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7 Uses of Class compbio.metadata.JobSubmissionException
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18 parent.document.title="Uses of Class compbio.metadata.JobSubmissionException";
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84 <B>Uses of Class<br>compbio.metadata.JobSubmissionException</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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90 Packages that use <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>
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94 <TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>
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98 <TD> </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>
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102 <TD> </TD>
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104 <TR BGCOLOR="white" CLASS="TableRowColor">
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105 <TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>
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106 <TD> </TD>
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108 <TR BGCOLOR="white" CLASS="TableRowColor">
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109 <TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>
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110 <TD> </TD>
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112 <TR BGCOLOR="white" CLASS="TableRowColor">
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113 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>
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114 <TD>A meta-data model for multiple sequence alignment web services
115 Classes in this package have no dependencies to other sources in the project. </TD>
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117 <TR BGCOLOR="white" CLASS="TableRowColor">
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118 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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119 <TD>Utilities commonly used by all runners. </TD>
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121 <TR BGCOLOR="white" CLASS="TableRowColor">
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122 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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123 <TD> </TD>
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128 <A NAME="compbio.data.msa"><!-- --></A>
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129 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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130 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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131 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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132 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>
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138 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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139 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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140 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>
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142 <TR BGCOLOR="white" CLASS="TableRowColor">
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143 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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144 <CODE> <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>
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145 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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148 Align a list of sequences with default settings.</TD>
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150 <TR BGCOLOR="white" CLASS="TableRowColor">
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151 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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152 <CODE> <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>
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153 <TD><CODE><B>SequenceAnnotation.</B><B><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#analize(java.util.List)">analize</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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156 Analyse the sequences.</TD>
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158 <TR BGCOLOR="white" CLASS="TableRowColor">
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159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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160 <CODE> <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>
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161 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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162 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>
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165 Align a list of sequences with options.</TD>
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167 <TR BGCOLOR="white" CLASS="TableRowColor">
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168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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169 <CODE> <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>
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170 <TD><CODE><B>SequenceAnnotation.</B><B><A HREF="../../../compbio/data/msa/SequenceAnnotation.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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171 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>>> options)</CODE>
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174 Analyse the sequences according to custom settings defined in options
177 <TR BGCOLOR="white" CLASS="TableRowColor">
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178 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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179 <CODE> <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>
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180 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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181 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)</CODE>
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184 Align a list of sequences with preset.</TD>
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186 <TR BGCOLOR="white" CLASS="TableRowColor">
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187 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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188 <CODE> <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>
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189 <TD><CODE><B>SequenceAnnotation.</B><B><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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190 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>> preset)</CODE>
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193 Analyse the sequences according to the preset settings.</TD>
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198 <A NAME="compbio.engine"><!-- --></A>
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199 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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200 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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201 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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202 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>
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208 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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209 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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210 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>
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212 <TR BGCOLOR="white" CLASS="TableRowColor">
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213 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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215 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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216 <TR ALIGN="right" VALIGN="">
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217 <TD NOWRAP><FONT SIZE="-1">
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218 <CODE><T> <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T></CODE></FONT></TD>
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221 </CODE></FONT></TD>
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222 <TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)">configureExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T> executable)</CODE>
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225 </TD>
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227 <TR BGCOLOR="white" CLASS="TableRowColor">
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228 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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230 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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231 <TR ALIGN="right" VALIGN="">
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232 <TD NOWRAP><FONT SIZE="-1">
