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JWS-109 & JWS-116 Moved the docs (source and html built) to a new location that is...
[jabaws.git] / website / dm_javadoc / compbio / data / sequence / class-use / UnknownFileFormatException.html
diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html b/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html
index ec5cd08..1c5d664 100644 (file)
--- a/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html
+++ b/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.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.UnknownFileFormatException\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
@@ -113,8 +113,17 @@ Uses of <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.ht
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static&nbsp;java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#openInputStream(java.lang.String)">openInputStream</A></B>(java.lang.String&nbsp;inFilePath)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads and parses Fasta or Clustal formatted file into a list of
+ FastaSequence objects</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>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;file)</CODE>\r
+<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(java.io.File&nbsp;file)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -122,23 +131,75 @@ Uses of <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.ht
 <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>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</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;instream)</CODE>\r
+<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(java.io.InputStream&nbsp;instream)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read Clustal formatted alignment.</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/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;result)</CODE>\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;<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/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</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>(<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;inStream)</CODE>\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