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7 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> </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>Classes and interfaces representing an input for engines. </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>An cluster engine classes responsible for execution of Executables on the clusters. </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>An local engine classes responsible for execution of Executables on the local computer
111 (the same machine as JVM running these classes). </TD>
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113 <TR BGCOLOR="white" CLASS="TableRowColor">
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114 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>
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115 <TD>A meta-data model for multiple sequence alignment web services
116 Classes in this package have no dependencies to other sources in the project. </TD>
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118 <TR BGCOLOR="white" CLASS="TableRowColor">
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119 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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120 <TD> </TD>
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125 <A NAME="compbio.data.msa"><!-- --></A>
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126 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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127 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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128 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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129 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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135 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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136 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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137 <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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139 <TR BGCOLOR="white" CLASS="TableRowColor">
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140 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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141 <CODE> java.lang.String</CODE></FONT></TD>
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142 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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145 Align a list of sequences with default settings.</TD>
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147 <TR BGCOLOR="white" CLASS="TableRowColor">
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148 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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149 <CODE> java.lang.String</CODE></FONT></TD>
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150 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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151 java.util.List<<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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154 Align a list of sequences with options.</TD>
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156 <TR BGCOLOR="white" CLASS="TableRowColor">
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157 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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158 <CODE> java.lang.String</CODE></FONT></TD>
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159 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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160 <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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163 Align a list of sequences with preset.</TD>
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168 <A NAME="compbio.engine"><!-- --></A>
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169 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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170 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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171 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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172 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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178 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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179 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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180 <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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182 <TR BGCOLOR="white" CLASS="TableRowColor">
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183 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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185 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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186 <TR ALIGN="right" VALIGN="">
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187 <TD NOWRAP><FONT SIZE="-1">
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188 <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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191 </CODE></FONT></TD>
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192 <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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195 </TD>
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197 <TR BGCOLOR="white" CLASS="TableRowColor">
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198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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200 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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201 <TR ALIGN="right" VALIGN="">
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202 <TD NOWRAP><FONT SIZE="-1">
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203 <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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206 </CODE></FONT></TD>
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207 <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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208 <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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211 </TD>
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213 <TR BGCOLOR="white" CLASS="TableRowColor">
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214 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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216 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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217 <TR ALIGN="right" VALIGN="">
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218 <TD NOWRAP><FONT SIZE="-1">
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219 <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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222 </CODE></FONT></TD>
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223 <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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224 java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> dataSet)</CODE>
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227 </TD>
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229 <TR BGCOLOR="white" CLASS="TableRowColor">
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230 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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231 <CODE> void</CODE></FONT></TD>
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232 <TD><CODE><B>SyncExecutor.</B><B><A HREF="../../../compbio/engine/SyncExecutor.html#executeJob()">executeJob</A></B>()</CODE>
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235 Execute the job</TD>
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237 <TR BGCOLOR="white" CLASS="TableRowColor">
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238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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239 <CODE>static <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>
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240 <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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243 </TD>
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245 <TR BGCOLOR="white" CLASS="TableRowColor">
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246 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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247 <CODE>static <A HREF="../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>
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248 <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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249 <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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252 </TD>
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254 <TR BGCOLOR="white" CLASS="TableRowColor">
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255 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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256 <CODE> java.lang.String</CODE></FONT></TD>
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257 <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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260 Submits job for the execution
261 Immediate execution is not guaranteed, this method puts the job in the queue.</TD>
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266 <A NAME="compbio.engine.client"><!-- --></A>
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267 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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268 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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269 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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270 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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276 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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277 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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278 <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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280 <TR BGCOLOR="white" CLASS="TableRowColor">
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281 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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282 <CODE> java.lang.String</CODE></FONT></TD>
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283 <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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286 </TD>
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291 <A NAME="compbio.engine.cluster.drmaa"><!-- --></A>
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292 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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293 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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294 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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295 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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301 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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302 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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303 <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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305 <TR BGCOLOR="white" CLASS="TableRowColor">
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306 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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307 <CODE> void</CODE></FONT></TD>
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308 <TD><CODE><B>JobRunner.</B><B><A HREF="../../../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()">executeJob</A></B>()</CODE>
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311 </TD>
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313 <TR BGCOLOR="white" CLASS="TableRowColor">
