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7 Uses of Package compbio.metadata
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18 parent.document.title="Uses of Package compbio.metadata";
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84 <B>Uses of Package<br>compbio.metadata</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/package-summary.html">compbio.metadata</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.data.msa.jaxws"><B>compbio.data.msa.jaxws</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"><B>compbio.engine</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.client"><B>compbio.engine.client</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.cluster.drmaa"><B>compbio.engine.cluster.drmaa</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.engine.local"><B>compbio.engine.local</B></A></TD>
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114 <TD> </TD>
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116 <TR BGCOLOR="white" CLASS="TableRowColor">
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117 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>
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118 <TD>A meta-data model for multiple sequence alignment web services
119 Classes in this package have no dependencies to other sources in the project. </TD>
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121 <TR BGCOLOR="white" CLASS="TableRowColor">
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122 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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123 <TD>Utilities commonly used by all runners. </TD>
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125 <TR BGCOLOR="white" CLASS="TableRowColor">
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126 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>
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127 <TD> </TD>
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129 <TR BGCOLOR="white" CLASS="TableRowColor">
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130 <TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>
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131 <TD> </TD>
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133 <TR BGCOLOR="white" CLASS="TableRowColor">
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134 <TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>
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135 <TD> </TD>
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137 <TR BGCOLOR="white" CLASS="TableRowColor">
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138 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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139 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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141 <TR BGCOLOR="white" CLASS="TableRowColor">
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142 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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143 <TD> </TD>
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148 <A NAME="compbio.data.msa"><!-- --></A>
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149 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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150 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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151 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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152 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>
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154 <TR BGCOLOR="white" CLASS="TableRowColor">
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155 <TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa"><B>ChunkHolder</B></A></B>
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158 Represents a chunk of a string data together with the position in a file for
159 the next read operation.</TD>
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161 <TR BGCOLOR="white" CLASS="TableRowColor">
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162 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa"><B>JobStatus</B></A></B>
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165 The status of the job.</TD>
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167 <TR BGCOLOR="white" CLASS="TableRowColor">
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168 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.data.msa"><B>JobSubmissionException</B></A></B>
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171 Exception for generic problems with JobSubmission it is often thrown as a
172 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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174 <TR BGCOLOR="white" CLASS="TableRowColor">
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175 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.data.msa"><B>Limit</B></A></B>
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178 A value object containing a maximum number of sequences and a maximum average
179 sequence length for a preset.</TD>
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181 <TR BGCOLOR="white" CLASS="TableRowColor">
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182 <TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.data.msa"><B>LimitExceededException</B></A></B>
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185 This exception is thrown if the task larger in size that the limit that
186 applies to the calculation.</TD>
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188 <TR BGCOLOR="white" CLASS="TableRowColor">
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189 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.data.msa"><B>LimitsManager</B></A></B>
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192 A collection of Limits</TD>
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194 <TR BGCOLOR="white" CLASS="TableRowColor">
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195 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.data.msa"><B>Option</B></A></B>
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198 Command line option/flag or multiple exclusive options with no value.</TD>
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200 <TR BGCOLOR="white" CLASS="TableRowColor">
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201 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa"><B>Preset</B></A></B>
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204 Collection of Options and Parameters with their values</TD>
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206 <TR BGCOLOR="white" CLASS="TableRowColor">
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207 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa"><B>PresetManager</B></A></B>
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210 Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>
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212 <TR BGCOLOR="white" CLASS="TableRowColor">
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213 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.data.msa"><B>ResultNotAvailableException</B></A></B>
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216 ResultNotAvailableException is thrown wherever the results of the calculation
217 cannot be obtained.</TD>
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219 <TR BGCOLOR="white" CLASS="TableRowColor">
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220 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.data.msa"><B>RunnerConfig</B></A></B>
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223 The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>
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225 <TR BGCOLOR="white" CLASS="TableRowColor">
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226 <TD><B><A HREF="../../compbio/metadata/class-use/UnsupportedRuntimeException.html#compbio.data.msa"><B>UnsupportedRuntimeException</B></A></B>
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229 Indicates that the server could not execute native executables.</TD>
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231 <TR BGCOLOR="white" CLASS="TableRowColor">
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232 <TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.data.msa"><B>WrongParameterException</B></A></B>
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235 WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
236 does not match the actual runnable or then attempting to set the value of
237 <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>
