<!--NewPage-->\r
<HTML>\r
<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:34 BST 2011 -->\r
<TITLE>\r
_SkeletalCommandBuilder\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
<BR>\r
Class _SkeletalCommandBuilder</H2>\r
<PRE>\r
-java.lang.Object\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 "><B>compbio.runner._SkeletalCommandBuilder</B>\r
</PRE>\r
<DL>\r
<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></DD>\r
</DL>\r
<DL>\r
-<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>, <A HREF="../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>, <A HREF="../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>, <A HREF="../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>, <A HREF="../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>, <A HREF="../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>, <A HREF="../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></DD>\r
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>, <A HREF="../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>, <A HREF="../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>, <A HREF="../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>, <A HREF="../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>, <A HREF="../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></DD>\r
</DL>\r
<HR>\r
+<B>Deprecated.</B>\r
+<P>\r
<DL>\r
-<DT><PRE>public abstract class <B>_SkeletalCommandBuilder</B><DT>extends java.lang.Object<DT>implements <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></DL>\r
+<DT><PRE><FONT SIZE="-1"><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Deprecated.html?is-external=true" title="class or interface in java.lang">@Deprecated</A>\r
+</FONT>public abstract class <B>_SkeletalCommandBuilder</B><DT>extends <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><DT>implements <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></DL>\r
</PRE>\r
\r
<P>\r
<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#_SkeletalCommandBuilder()">_SkeletalCommandBuilder</A></B>()</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
</TABLE>\r
\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A></B>(java.lang.String parameter)</CODE>\r
+<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A></B>(<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> parameter)</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List<java.lang.String> parameters)</CODE>\r
+<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</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><<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>> parameters)</CODE>\r
\r
<BR>\r
- Adds parameter to the list of parameters for a native executable</TD>\r
+ <B>Deprecated.</B> Adds parameter to the list of parameters for a native executable</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A></B>(java.lang.String[] parameters)</CODE>\r
+<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A></B>(<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>[] parameters)</CODE>\r
+\r
+<BR>\r
+ <B>Deprecated.</B> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <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/runner/_SkeletalCommandBuilder.html#getClusterJobSettings()">getClusterJobSettings</A></B>()</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> java.lang.String</CODE></FONT></TD>\r
+<CODE> <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/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A></B>()</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> java.lang.String</CODE></FONT></TD>\r
+<CODE> <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/runner/_SkeletalCommandBuilder.html#getError()">getError</A></B>()</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String presetName)</CODE>\r
+<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A></B>(<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> presetName)</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A></B>()</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> java.lang.String</CODE></FONT></TD>\r
+<CODE> <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/runner/_SkeletalCommandBuilder.html#getName()">getName</A></B>()</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> java.lang.String</CODE></FONT></TD>\r
+<CODE> <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/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A></B>()</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
</TR>\r
</TABLE>\r
</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String directory)</CODE>\r
+<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A></B>(<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> directory)</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconfig)</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A></B>(java.lang.String email)</CODE>\r
+<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A></B>(<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> email)</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></B>(java.lang.String name)</CODE>\r
+<TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></B>(<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> name)</CODE>\r
\r
<BR>\r
- </TD>\r
+ <B>Deprecated.</B> </TD>\r
</TR>\r
</TABLE>\r
<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.Object</B></TH>\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>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\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
<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
<PRE>\r
public <B>_SkeletalCommandBuilder</B>()</PRE>\r
<DL>\r
-</DL>\r
+<DD><B>Deprecated.</B> </DL>\r
\r
<!-- ============ METHOD DETAIL ========== -->\r
\r
<A NAME="setEmail(java.lang.String)"><!-- --></A><H3>\r
setEmail</H3>\r
<PRE>\r
-public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setEmail</B>(java.lang.String email)</PRE>\r
+public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setEmail</B>(<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> email)</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
</DL>\r
</DD>\r
<DD><DL>\r
<A NAME="setName(java.lang.String)"><!-- --></A><H3>\r
setName</H3>\r
<PRE>\r
-public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setName</B>(java.lang.String name)</PRE>\r
+public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setName</B>(<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> name)</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
</DL>\r
</DD>\r
<DD><DL>\r
<A NAME="getName()"><!-- --></A><H3>\r
getName</H3>\r
<PRE>\r
-public java.lang.String <B>getName</B>()</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>getName</B>()</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
</DL>\r
</DD>\r
<DD><DL>\r
<A NAME="getEmail()"><!-- --></A><H3>\r
getEmail</H3>\r
<PRE>\r
-public java.lang.String <B>getEmail</B>()</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>getEmail</B>()</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
</DL>\r
</DD>\r
<DD><DL>\r
<A NAME="addParameters(java.lang.String[])"><!-- --></A><H3>\r
addParameters</H3>\r
<PRE>\r
-public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</B>(java.lang.String[] parameters)</PRE>\r
+public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</B>(<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>[] parameters)</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
</DL>\r
</DD>\r
<DD><DL>\r
<A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
addParameters</H3>\r
<PRE>\r
-public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</B>(java.util.List<java.lang.String> parameters)</PRE>\r
+public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</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><<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>> parameters)</PRE>\r
<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
+<DD><B>Deprecated.</B> <DD><B>Description copied from interface: <CODE><A HREF="../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
<DD>Adds parameter to the list of parameters for a native executable\r
<P>\r
<DD><DL>\r
<PRE>\r
public <A HREF="../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>> <B>getParameters</B>(<A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>\r
</DD>\r
<DD><DL>\r
<A NAME="addParameter(java.lang.String)"><!-- --></A><H3>\r
addParameter</H3>\r
<PRE>\r
-public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameter</B>(java.lang.String parameter)</PRE>\r
+public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameter</B>(<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> parameter)</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
</DL>\r
</DD>\r
<DD><DL>\r
<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
getResults</H3>\r
<PRE>\r
-public <V> V <B>getResults</B>(java.lang.String directory)</PRE>\r
+public <V> V <B>getResults</B>(<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> directory)</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>\r
</DD>\r
<DD><DL>\r
<PRE>\r
public <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?> <B>loadRunConfiguration</B>(<A HREF="../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconfig)</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>\r
</DD>\r
<DD><DL>\r
<A NAME="getOutput()"><!-- --></A><H3>\r
getOutput</H3>\r
<PRE>\r
-public java.lang.String <B>getOutput</B>()</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>getOutput</B>()</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>\r
</DD>\r
<DD><DL>\r
<A NAME="getError()"><!-- --></A><H3>\r
getError</H3>\r
<PRE>\r
-public java.lang.String <B>getError</B>()</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>getError</B>()</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getError()">getError</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>\r
</DD>\r
<DD><DL>\r
<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
getLimit</H3>\r
<PRE>\r
-public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>> <B>getLimit</B>(java.lang.String presetName)</PRE>\r
+public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>> <B>getLimit</B>(<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> presetName)</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>\r
</DD>\r
<DD><DL>\r
<PRE>\r
public <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>> <B>getLimits</B>()</PRE>\r
<DL>\r
-<DD><DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>\r
</DD>\r
<DD><DL>\r
</DL>\r
</DD>\r
</DL>\r
+<HR>\r
+\r
+<A NAME="getClusterJobSettings()"><!-- --></A><H3>\r
+getClusterJobSettings</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>getClusterJobSettings</B>()</PRE>\r
+<DL>\r
+<DD><B>Deprecated.</B> <DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getClusterJobSettings()">getClusterJobSettings</A></CODE> in interface <CODE><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
<!-- ========= END OF CLASS DATA ========= -->\r
<HR>\r
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git://source.jalview.org / jabaws.git / blobdiff