website/dm_javadoc/compbio/metadata/class-use/Option.html

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   7 Uses of Class compbio.metadata.Option\r
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  42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
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  83 <H2>\r
  84 <B>Uses of Class<br>compbio.metadata.Option</B></H2>\r
  85 </CENTER>\r
  86 \r
  87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
  88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
  89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
  90 Packages that use <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
  91 </TR>\r
  92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  93 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
  94 <TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.&nbsp;</TD>\r
  95 </TR>\r
  96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  97 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
  98 <TD>A meta-data model for multiple sequence alignment web services
  99  Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
 100 </TR>\r
 101 </TABLE>\r
 102 &nbsp;\r
 103 <P>\r
 104 <A NAME="compbio.data.msa"><!-- --></A>\r
 105 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 106 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 107 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 108 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
 109 </TR>\r
 110 </TABLE>\r
 111 &nbsp;\r
 112 <P>\r
 113 \r
 114 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 115 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 116 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
 117 </TR>\r
 118 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 119 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 120 <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
 121 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.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
 122             <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/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
 123 \r
 124 <BR>\r
 125 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
 126 </TR>\r
 127 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 128 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 129 <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
 130 <TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</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
 131               <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/data/msa/Annotation.html" title="type parameter in Annotation">T</A>&gt;&gt;&nbsp;options)</CODE>\r
 132 \r
 133 <BR>\r
 134 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to custom settings defined in options
 135  list.</TD>\r
 136 </TR>\r
 137 </TABLE>\r
 138 &nbsp;\r
 139 <P>\r
 140 <A NAME="compbio.metadata"><!-- --></A>\r
 141 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 142 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 143 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 144 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
 145 </TR>\r
 146 </TABLE>\r
 147 &nbsp;\r
 148 <P>\r
 149 \r
 150 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 151 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 152 <TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
 153 </TR>\r
 154 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 155 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 156 <CODE>&nbsp;class</CODE></FONT></TD>\r
 157 <TD><CODE><B><A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter&lt;T&gt;</A></B></CODE>\r
 158 \r
 159 <BR>\r
 160 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A single value containing an option supported by the web service e.g.</TD>\r
 161 </TR>\r
 162 </TABLE>\r
 163 &nbsp;\r
 164 <P>\r
 165 \r
 166 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 167 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 168 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
 169 </TR>\r
 170 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 172 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
 173 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</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;name)</CODE>\r
 174 \r
 175 <BR>\r
 176 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the argument by its name if found, NULL otherwise.</TD>\r
 177 </TR>\r
 178 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 179 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 180 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
 181 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</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;optionName)</CODE>\r
 182 \r
 183 <BR>\r
 184 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the argument by option name, NULL if the argument is not found</TD>\r
 185 </TR>\r
 186 </TABLE>\r
 187 &nbsp;\r
 188 <P>\r
 189 \r
 190 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 191 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 192 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
 193 </TR>\r
 194 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 195 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 196 <CODE>&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/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
 197 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>\r
 198 \r
 199 <BR>\r
 200 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns list of <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
 201  runner</TD>\r
 202 </TR>\r
 203 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 204 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 205 <CODE>&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/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&gt;</CODE></FONT></TD>\r
 206 <TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&nbsp;rconfig)</CODE>\r
 207 \r
 208 <BR>\r
 209 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Converts list of options as String to type Option</TD>\r
 210 </TR>\r
 211 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 212 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 213 <CODE>&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/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
 214 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>\r
 215 \r
 216 <BR>\r
 217 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the list of the Options supported by the executable of type T</TD>\r
 218 </TR>\r
 219 </TABLE>\r
 220 &nbsp;\r
 221 <P>\r
 222 \r
 223 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 224 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 225 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
 226 </TR>\r
 227 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 228 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 229 <CODE>&nbsp;void</CODE></FONT></TD>\r
 230 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)">addOption</A></B>(<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&nbsp;option)</CODE>\r
 231 \r
 232 <BR>\r
 233 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds Option to the internal list of options</TD>\r
 234 </TR>\r
 235 </TABLE>\r
 236 &nbsp;\r
 237 <P>\r
 238 \r
 239 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 240 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 241 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
 242 </TR>\r
 243 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 244 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 245 <CODE>&nbsp;void</CODE></FONT></TD>\r
 246 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</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/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;&nbsp;parameters)</CODE>\r
 247 \r
 248 <BR>\r
 249 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds the list of options or parameters to the internal list of options</TD>\r
 250 </TR>\r
 251 </TABLE>\r
 252 &nbsp;\r
 253 <P>\r
 254 \r
 255 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 256 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 257 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
 258 </TR>\r
 259 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 260 <TD><CODE><B><A HREF="../../../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)">WrongParameterException</A></B>(<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&nbsp;option)</CODE>\r
 261 \r
 262 <BR>\r
 263 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 264 </TR>\r
 265 </TABLE>\r
 266 &nbsp;\r
 267 <P>\r
 268 <HR>\r
 269 \r
 270 \r
 271 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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 280   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 281   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 282   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
 283   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
 284   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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