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7 Uses of Class compbio.data.sequence.UnknownFileFormatException
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84 <B>Uses of Class<br>compbio.data.sequence.UnknownFileFormatException</B></H2>
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90 Packages that use <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>
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94 <TD>A data model for multiple sequence alignment web services and utility methods
95 that work on the objects of this model. </TD>
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100 <A NAME="compbio.data.sequence"><!-- --></A>
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103 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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104 Uses of <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>
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112 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that throw <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>
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114 <TR BGCOLOR="white" CLASS="TableRowColor">
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115 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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116 <CODE>static java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>
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117 <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>
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120 Reads and parses Fasta or Clustal formatted file into a list of
121 FastaSequence objects</TD>
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123 <TR BGCOLOR="white" CLASS="TableRowColor">
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124 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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125 <CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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126 <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>
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129 </TD>
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131 <TR BGCOLOR="white" CLASS="TableRowColor">
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132 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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133 <CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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134 <TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(java.io.InputStream instream)</CODE>
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137 Read Clustal formatted alignment.</TD>
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139 <TR BGCOLOR="white" CLASS="TableRowColor">
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140 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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141 <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>
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142 <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>
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145 > Foobar_dundeefriends
147 # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
153 # RESIDUE COILS REM465 HOTLOOPS
155 M 0.86010 0.88512 0.37094
157 T 0.79983 0.85864 0.44331
159 >Next Sequence name</TD>
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161 <TR BGCOLOR="white" CLASS="TableRowColor">
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162 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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163 <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>
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164 <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>
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167 > Foobar_dundeefriends
169 # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
175 # RESIDUE COILS REM465 HOTLOOPS
177 M 0.86010 0.88512 0.37094
179 T 0.79983 0.85864 0.44331
181 >Next Sequence name</TD>
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183 <TR BGCOLOR="white" CLASS="TableRowColor">
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184 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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185 <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>
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186 <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>
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189 Read IUPred output</TD>
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191 <TR BGCOLOR="white" CLASS="TableRowColor">
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192 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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193 <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>
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194 <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>
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197 </TD>
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199 <TR BGCOLOR="white" CLASS="TableRowColor">
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200 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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201 <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>
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202 <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>
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205 Reader for JRonn horizontal file format</TD>
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