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242 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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243 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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244 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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245 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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246 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>
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248 <TR BGCOLOR="white" CLASS="TableRowColor">
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249 <TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa.jaxws"><B>ChunkHolder</B></A></B>
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252 Represents a chunk of a string data together with the position in a file for
253 the next read operation.</TD>
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255 <TR BGCOLOR="white" CLASS="TableRowColor">
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256 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa.jaxws"><B>JobStatus</B></A></B>
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259 The status of the job.</TD>
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261 <TR BGCOLOR="white" CLASS="TableRowColor">
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262 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.data.msa.jaxws"><B>Limit</B></A></B>
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265 A value object containing a maximum number of sequences and a maximum average
266 sequence length for a preset.</TD>
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268 <TR BGCOLOR="white" CLASS="TableRowColor">
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269 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.data.msa.jaxws"><B>LimitsManager</B></A></B>
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272 A collection of Limits</TD>
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274 <TR BGCOLOR="white" CLASS="TableRowColor">
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275 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.data.msa.jaxws"><B>Option</B></A></B>
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278 Command line option/flag or multiple exclusive options with no value.</TD>
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280 <TR BGCOLOR="white" CLASS="TableRowColor">
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281 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa.jaxws"><B>Preset</B></A></B>
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284 Collection of Options and Parameters with their values</TD>
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286 <TR BGCOLOR="white" CLASS="TableRowColor">
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287 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa.jaxws"><B>PresetManager</B></A></B>
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290 Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>
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292 <TR BGCOLOR="white" CLASS="TableRowColor">
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293 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.data.msa.jaxws"><B>RunnerConfig</B></A></B>
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296 The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>
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301 <A NAME="compbio.engine"><!-- --></A>
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302 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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303 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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304 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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305 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>
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307 <TR BGCOLOR="white" CLASS="TableRowColor">
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308 <TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.engine"><B>ChunkHolder</B></A></B>
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311 Represents a chunk of a string data together with the position in a file for
312 the next read operation.</TD>
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314 <TR BGCOLOR="white" CLASS="TableRowColor">
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315 <TD><B><A HREF="../../compbio/metadata/class-use/JobExecutionException.html#compbio.engine"><B>JobExecutionException</B></A></B>
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318 JobExecutionException is thrown wherever the results of the calculation
319 cannot be obtained.</TD>
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321 <TR BGCOLOR="white" CLASS="TableRowColor">
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322 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine"><B>JobStatus</B></A></B>
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325 The status of the job.</TD>
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327 <TR BGCOLOR="white" CLASS="TableRowColor">
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328 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine"><B>JobSubmissionException</B></A></B>
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331 Exception for generic problems with JobSubmission it is often thrown as a
332 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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334 <TR BGCOLOR="white" CLASS="TableRowColor">
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335 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine"><B>ResultNotAvailableException</B></A></B>
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338 ResultNotAvailableException is thrown wherever the results of the calculation
339 cannot be obtained.</TD>
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344 <A NAME="compbio.engine.client"><!-- --></A>
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345 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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346 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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347 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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348 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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350 <TR BGCOLOR="white" CLASS="TableRowColor">
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351 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine.client"><B>JobStatus</B></A></B>
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354 The status of the job.</TD>
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356 <TR BGCOLOR="white" CLASS="TableRowColor">
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357 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine.client"><B>JobSubmissionException</B></A></B>
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360 Exception for generic problems with JobSubmission it is often thrown as a
361 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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363 <TR BGCOLOR="white" CLASS="TableRowColor">
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364 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.engine.client"><B>Limit</B></A></B>
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367 A value object containing a maximum number of sequences and a maximum average
368 sequence length for a preset.</TD>
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370 <TR BGCOLOR="white" CLASS="TableRowColor">
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371 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.engine.client"><B>LimitsManager</B></A></B>
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374 A collection of Limits</TD>
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376 <TR BGCOLOR="white" CLASS="TableRowColor">
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377 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.engine.client"><B>Option</B></A></B>
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380 Command line option/flag or multiple exclusive options with no value.</TD>
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382 <TR BGCOLOR="white" CLASS="TableRowColor">
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383 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.engine.client"><B>PresetManager</B></A></B>
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386 Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>
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388 <TR BGCOLOR="white" CLASS="TableRowColor">
