X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2F_impl%2FRPSBlast.html;h=35a934e642107a81d416000958f12f8ca4e960cf;hb=2da44d18582e4d851e137573346a4916435c220b;hp=64cecfd14e482e475c7a9a2eedaea670dcf0663f;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/website/full_javadoc/compbio/runner/_impl/RPSBlast.html b/website/full_javadoc/compbio/runner/_impl/RPSBlast.html
index 64cecfd..35a934e 100644
--- a/website/full_javadoc/compbio/runner/_impl/RPSBlast.html
+++ b/website/full_javadoc/compbio/runner/_impl/RPSBlast.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:41 GMT 2011 -->
 <TITLE>
 RPSBlast
 </TITLE>
 
-<META NAME="date" CONTENT="2010-02-17">
+<META NAME="date" CONTENT="2011-12-07">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">
 
@@ -92,7 +92,7 @@ compbio.runner._impl</FONT>
 <BR>
 Class RPSBlast</H2>
 <PRE>
-java.lang.Object
+<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>
   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>
       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.RPSBlast</B>
 </PRE>
@@ -137,7 +137,7 @@ java.lang.Object
 <B>Constructor Summary</B></FONT></TH>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#RPSBlast(java.lang.String)">RPSBlast</A></B>(java.lang.String&nbsp;workDirectory)</CODE>
+<TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#RPSBlast(java.lang.String)">RPSBlast</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>&nbsp;workDirectory)</CODE>
 
 <BR>
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
@@ -154,7 +154,7 @@ java.lang.Object
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>
+<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>
 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>
 
 <BR>
@@ -162,7 +162,7 @@ java.lang.Object
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>
+<CODE>static&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>
 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getCommandName()">getCommandName</A></B>()</CODE>
 
 <BR>
@@ -170,7 +170,7 @@ java.lang.Object
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>
+<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="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>
 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>
 
 <BR>
@@ -178,7 +178,7 @@ java.lang.Object
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>
+<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>
 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getInput()">getInput</A></B>()</CODE>
 
 <BR>
@@ -186,7 +186,7 @@ java.lang.Object
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>
+<CODE>static&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>
 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getTestCommand()">getTestCommand</A></B>()</CODE>
 
 <BR>
@@ -199,16 +199,16 @@ java.lang.Object
 <TH ALIGN="left"><B>Methods inherited from class compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TH>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
-<TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>
+<TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>
 </TR>
 </TABLE>
 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
+<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>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+<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>
 </TR>
 </TABLE>
 &nbsp;
@@ -227,7 +227,7 @@ java.lang.Object
 <A NAME="RPSBlast(java.lang.String)"><!-- --></A><H3>
 RPSBlast</H3>
 <PRE>
-public <B>RPSBlast</B>(java.lang.String&nbsp;workDirectory)</PRE>
+public <B>RPSBlast</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>&nbsp;workDirectory)</PRE>
 <DL>
 </DL>
 
@@ -244,7 +244,7 @@ public <B>RPSBlast</B>(java.lang.String&nbsp;workDirectory)</PRE>
 <A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
 getCommand</H3>
 <PRE>
-public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>
+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>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>
 <DL>
 <DD><DL>
 </DL>
@@ -255,7 +255,7 @@ public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/clien
 <A NAME="getTestCommand()"><!-- --></A><H3>
 getTestCommand</H3>
 <PRE>
-public static java.lang.String <B>getTestCommand</B>()</PRE>
+public static <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>getTestCommand</B>()</PRE>
 <DL>
 <DD><DL>
 </DL>
@@ -266,7 +266,7 @@ public static java.lang.String <B>getTestCommand</B>()</PRE>
 <A NAME="getCommandName()"><!-- --></A><H3>
 getCommandName</H3>
 <PRE>
-public static java.lang.String <B>getCommandName</B>()</PRE>
+public static <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>getCommandName</B>()</PRE>
 <DL>
 <DD><DL>
 </DL>
@@ -277,7 +277,7 @@ public static java.lang.String <B>getCommandName</B>()</PRE>
 <A NAME="getCreatedFiles()"><!-- --></A><H3>
 getCreatedFiles</H3>
 <PRE>
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>
+public <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; <B>getCreatedFiles</B>()</PRE>
 <DL>
 <DD><DL>
 </DL>
@@ -288,7 +288,7 @@ public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>
 <A NAME="getInput()"><!-- --></A><H3>
 getInput</H3>
 <PRE>
-public java.lang.String <B>getInput</B>()</PRE>
+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>getInput</B>()</PRE>
 <DL>
 <DD><DL>
 </DL>
