<!--NewPage-->\r
<HTML>\r
<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:28 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="2010-02-17">\r
+<META NAME="date" CONTENT="2011-12-07">\r
\r
<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
\r
</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
- Classes in this package have no dependencies to other sources in the project. </TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
</TR>\r
</TABLE>\r
\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></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 inFilePath)</CODE>\r
+\r
+<BR>\r
+ 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 <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>(java.io.File file)</CODE>\r
\r
<BR>\r
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 java.util.HashMap<java.lang.String,java.util.Set<<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>></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 input)</CODE>\r
+\r
+<BR>\r
+ > 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 java.util.HashMap<java.lang.String,java.util.Set<<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>></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 input)</CODE>\r
+\r
+<BR>\r
+ > 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 java.util.Map<java.lang.String,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></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 result)</CODE>\r
+\r
+<BR>\r
+ 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 java.util.Map<java.lang.String,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></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 result)</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 java.util.Map<java.lang.String,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></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 inStream)</CODE>\r
+\r
+<BR>\r
+ Reader for JRonn horizontal file format</TD>\r
+</TR>\r
</TABLE>\r
\r
<P>\r
git://source.jalview.org / jabaws.git / blobdiff