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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / dm_javadoc / compbio / data / sequence / class-use / Score.html
diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/Score.html b/website/dm_javadoc/compbio/data/sequence/class-use/Score.html
index 832289f..6f1eb8c 100644 (file)
--- a/website/dm_javadoc/compbio/data/sequence/class-use/Score.html
+++ b/website/dm_javadoc/compbio/data/sequence/class-use/Score.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Tue Dec 21 18:32:59 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:08:24 GMT 2011 -->\r
 <TITLE>\r
 Uses of Class compbio.data.sequence.Score\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-12-21">\r
+<META NAME="date" CONTENT="2011-12-07">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
 \r
@@ -90,10 +90,6 @@ function windowTitle()
 Packages that use <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.&nbsp;</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
 <TD>A data model for multiple sequence alignment web services and utility methods
  that work on the objects of this model.&nbsp;</TD>\r
@@ -101,11 +97,11 @@ Packages that use <A HREF="../../../../compbio/data/sequence/Score.html" title="
 </TABLE>\r
 &nbsp;\r
 <P>\r
-<A NAME="compbio.data.msa"><!-- --></A>\r
+<A NAME="compbio.data.sequence"><!-- --></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
-Uses of <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+Uses of <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
 </TR>\r
 </TABLE>\r
 &nbsp;\r
@@ -113,24 +109,39 @@ Uses of <A HREF="../../../../compbio/data/sequence/Score.html" title="class in c
 \r
 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>\r
+<TH ALIGN="left" COLSPAN="2">Fields in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type parameters of type <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>Annotation.</B><B><A HREF="../../../../compbio/data/msa/Annotation.html#getAnnotation(java.lang.String)">getAnnotation</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;jobId)</CODE>\r
+<CODE>&nbsp;java.util.TreeSet&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>ScoreManager.ScoreHolder.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#scores">scores</A></B></CODE>\r
 \r
 <BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</TD>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 </TABLE>\r
 &nbsp;\r
 <P>\r
-<A NAME="compbio.data.sequence"><!-- --></A>\r
+\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
-Uses of <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></CODE></FONT></TD>\r
+<TD><CODE><B>ScoreManager.ScoreHolder.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.Enum)">getScoreByMethod</A></B>(java.lang.Enum&lt;?&gt;&nbsp;method)</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>&nbsp;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></CODE></FONT></TD>\r
+<TD><CODE><B>ScoreManager.ScoreHolder.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.String)">getScoreByMethod</A></B>(java.lang.String&nbsp;method)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 </TABLE>\r
 &nbsp;\r
@@ -142,12 +153,112 @@ Uses of <A HREF="../../../../compbio/data/sequence/Score.html" title="class in c
 </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/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)">readAAConResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;results)</CODE>\r
+<CODE>&nbsp;java.util.Map&lt;java.lang.String,java.util.TreeSet&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#asMap()">asMap</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>&nbsp;java.util.Set&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#asSet()">asSet</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;java.util.HashSet&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)">readAAConResults</A></B>(java.io.InputStream&nbsp;results)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read AACon result with no alignment files.</TD>\r
 </TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static&nbsp;java.util.HashMap&lt;java.lang.String,java.util.Set&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readDisembl(java.io.InputStream)">readDisembl</A></B>(java.io.InputStream&nbsp;input)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;> Foobar_dundeefriends
+ 
+ # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
+ 
+ # REM465 355-368
+ 
+ # HOTLOOPS 190-204
+ 
+ # RESIDUE COILS REM465 HOTLOOPS
+ 
+ M 0.86010 0.88512 0.37094
+ 
+ T 0.79983 0.85864 0.44331
+ 
+ >Next Sequence name</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static&nbsp;java.util.HashMap&lt;java.lang.String,java.util.Set&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readGlobPlot(java.io.InputStream)">readGlobPlot</A></B>(java.io.InputStream&nbsp;input)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;> Foobar_dundeefriends
+ 
+ # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
+ 
+ # REM465 355-368
+ 
+ # HOTLOOPS 190-204
+ 
+ # RESIDUE COILS REM465 HOTLOOPS
+ 
+ M 0.86010 0.88512 0.37094
+ 
+ T 0.79983 0.85864 0.44331
+ 
+ >Next Sequence name</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static&nbsp;java.util.Map&lt;java.lang.String,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readIUPred(java.io.File)">readIUPred</A></B>(java.io.File&nbsp;result)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read IUPred output</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static&nbsp;java.util.Map&lt;java.lang.String,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)">readJRonn</A></B>(java.io.File&nbsp;result)</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;java.util.Map&lt;java.lang.String,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)">readJRonn</A></B>(java.io.InputStream&nbsp;inStream)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reader for JRonn horizontal file format</TD>\r
+</TR>\r
+</TABLE>\r
+&nbsp;\r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;int</CODE></FONT></TD>\r
+<TD><CODE><B>Score.</B><B><A HREF="../../../../compbio/data/sequence/Score.html#compareTo(compbio.data.sequence.Score)">compareTo</A></B>(<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&nbsp;o)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
 </TABLE>\r
 &nbsp;\r
 <P>\r
@@ -158,9 +269,33 @@ Uses of <A HREF="../../../../compbio/data/sequence/Score.html" title="class in c
 </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/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
+<TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#newInstance(java.util.Map)">newInstance</A></B>(java.util.Map&lt;java.lang.String,java.util.Set&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;&nbsp;data)</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/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
+<TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleScore(java.util.Map)">newInstanceSingleScore</A></B>(java.util.Map&lt;java.lang.String,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&nbsp;seqScoresMap)</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/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
+<TD><CODE><B>ScoreManager.</B><B><A HREF="../../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleSequence(java.util.Set)">newInstanceSingleSequence</A></B>(java.util.Set&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&nbsp;data)</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;void</CODE></FONT></TD>\r
-<TD><CODE><B>Score.</B><B><A HREF="../../../../compbio/data/sequence/Score.html#write(java.util.Set, java.io.OutputStream)">write</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&nbsp;scores,\r
-      <A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;output)</CODE>\r
+<TD><CODE><B>Score.</B><B><A HREF="../../../../compbio/data/sequence/Score.html#write(java.util.TreeSet, java.io.Writer)">write</A></B>(java.util.TreeSet&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&nbsp;scores,\r
+      java.io.Writer&nbsp;writer)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Outputs the List of Score objects into the Output stream.</TD>\r