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389 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine.client"><B>ResultNotAvailableException</B></A></B>
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392 ResultNotAvailableException is thrown wherever the results of the calculation
393 cannot be obtained.</TD>
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395 <TR BGCOLOR="white" CLASS="TableRowColor">
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396 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.engine.client"><B>RunnerConfig</B></A></B>
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399 The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>
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401 <TR BGCOLOR="white" CLASS="TableRowColor">
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402 <TD><B><A HREF="../../compbio/metadata/class-use/UnsupportedRuntimeException.html#compbio.engine.client"><B>UnsupportedRuntimeException</B></A></B>
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405 Indicates that the server could not execute native executables.</TD>
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410 <A NAME="compbio.engine.cluster.drmaa"><!-- --></A>
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411 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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412 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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413 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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414 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>
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416 <TR BGCOLOR="white" CLASS="TableRowColor">
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417 <TD><B><A HREF="../../compbio/metadata/class-use/JobExecutionException.html#compbio.engine.cluster.drmaa"><B>JobExecutionException</B></A></B>
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420 JobExecutionException is thrown wherever the results of the calculation
421 cannot be obtained.</TD>
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423 <TR BGCOLOR="white" CLASS="TableRowColor">
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424 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine.cluster.drmaa"><B>JobStatus</B></A></B>
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427 The status of the job.</TD>
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429 <TR BGCOLOR="white" CLASS="TableRowColor">
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430 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine.cluster.drmaa"><B>JobSubmissionException</B></A></B>
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433 Exception for generic problems with JobSubmission it is often thrown as a
434 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
\r
436 <TR BGCOLOR="white" CLASS="TableRowColor">
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437 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine.cluster.drmaa"><B>ResultNotAvailableException</B></A></B>
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440 ResultNotAvailableException is thrown wherever the results of the calculation
441 cannot be obtained.</TD>
\r
446 <A NAME="compbio.engine.local"><!-- --></A>
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447 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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448 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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449 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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450 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>
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452 <TR BGCOLOR="white" CLASS="TableRowColor">
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453 <TD><B><A HREF="../../compbio/metadata/class-use/JobExecutionException.html#compbio.engine.local"><B>JobExecutionException</B></A></B>
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456 JobExecutionException is thrown wherever the results of the calculation
457 cannot be obtained.</TD>
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459 <TR BGCOLOR="white" CLASS="TableRowColor">
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460 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine.local"><B>JobStatus</B></A></B>
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463 The status of the job.</TD>
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465 <TR BGCOLOR="white" CLASS="TableRowColor">
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466 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine.local"><B>JobSubmissionException</B></A></B>
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469 Exception for generic problems with JobSubmission it is often thrown as a
470 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
\r
472 <TR BGCOLOR="white" CLASS="TableRowColor">
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473 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine.local"><B>ResultNotAvailableException</B></A></B>
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476 ResultNotAvailableException is thrown wherever the results of the calculation
477 cannot be obtained.</TD>
\r
482 <A NAME="compbio.metadata"><!-- --></A>
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483 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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484 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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485 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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486 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>
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488 <TR BGCOLOR="white" CLASS="TableRowColor">
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489 <TD><B><A HREF="../../compbio/metadata/class-use/Argument.html#compbio.metadata"><B>Argument</B></A></B>
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492 An unmodifiable view for the options and parameters, with one exception - it
493 allows to set a value</TD>
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495 <TR BGCOLOR="white" CLASS="TableRowColor">
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496 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.metadata"><B>JobStatus</B></A></B>
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499 The status of the job.</TD>
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501 <TR BGCOLOR="white" CLASS="TableRowColor">
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502 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.metadata"><B>JobSubmissionException</B></A></B>
\r
505 Exception for generic problems with JobSubmission it is often thrown as a
506 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
\r
508 <TR BGCOLOR="white" CLASS="TableRowColor">
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509 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.metadata"><B>Limit</B></A></B>
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512 A value object containing a maximum number of sequences and a maximum average
513 sequence length for a preset.</TD>
\r
515 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
516 <TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.metadata"><B>LimitExceededException</B></A></B>
\r
519 This exception is thrown if the task larger in size that the limit that
520 applies to the calculation.</TD>
\r
522 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
523 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.metadata"><B>Option</B></A></B>
\r
526 Command line option/flag or multiple exclusive options with no value.</TD>
\r
528 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
529 <TD><B><A HREF="../../compbio/metadata/class-use/Parameter.html#compbio.metadata"><B>Parameter</B></A></B>
\r
532 A single value containing an option supported by the web service e.g.</TD>
\r
534 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
535 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.metadata"><B>Preset</B></A></B>
\r
538 Collection of Options and Parameters with their values</TD>
\r
540 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
541 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.metadata"><B>PresetManager</B></A></B>
\r
544 Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>
\r
546 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
547 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.metadata"><B>RunnerConfig</B></A></B>
\r
550 The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>
\r
552 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
