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remove old datamodel javadoc
[jabaws.git] / website / full_javadoc / compbio / runner / Util.html
diff --git a/website/full_javadoc/compbio/runner/Util.html b/website/full_javadoc/compbio/runner/Util.html
index d09afc7..8db9c58 100644 (file)
--- a/website/full_javadoc/compbio/runner/Util.html
+++ b/website/full_javadoc/compbio/runner/Util.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 14:32:34 BST 2011 -->\r
 <TITLE>\r
 Util\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
@@ -92,12 +92,12 @@ compbio.runner</FONT>
 <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
@@ -114,7 +114,15 @@ java.lang.Object
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
+<CODE>static&nbsp;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
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<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>\r
 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#SPACE">SPACE</A></B></CODE>\r
 \r
 <BR>\r
@@ -152,15 +160,14 @@ java.lang.Object
 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 <TR ALIGN="right" VALIGN="">\r
 <TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt;</CODE></FONT></TD>\r
+<CODE>&lt;T&gt; <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt;</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&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;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>&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
 \r
 <BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
@@ -168,35 +175,29 @@ java.lang.Object
 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 <TR ALIGN="right" VALIGN="">\r
 <TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt;</CODE></FONT></TD>\r
+<CODE>&lt;T&gt; <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt;</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&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;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>&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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>&lt;T&gt; <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt;</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&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
+<CODE>static&nbsp;<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>&nbsp;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>&nbsp;clustFile)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;<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&nbsp;workDirectory,\r
-                java.lang.String&nbsp;clustFile)</CODE>\r
+<CODE>static&nbsp;<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>&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>,<A HREF="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</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>&nbsp;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>&nbsp;clustFile)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -204,7 +205,7 @@ java.lang.Object
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;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&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;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>&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
            <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
 \r
 <BR>\r
@@ -214,10 +215,10 @@ java.lang.Object
 &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
@@ -233,10 +234,20 @@ java.lang.Object
 </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
@@ -269,31 +280,10 @@ public <B>Util</B>()</PRE>
 </TR>\r
 </TABLE>\r
 \r
-<A NAME="getLimits(java.lang.Class)"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public static &lt;T&gt; <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt; <B>getLimits</B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;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 &lt;T&gt; <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt; <B>getSupportedOptions</B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
+public static &lt;T&gt; <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt; <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>&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -304,7 +294,7 @@ public static &lt;T&gt; <A HREF="../../compbio/metadata/RunnerConfig.html" title
 <A NAME="getPresets(java.lang.Class)"><!-- --></A><H3>\r
 getPresets</H3>\r
 <PRE>\r
-public static &lt;T&gt; <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt; <B>getPresets</B>(java.lang.Class&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
+public static &lt;T&gt; <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt; <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>&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -315,20 +305,41 @@ public static &lt;T&gt; <A HREF="../../compbio/metadata/PresetManager.html" titl
 <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&nbsp;workDirectory,\r
-                                              java.lang.String&nbsp;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>&nbsp;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>&nbsp;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>&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>,<A HREF="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt; <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>&nbsp;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>&nbsp;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
@@ -336,11 +347,14 @@ public static final <A HREF="../../compbio/data/sequence/Alignment.html" title="
 <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&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-                              <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;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>&lt;<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+                              <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;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