+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
-<TITLE>\r
-Util\r
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-function windowTitle()\r
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- <A HREF="../../index.html?compbio/runner/Util.html" target="_top"><B>FRAMES</B></A> \r
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- <SCRIPT type="text/javascript">\r
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- document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-<H2>\r
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-compbio.runner</FONT>\r
-<BR>\r
-Class Util</H2>\r
-<PRE>\r
-java.lang.Object\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
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\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
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#SPACE">SPACE</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/runner/Util.html#Util()">Util</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\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/LimitsManager.html" title="class in compbio.metadata">LimitsManager</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
-\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
-</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/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#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
-\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
-\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
-\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 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
- <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)</CODE>\r
-\r
-<BR>\r
- </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
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="SPACE"><!-- --></A><H3>\r
-SPACE</H3>\r
-<PRE>\r
-public static final java.lang.String <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
-</DL>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Util()"><!-- --></A><H3>\r
-Util</H3>\r
-<PRE>\r
-public <B>Util</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\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
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\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
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\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
- 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
-<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>\r
-</DL>\r
-<HR>\r
-\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
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
- <TR ALIGN="center" VALIGN="top">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Util.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
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-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><B>PREV CLASS</B></A> \r
- NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/runner/Util.html" target="_top"><B>FRAMES</B></A> \r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
- //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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