B>(java.util.List&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments,\r
+<CODE>static&nbsp;<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="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</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;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments,\r
                          <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
 \r
 <BR>\r
@@ -352,16 +352,16 @@ Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in co
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
+<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="type parameter in GenericMetadataService">T</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>GenericMetadataService.</B><B><A HREF="../../../compbio/ws/server/GenericMetadataService.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
+<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -384,8 +384,24 @@ Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in co
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
+<CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>ClustalOWS.</B><B><A HREF="../../../compbio/ws/server/ClustalOWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r