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314 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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315 <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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316 <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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319 </TD>
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321 <TR BGCOLOR="white" CLASS="TableRowColor">
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322 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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323 <CODE> java.lang.String</CODE></FONT></TD>
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324 <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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327 </TD>
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333 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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334 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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335 <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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337 <TR BGCOLOR="white" CLASS="TableRowColor">
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338 <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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341 </TD>
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346 <A NAME="compbio.engine.local"><!-- --></A>
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347 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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348 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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349 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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350 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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356 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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357 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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358 <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>
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360 <TR BGCOLOR="white" CLASS="TableRowColor">
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361 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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362 <CODE> void</CODE></FONT></TD>
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363 <TD><CODE><B>LocalRunner.</B><B><A HREF="../../../compbio/engine/local/LocalRunner.html#executeJob()">executeJob</A></B>()</CODE>
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366 </TD>
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368 <TR BGCOLOR="white" CLASS="TableRowColor">
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369 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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370 <CODE> java.lang.String</CODE></FONT></TD>
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371 <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>
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374 </TD>
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380 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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381 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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382 <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>
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384 <TR BGCOLOR="white" CLASS="TableRowColor">
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385 <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,
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386 java.lang.String workDirectory)</CODE>
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389 </TD>
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394 <A NAME="compbio.metadata"><!-- --></A>
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395 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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396 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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397 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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398 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>
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404 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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405 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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406 <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>
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408 <TR BGCOLOR="white" CLASS="TableRowColor">
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409 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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410 <CODE> class</CODE></FONT></TD>
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411 <TD><CODE><B><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></B></CODE>
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414 Thrown if the task larger in size that the limit that applies to the
417 <TR BGCOLOR="white" CLASS="TableRowColor">
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418 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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419 <CODE> class</CODE></FONT></TD>
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420 <TD><CODE><B><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></B></CODE>
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423 Indicates that the server could not execute native executables.</TD>
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428 <A NAME="compbio.ws.server"><!-- --></A>
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429 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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430 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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431 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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432 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>
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438 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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439 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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440 <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>
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442 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
443 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
444 <CODE> java.lang.String</CODE></FONT></TD>
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445 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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448 </TD>
\r
450 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
451 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
452 <CODE> java.lang.String</CODE></FONT></TD>
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453 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
456 </TD>
\r
458 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
459 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
460 <CODE> java.lang.String</CODE></FONT></TD>
\r
461 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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464 </TD>
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466 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
467 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
468 <CODE> java.lang.String</CODE></FONT></TD>
\r
469 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
472 </TD>
\r
474 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
475 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
476 <CODE> java.lang.String</CODE></FONT></TD>
\r
477 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
480 </TD>
\r
482 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
483 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
485 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
\r
486 <TR ALIGN="right" VALIGN="">
\r
487 <TD NOWRAP><FONT SIZE="-1">
\r
488 <CODE><T> java.lang.String</CODE></FONT></TD>
\r
491 </CODE></FONT></TD>
\r
492 <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, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)">align</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
493 <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T> confExec,
\r
494 org.apache.log4j.Logger statLog,
\r
495 javax.xml.ws.WebServiceContext wsContext,
\r
496 java.lang.String callingMethod,
\r
497 <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><T> limit)</CODE>
\r
500 </TD>
\r
502 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
503 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
504 <CODE> java.lang.String</CODE></FONT></TD>
\r
505 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
506 java.util.List<<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
509 </TD>
\r
511 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
512 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
513 <CODE> java.lang.String</CODE></FONT></TD>
\r
514 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
515 java.util.List<<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
518 </TD>
\r
520 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
521 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
522 <CODE> java.lang.String</CODE></FONT></TD>
\r
523 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
524 java.util.List<<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
527 </TD>
\r
529 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
530 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
531 <CODE> java.lang.String</CODE></FONT></TD>
\r
532 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
533 java.util.List<<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
536 </TD>
\r
538 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
539 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
540 <CODE> java.lang.String</CODE></FONT></TD>
\r
541 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
542 java.util.List<<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
545 </TD>
\r
547 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
548 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
549 <CODE> java.lang.String</CODE></FONT></TD>
\r
550 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
551 <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
554 </TD>
\r
556 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
557 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
558 <CODE> java.lang.String</CODE></FONT></TD>
\r
559 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
560 <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
563 </TD>
\r
565 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
566 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
567 <CODE> java.lang.String</CODE></FONT></TD>
\r
568 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
569 <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
572 </TD>
\r
574 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
575 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
576 <CODE> java.lang.String</CODE></FONT></TD>
\r
577 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
578 <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
581 </TD>
\r
583 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
584 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
585 <CODE> java.lang.String</CODE></FONT></TD>
\r
586 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
587 <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
590 </TD>
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598 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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599 <A NAME="navbar_bottom"><!-- --></A>
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600 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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604 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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606 <TR ALIGN="center" VALIGN="top">
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607 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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