website/full_javadoc/compbio/runner/msa/class-use/Probcons.html

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   7 Uses of Class compbio.runner.msa.Probcons\r
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  84 <B>Uses of Class<br>compbio.runner.msa.Probcons</B></H2>\r
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  90 Packages that use <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></FONT></TH>\r
  91 </TR>\r
  92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  93 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
  94 <TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
  95 </TR>\r
  96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  97 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
  98 <TD>&nbsp;&nbsp;</TD>\r
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 100 </TABLE>\r
 101 &nbsp;\r
 102 <P>\r
 103 <A NAME="compbio.runner.msa"><!-- --></A>\r
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 105 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 106 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 107 Uses of <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
 108 </TR>\r
 109 </TABLE>\r
 110 &nbsp;\r
 111 <P>\r
 112 \r
 113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 114 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 115 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></FONT></TH>\r
 116 </TR>\r
 117 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 118 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 119 <CODE>&nbsp;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></CODE></FONT></TD>\r
 120 <TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#setInput(java.lang.String)">setInput</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;inFile)</CODE>\r
 121 \r
 122 <BR>\r
 123 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 124 </TR>\r
 125 </TABLE>\r
 126 &nbsp;\r
 127 <P>\r
 128 \r
 129 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 130 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 131 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></FONT></TH>\r
 132 </TR>\r
 133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 135 <CODE>&nbsp;<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;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
 136 <TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getType()">getType</A></B>()</CODE>\r
 137 \r
 138 <BR>\r
 139 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 140 </TR>\r
 141 </TABLE>\r
 142 &nbsp;\r
 143 <P>\r
 144 <A NAME="compbio.ws.server"><!-- --></A>\r
 145 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 146 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 147 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 148 Uses of <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
 149 </TR>\r
 150 </TABLE>\r
 151 &nbsp;\r
 152 <P>\r
 153 \r
 154 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 155 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 156 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></FONT></TH>\r
 157 </TR>\r
 158 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 160 <CODE>&nbsp;<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
 161 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getLimit(java.lang.String)">getLimit</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;presetName)</CODE>\r
 162 \r
 163 <BR>\r
 164 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 165 </TR>\r
 166 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 167 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 168 <CODE>&nbsp;<A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
 169 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getLimits()">getLimits</A></B>()</CODE>\r
 170 \r
 171 <BR>\r
 172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 173 </TR>\r
 174 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 175 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 176 <CODE>&nbsp;<A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
 177 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getPresets()">getPresets</A></B>()</CODE>\r
 178 \r
 179 <BR>\r
 180 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 181 </TR>\r
 182 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 183 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 184 <CODE>&nbsp;<A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
 185 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
 186 \r
 187 <BR>\r
 188 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 189 </TR>\r
 190 </TABLE>\r
 191 &nbsp;\r
 192 <P>\r
 193 \r
 194 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 195 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 196 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></FONT></TH>\r
 197 </TR>\r
 198 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 199 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 200 <CODE>&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
 201 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</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
 202             <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/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
 203 \r
 204 <BR>\r
 205 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 206 </TR>\r
 207 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 208 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 209 <CODE>&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
 210 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</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
 211             <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&nbsp;preset)</CODE>\r
 212 \r
 213 <BR>\r
 214 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 215 </TR>\r
 216 </TABLE>\r
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