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233 <CODE><T> <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T></CODE></FONT></TD>
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236 </CODE></FONT></TD>
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237 <TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)">configureExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T> executable,
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238 <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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241 </TD>
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243 <TR BGCOLOR="white" CLASS="TableRowColor">
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244 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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246 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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247 <TR ALIGN="right" VALIGN="">
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248 <TD NOWRAP><FONT SIZE="-1">
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249 <CODE><T> <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T></CODE></FONT></TD>
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252 </CODE></FONT></TD>
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253 <TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T> executable,
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254 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> dataSet)</CODE>
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257 </TD>
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259 <TR BGCOLOR="white" CLASS="TableRowColor">
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260 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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261 <CODE> void</CODE></FONT></TD>
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262 <TD><CODE><B>SyncExecutor.</B><B><A HREF="../../../compbio/engine/SyncExecutor.html#executeJob()">executeJob</A></B>()</CODE>
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265 Execute the job</TD>
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267 <TR BGCOLOR="white" CLASS="TableRowColor">
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268 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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269 <CODE>static <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>
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270 <TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)">getSyncEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
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273 </TD>
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275 <TR BGCOLOR="white" CLASS="TableRowColor">
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276 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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277 <CODE>static <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>
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278 <TD><CODE><B>Configurator.</B><B><A HREF="../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getSyncEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable,
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279 <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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282 </TD>
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284 <TR BGCOLOR="white" CLASS="TableRowColor">
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285 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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286 <CODE> <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>
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287 <TD><CODE><B>AsyncExecutor.</B><B><A HREF="../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
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290 Submits job for the execution
291 Immediate execution is not guaranteed, this method puts the job in the queue.</TD>
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296 <A NAME="compbio.engine.client"><!-- --></A>
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297 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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298 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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299 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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300 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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306 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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307 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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308 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>
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310 <TR BGCOLOR="white" CLASS="TableRowColor">
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311 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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312 <CODE> <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>
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313 <TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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316 </TD>
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321 <A NAME="compbio.engine.cluster.drmaa"><!-- --></A>
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322 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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323 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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324 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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325 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>
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331 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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332 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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333 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>
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335 <TR BGCOLOR="white" CLASS="TableRowColor">
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336 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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337 <CODE> void</CODE></FONT></TD>
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338 <TD><CODE><B>JobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()">executeJob</A></B>()</CODE>
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341 </TD>
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343 <TR BGCOLOR="white" CLASS="TableRowColor">
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344 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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345 <CODE>static <A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A></CODE></FONT></TD>
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346 <TD><CODE><B>JobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)">getInstance</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
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349 </TD>
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351 <TR BGCOLOR="white" CLASS="TableRowColor">
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352 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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353 <CODE> <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>
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354 <TD><CODE><B>AsyncJobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
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357 </TD>
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363 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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364 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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365 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>
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367 <TR BGCOLOR="white" CLASS="TableRowColor">
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368 <TD><CODE><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner(compbio.engine.client.ConfiguredExecutable)">JobRunner</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> confExec)</CODE>
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371 </TD>
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376 <A NAME="compbio.engine.local"><!-- --></A>
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377 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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378 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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379 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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380 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>
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386 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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387 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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388 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>
\r
