<!--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 Wed Dec 07 12:30:40 GMT 2011 -->\r
<TITLE>\r
Util\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
<BR>\r
Class Util</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.Util</B>\r
</PRE>\r
<HR>\r
<DL>\r
-<DT><PRE>public final class <B>Util</B><DT>extends java.lang.Object</DL>\r
+<DT><PRE>public final class <B>Util</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></DL>\r
</PRE>\r
\r
<P>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.lang.String</CODE></FONT></TD>\r
+<CODE>static org.apache.log4j.Logger</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#log">log</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>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></CODE></FONT></TD>\r
<TD><CODE><B><A HREF="../../compbio/runner/Util.html#SPACE">SPACE</A></B></CODE>\r
\r
<BR>\r
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
<TR ALIGN="right" VALIGN="">\r
<TD NOWRAP><FONT SIZE="-1">\r
-<CODE><T> <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><T></CODE></FONT></TD>\r
+<CODE><T> <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><T></CODE></FONT></TD>\r
</TR>\r
</TABLE>\r
</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#getLimits(java.lang.Class)">getLimits</A></B>(java.lang.Class<? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</CODE>\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</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><? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</CODE>\r
\r
<BR>\r
- For now just assume that all parameters which came in needs setting it
- will be a client responsibility to prepare RunnerConfig object then</TD>\r
+ </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
<TR ALIGN="right" VALIGN="">\r
<TD NOWRAP><FONT SIZE="-1">\r
-<CODE><T> <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><T></CODE></FONT></TD>\r
+<CODE><T> <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T></CODE></FONT></TD>\r
</TR>\r
</TABLE>\r
</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</A></B>(java.lang.Class<? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</CODE>\r
+<TD><CODE><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><? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</CODE>\r
\r
<BR>\r
</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE><T> <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T></CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(java.lang.Class<? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</CODE>\r
+<CODE>static <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</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> workDirectory,\r
+ <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> clustFile)</CODE>\r
\r
<BR>\r
</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</A></B>(java.lang.String workDirectory,\r
- java.lang.String clustFile)</CODE>\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<A HREF="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#readJronnFile(java.lang.String, java.lang.String)">readJronnFile</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> workDirectory,\r
+ <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> clustFile)</CODE>\r
\r
<BR>\r
</TD>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</A></B>(java.util.List<<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</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="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)</CODE>\r
\r
<BR>\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
\r
</TR>\r
</TABLE>\r
\r
+<A NAME="log"><!-- --></A><H3>\r
+log</H3>\r
+<PRE>\r
+public static org.apache.log4j.Logger <B>log</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
<A NAME="SPACE"><!-- --></A><H3>\r
SPACE</H3>\r
<PRE>\r
-public static final java.lang.String <B>SPACE</B></PRE>\r
+public static final <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>SPACE</B></PRE>\r
<DL>\r
<DL>\r
<DT><B>See Also:</B><DD><A HREF="../../constant-values.html#compbio.runner.Util.SPACE">Constant Field Values</A></DL>\r
</TR>\r
</TABLE>\r
\r
-<A NAME="getLimits(java.lang.Class)"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public static <T> <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><T> <B>getLimits</B>(java.lang.Class<? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</PRE>\r
-<DL>\r
-<DD>For now just assume that all parameters which came in needs setting it
- will be a client responsibility to prepare RunnerConfig object then\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>rconfig</CODE> - \r
-<DT><B>Returns:</B><DD>public static List<String> toOptionString(RunnerConfig<?>
- rconfig) { String option = ""; List<String> options = new
- ArrayList<String>(); for (Parameter<?> par :
- rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())
- { option = par.getOptionName(); } else { option =
- par.getOptionName() + "=" + par.getPossibleValues().get(0); } //
- separate options options.add(option); } return options; }</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
<A NAME="getSupportedOptions(java.lang.Class)"><!-- --></A><H3>\r
getSupportedOptions</H3>\r
<PRE>\r
-public static <T> <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T> <B>getSupportedOptions</B>(java.lang.Class<? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</PRE>\r
+public static <T> <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T> <B>getSupportedOptions</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><? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="getPresets(java.lang.Class)"><!-- --></A><H3>\r
getPresets</H3>\r
<PRE>\r
-public static <T> <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><T> <B>getPresets</B>(java.lang.Class<? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</PRE>\r
+public static <T> <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><T> <B>getPresets</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><? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="readClustalFile(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
readClustalFile</H3>\r
<PRE>\r
-public static final <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(java.lang.String workDirectory,\r
- java.lang.String clustFile)\r
+public static final <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</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> workDirectory,\r
+ <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> clustFile)\r
throws <A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
- java.io.IOException,\r
- java.io.FileNotFoundException,\r
- java.lang.NullPointerException</PRE>\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="readJronnFile(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
+readJronnFile</H3>\r
+<PRE>\r
+public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<A HREF="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> <B>readJronnFile</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> workDirectory,\r
+ <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> clustFile)\r
+ throws <A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></PRE>\r
<DL>\r
<DD><DL>\r
\r
<DT><B>Throws:</B>\r
<DD><CODE><A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
-<DD><CODE>java.io.IOException</CODE>\r
-<DD><CODE>java.io.FileNotFoundException</CODE>\r
-<DD><CODE>java.lang.NullPointerException</CODE></DL>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE></DL>\r
</DD>\r
</DL>\r
<HR>\r
<A NAME="writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
writeInput</H3>\r
<PRE>\r
-public static void <B>writeInput</B>(java.util.List<<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
- <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)</PRE>\r
+public static void <B>writeInput</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="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)\r
+ throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
<DL>\r
<DD><DL>\r
-</DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
</DD>\r
</DL>\r
<!-- ========= END OF CLASS DATA ========= -->\r