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remove old datamodel javadoc
[jabaws.git] / website / full_javadoc / compbio / runner / _impl / PSIBlast.html
diff --git a/website/full_javadoc/compbio/runner/_impl/PSIBlast.html b/website/full_javadoc/compbio/runner/_impl/PSIBlast.html
index b14bdb4..3f9faab 100644 (file)
--- a/website/full_javadoc/compbio/runner/_impl/PSIBlast.html
+++ b/website/full_javadoc/compbio/runner/_impl/PSIBlast.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:35 BST 2011 -->\r
 <TITLE>\r
 PSIBlast\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
@@ -92,7 +92,7 @@ compbio.runner._impl</FONT>
 <BR>\r
 Class PSIBlast</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 "><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>\r
       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.PSIBlast</B>\r
 </PRE>\r
@@ -137,7 +137,7 @@ java.lang.Object
 <B>Constructor Summary</B></FONT></TH>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html#PSIBlast(java.lang.String)">PSIBlast</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
+<TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html#PSIBlast(java.lang.String)">PSIBlast</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>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -154,7 +154,7 @@ java.lang.Object
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\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/runner/_impl/PSIBlast.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>\r
 \r
 <BR>\r
@@ -162,7 +162,7 @@ java.lang.Object
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\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/runner/_impl/PSIBlast.html#getCommandName()">getCommandName</A></B>()</CODE>\r
 \r
 <BR>\r
@@ -170,7 +170,7 @@ java.lang.Object
 </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;java.lang.String&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="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><A HREF="../../../compbio/runner/_impl/PSIBlast.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 \r
 <BR>\r
@@ -178,7 +178,7 @@ java.lang.Object
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\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/runner/_impl/PSIBlast.html#getInput()">getInput</A></B>()</CODE>\r
 \r
 <BR>\r
@@ -187,7 +187,7 @@ java.lang.Object
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html#removeOutput(java.lang.String)">removeOutput</A></B>(java.lang.String&nbsp;outfile)</CODE>\r
+<TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html#removeOutput(java.lang.String)">removeOutput</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;outfile)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -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>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
-<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>\r
+<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>\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.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
 &nbsp;\r
@@ -227,7 +227,7 @@ java.lang.Object
 <A NAME="PSIBlast(java.lang.String)"><!-- --></A><H3>\r
 PSIBlast</H3>\r
 <PRE>\r
-public <B>PSIBlast</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
+public <B>PSIBlast</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>\r
 <DL>\r
 </DL>\r
 \r
@@ -244,7 +244,7 @@ public <B>PSIBlast</B>(java.lang.String&nbsp;workDirectory)</PRE>
 <A NAME="removeOutput(java.lang.String)"><!-- --></A><H3>\r
 removeOutput</H3>\r
 <PRE>\r
-public boolean <B>removeOutput</B>(java.lang.String&nbsp;outfile)</PRE>\r
+public boolean <B>removeOutput</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;outfile)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -255,7 +255,7 @@ public boolean <B>removeOutput</B>(java.lang.String&nbsp;outfile)</PRE>
 <A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 getCommand</H3>\r
 <PRE>\r
-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>\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>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -266,7 +266,7 @@ public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/clien
 <A NAME="getCommandName()"><!-- --></A><H3>\r
 getCommandName</H3>\r
 <PRE>\r
-public java.lang.String <B>getCommandName</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>getCommandName</B>()</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -277,7 +277,7 @@ public java.lang.String <B>getCommandName</B>()</PRE>
 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 getCreatedFiles</H3>\r
 <PRE>\r
-public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
+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>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -288,7 +288,7 @@ public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>
 <A NAME="getInput()"><!-- --></A><H3>\r
 getInput</H3>\r
 <PRE>\r
-public java.lang.String <B>getInput</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>getInput</B>()</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r