390 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
391 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
392 <CODE> void</CODE></FONT></TD>
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393 <TD><CODE><B>LocalRunner.</B><B><A HREF="../../../compbio/engine/local/LocalRunner.html#executeJob()">executeJob</A></B>()</CODE>
\r
396 </TD>
\r
398 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
399 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
400 <CODE> <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
401 <TD><CODE><B>AsyncLocalRunner.</B><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>
\r
404 </TD>
\r
410 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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411 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
412 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>
\r
414 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
415 <TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)">ExecutableWrapper</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable,
\r
416 <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> workDirectory)</CODE>
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419 </TD>
\r
424 <A NAME="compbio.metadata"><!-- --></A>
\r
425 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
426 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
427 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
428 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>
\r
434 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
435 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
436 <TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>
\r
438 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
439 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
440 <CODE> class</CODE></FONT></TD>
\r
441 <TD><CODE><B><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></B></CODE>
\r
444 This exception is thrown if the task larger in size that the limit that
445 applies to the calculation.</TD>
\r
447 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
448 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
449 <CODE> class</CODE></FONT></TD>
\r
450 <TD><CODE><B><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></B></CODE>
\r
453 Indicates that the server could not execute native executables.</TD>
\r
458 <A NAME="compbio.runner"><!-- --></A>
\r
459 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
460 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
461 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
462 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
\r
468 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
469 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
470 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>
\r
472 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
473 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
474 <CODE>static void</CODE></FONT></TD>
\r
475 <TD><CODE><B>Util.</B><B><A HREF="../../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
476 <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)</CODE>
\r
479 </TD>
\r
484 <A NAME="compbio.ws.server"><!-- --></A>
\r
485 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
486 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
487 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
488 Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>
\r
494 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
495 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
496 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>
\r
498 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
499 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
500 <CODE> <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
501 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#align(java.util.List)">align</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
504 </TD>
\r
506 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
507 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
508 <CODE> <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
509 <TD><CODE><B>_MsaService.</B><B><A HREF="../../../compbio/ws/server/_MsaService.html#align(java.util.List)">align</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
512 </TD>
\r
514 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
515 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
516 <CODE> <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
517 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#align(java.util.List)">align</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
520 </TD>
\r
522 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
523 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
524 <CODE> <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
525 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#align(java.util.List)">align</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
528 </TD>
\r
530 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
531 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
532 <CODE> <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
533 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#align(java.util.List)">align</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
536 </TD>
\r
538 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
539 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
540 <CODE> <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
541 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#align(java.util.List)">align</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
544 </TD>
\r
546 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
547 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
548 <CODE> <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
549 <TD><CODE><B>ClustalOWS.</B><B><A HREF="../../../compbio/ws/server/ClustalOWS.html#align(java.util.List)">align</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
552 </TD>
\r
554 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
555 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
557 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
\r
558 <TR ALIGN="right" VALIGN="">
\r
559 <TD NOWRAP><FONT SIZE="-1">
\r
560 <CODE><T> <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
563 </CODE></FONT></TD>
\r
564 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)">align</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
565 <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T> confExec,
\r
566 org.apache.log4j.Logger logger,
\r
567 <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> callingMethod,
\r
568 <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><T> limit)</CODE>
\r
571 </TD>
\r
573 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
574 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
575 <CODE> <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
576 <TD><CODE><B>AAConWS.</B><B><A HREF="../../../compbio/ws/server/AAConWS.html#analize(java.util.List)">analize</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
579 </TD>
\r
581 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
582 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
583 <CODE> <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
584 <TD><CODE><B>SequenceAnnotationService.</B><B><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#analize(java.util.List)">analize</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
587 </TD>
\r
589 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
590 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
592 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
\r
593 <TR ALIGN="right" VALIGN="">
\r
594 <TD NOWRAP><FONT SIZE="-1">
\r
595 <CODE><T> <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
598 </CODE></FONT></TD>
\r
599 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#analize(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)">analize</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
600 <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T> confExec,
\r
601 org.apache.log4j.Logger log,
\r
602 <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> method,
\r
603 <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><T> limit)</CODE>
\r
606 </TD>
\r
608 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
609 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
610 <CODE> <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
611 <TD><CODE><B>ClustalOWS.</B><B><A HREF="../../../compbio/ws/server/ClustalOWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
612 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>>> options)</CODE>
\r
615 </TD>
\r
617 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
618 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
619 <CODE> <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
620 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
621 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>>> options)</CODE>
\r
624 </TD>
\r
626 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
627 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
628 <CODE> <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
629 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
630 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>>> options)</CODE>
\r
633 </TD>
\r
635 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
636 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
637 <CODE> <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
638 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