553 <TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.html#compbio.metadata"><B>ValueConstrain</B></A></B>
\r
556 The type and the lower and upper boundaries for numerical value.</TD>
\r
558 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
559 <TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.Type.html#compbio.metadata"><B>ValueConstrain.Type</B></A></B>
\r
562 </TD>
\r
564 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
565 <TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.metadata"><B>WrongParameterException</B></A></B>
\r
568 WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
569 does not match the actual runnable or then attempting to set the value of
570 <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>
\r
575 <A NAME="compbio.runner"><!-- --></A>
\r
576 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
577 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
578 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
579 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
\r
581 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
582 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.runner"><B>JobSubmissionException</B></A></B>
\r
585 Exception for generic problems with JobSubmission it is often thrown as a
586 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
\r
588 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
589 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner"><B>Limit</B></A></B>
\r
592 A value object containing a maximum number of sequences and a maximum average
593 sequence length for a preset.</TD>
\r
595 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
596 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner"><B>LimitsManager</B></A></B>
\r
599 A collection of Limits</TD>
\r
601 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
602 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.runner"><B>Option</B></A></B>
\r
605 Command line option/flag or multiple exclusive options with no value.</TD>
\r
607 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
608 <TD><B><A HREF="../../compbio/metadata/class-use/Parameter.html#compbio.runner"><B>Parameter</B></A></B>
\r
611 A single value containing an option supported by the web service e.g.</TD>
\r
613 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
614 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.runner"><B>PresetManager</B></A></B>
\r
617 Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>
\r
619 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
620 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.runner"><B>RunnerConfig</B></A></B>
\r
623 The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>
\r
628 <A NAME="compbio.runner._impl"><!-- --></A>
\r
629 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
630 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
631 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
632 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>
\r
634 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
635 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner._impl"><B>Limit</B></A></B>
\r
638 A value object containing a maximum number of sequences and a maximum average
639 sequence length for a preset.</TD>
\r
641 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
642 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner._impl"><B>LimitsManager</B></A></B>
\r
645 A collection of Limits</TD>
\r
650 <A NAME="compbio.runner.conservation"><!-- --></A>
\r
651 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
652 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
653 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
654 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></FONT></TH>
\r
656 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
657 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.conservation"><B>ResultNotAvailableException</B></A></B>
\r
660 ResultNotAvailableException is thrown wherever the results of the calculation
661 cannot be obtained.</TD>
\r
666 <A NAME="compbio.runner.disorder"><!-- --></A>
\r
667 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
668 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
669 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
670 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>
\r
672 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
673 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.disorder"><B>ResultNotAvailableException</B></A></B>
\r
676 ResultNotAvailableException is thrown wherever the results of the calculation
677 cannot be obtained.</TD>
\r
682 <A NAME="compbio.runner.msa"><!-- --></A>
\r
683 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
684 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
685 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
686 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>
\r
688 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
689 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.msa"><B>ResultNotAvailableException</B></A></B>
\r
692 ResultNotAvailableException is thrown wherever the results of the calculation
693 cannot be obtained.</TD>
\r
698 <A NAME="compbio.ws.server"><!-- --></A>
\r
699 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
700 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
701 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
702 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>
\r
704 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
705 <TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.ws.server"><B>ChunkHolder</B></A></B>
\r
708 Represents a chunk of a string data together with the position in a file for
709 the next read operation.</TD>
\r
711 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
712 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.ws.server"><B>JobStatus</B></A></B>
\r
715 The status of the job.</TD>
\r
717 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
718 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.ws.server"><B>JobSubmissionException</B></A></B>
\r
721 Exception for generic problems with JobSubmission it is often thrown as a
722 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
\r
724 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
725 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.ws.server"><B>Limit</B></A></B>
\r
728 A value object containing a maximum number of sequences and a maximum average
729 sequence length for a preset.</TD>
\r
731 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
732 <TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.ws.server"><B>LimitExceededException</B></A></B>
\r
735 This exception is thrown if the task larger in size that the limit that
736 applies to the calculation.</TD>
\r
738 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
739 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.ws.server"><B>LimitsManager</B></A></B>
\r
742 A collection of Limits</TD>
\r
744 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
745 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.ws.server"><B>Option</B></A></B>
\r
748 Command line option/flag or multiple exclusive options with no value.</TD>
\r
750 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
751 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.ws.server"><B>Preset</B></A></B>
\r
754 Collection of Options and Parameters with their values</TD>
\r
756 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
757 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.ws.server"><B>PresetManager</B></A></B>
\r
760 Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>
\r
762 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
763 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.ws.server"><B>ResultNotAvailableException</B></A></B>
\r
766 ResultNotAvailableException is thrown wherever the results of the calculation
767 cannot be obtained.</TD>
\r
769 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
770 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.ws.server"><B>RunnerConfig</B></A></B>
\r
773 The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>
\r
775 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
776 <TD><B><A HREF="../../compbio/metadata/class-use/UnsupportedRuntimeException.html#compbio.ws.server"><B>UnsupportedRuntimeException</B></A></B>
\r
779 Indicates that the server could not execute native executables.</TD>
\r
781 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
782 <TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.ws.server"><B>WrongParameterException</B></A></B>
\r
785 WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
786 does not match the actual runnable or then attempting to set the value of
787 <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>
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