639 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>>> options)</CODE>
\r
642 </TD>
\r
644 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
645 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
646 <CODE> <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
647 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
648 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>>> options)</CODE>
\r
651 </TD>
\r
653 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
654 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
655 <CODE> <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
656 <TD><CODE><B>_MsaService.</B><B><A HREF="../../../compbio/ws/server/_MsaService.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
657 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>>> options)</CODE>
\r
660 </TD>
\r
662 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
663 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
664 <CODE> <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
665 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
666 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>>> options)</CODE>
\r
669 </TD>
\r
671 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
672 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
673 <CODE> <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
674 <TD><CODE><B>DisemblWS.</B><B><A HREF="../../../compbio/ws/server/DisemblWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
675 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>>> options)</CODE>
\r
678 </TD>
\r
680 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
681 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
682 <CODE> <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
683 <TD><CODE><B>GlobPlotWS.</B><B><A HREF="../../../compbio/ws/server/GlobPlotWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
684 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>>> options)</CODE>
\r
687 </TD>
\r
689 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
690 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
691 <CODE> <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
692 <TD><CODE><B>SequenceAnnotationService.</B><B><A HREF="../../../compbio/ws/server/SequenceAnnotationService.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
693 <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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>>> options)</CODE>
\r
696 </TD>
\r
698 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
699 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
700 <CODE> <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
701 <TD><CODE><B>ClustalOWS.</B><B><A HREF="../../../compbio/ws/server/ClustalOWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
702 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>> preset)</CODE>
\r
705 </TD>
\r
707 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
708 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
709 <CODE> <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
710 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
711 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> preset)</CODE>
\r
714 </TD>
\r
716 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
717 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
718 <CODE> <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
719 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
720 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>> preset)</CODE>
\r
723 </TD>
\r
725 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
726 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
727 <CODE> <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
728 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
729 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>> preset)</CODE>
\r
732 </TD>
\r
734 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
735 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
736 <CODE> <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
737 <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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
738 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>> preset)</CODE>
\r
741 </TD>
\r
743 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
744 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
745 <CODE> <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
746 <TD><CODE><B>_MsaService.</B><B><A HREF="../../../compbio/ws/server/_MsaService.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
747 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>> preset)</CODE>
\r
750 </TD>
\r
752 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
753 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
754 <CODE> <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
755 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
756 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>> preset)</CODE>
\r
759 </TD>
\r
761 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
762 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
763 <CODE> <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
764 <TD><CODE><B>DisemblWS.</B><B><A HREF="../../../compbio/ws/server/DisemblWS.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
765 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>> preset)</CODE>
\r
768 </TD>
\r
770 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
771 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
772 <CODE> <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
773 <TD><CODE><B>GlobPlotWS.</B><B><A HREF="../../../compbio/ws/server/GlobPlotWS.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
774 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>> preset)</CODE>
\r
777 </TD>
\r
779 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
780 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
781 <CODE> <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
782 <TD><CODE><B>IUPredWS.</B><B><A HREF="../../../compbio/ws/server/IUPredWS.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
783 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>> preset)</CODE>
\r
786 </TD>
\r
788 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
789 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
790 <CODE> <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
791 <TD><CODE><B>SequenceAnnotationService.</B><B><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
792 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>> preset)</CODE>
\r
795 </TD>
\r
797 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
798 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
799 <CODE>static void</CODE></FONT></TD>
\r
800 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateAAConInput(java.util.List)">validateAAConInput</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
803 </TD>
\r
805 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
806 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
807 <CODE>static void</CODE></FONT></TD>
\r
808 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateFastaInput(java.util.List)">validateFastaInput</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
811 </TD>
\r
819 <!-- ======= START OF BOTTOM NAVBAR ====== -->
\r
820 <A NAME="navbar_bottom"><!-- --></A>
\r
821 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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822 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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824 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
\r
825 <A NAME="navbar_bottom_firstrow"><!-- --></A>
\r
826 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
\r
827 <TR ALIGN="center" VALIGN="top">
\r
828 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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829 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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830 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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831 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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832 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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833 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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839 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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845 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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847 NEXT</FONT></TD>
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848 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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849 <A HREF="../../../index.html?compbio/metadata/\class-useJobSubmissionException.html" target="_top"><B>FRAMES</B></A>
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850 <A HREF="JobSubmissionException.html" target="_top"><B>NO FRAMES</B></A>
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851 <SCRIPT type="text/javascript">
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854 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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859 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
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866 <A NAME="skip-navbar_bottom"></A>
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867 <!-- ======== END OF BOTTOM NAVBAR ======= -->
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