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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> </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>Classes and interfaces representing an input for engines. </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>An cluster engine classes responsible for execution of Executables on the clusters. </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>An local engine classes responsible for execution of Executables on the local computer
115 (the same machine as JVM running these classes). </TD>
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117 <TR BGCOLOR="white" CLASS="TableRowColor">
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118 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>
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119 <TD>A meta-data model for multiple sequence alignment web services
120 Classes in this package have no dependencies to other sources in the project. </TD>
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122 <TR BGCOLOR="white" CLASS="TableRowColor">
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123 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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124 <TD>Utilities commonly used by all runners. </TD>
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126 <TR BGCOLOR="white" CLASS="TableRowColor">
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127 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>
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128 <TD> </TD>
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130 <TR BGCOLOR="white" CLASS="TableRowColor">
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131 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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132 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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134 <TR BGCOLOR="white" CLASS="TableRowColor">
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135 <TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>
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136 <TD> </TD>
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138 <TR BGCOLOR="white" CLASS="TableRowColor">
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139 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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140 <TD> </TD>
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145 <A NAME="compbio.data.msa"><!-- --></A>
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146 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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147 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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148 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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149 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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151 <TR BGCOLOR="white" CLASS="TableRowColor">
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152 <TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa"><B>ChunkHolder</B></A></B>
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155 Represents a chunk of string data together with the position in a file from
156 where corresponding to of the data.</TD>
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158 <TR BGCOLOR="white" CLASS="TableRowColor">
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159 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa"><B>JobStatus</B></A></B>
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162 The status of the job.</TD>
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164 <TR BGCOLOR="white" CLASS="TableRowColor">
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165 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.data.msa"><B>JobSubmissionException</B></A></B>
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168 Exception for generic problems with JobSubmission it is often thrown as a
169 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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171 <TR BGCOLOR="white" CLASS="TableRowColor">
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172 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.data.msa"><B>Limit</B></A></B>
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175 A value object containing a maximum number of sequences and a maximum average
176 sequence length for a preset.</TD>
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178 <TR BGCOLOR="white" CLASS="TableRowColor">
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179 <TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.data.msa"><B>LimitExceededException</B></A></B>
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182 Thrown if the task larger in size that the limit that applies to the
185 <TR BGCOLOR="white" CLASS="TableRowColor">
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186 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.data.msa"><B>LimitsManager</B></A></B>
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189 A collection of Limits</TD>
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191 <TR BGCOLOR="white" CLASS="TableRowColor">
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192 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.data.msa"><B>Option</B></A></B>
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195 Command line option/flag or multiple exclusive options with no value.</TD>
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197 <TR BGCOLOR="white" CLASS="TableRowColor">
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198 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa"><B>Preset</B></A></B>
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201 Collection of Options and Parameters with their values</TD>
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203 <TR BGCOLOR="white" CLASS="TableRowColor">
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204 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa"><B>PresetManager</B></A></B>
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207 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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209 <TR BGCOLOR="white" CLASS="TableRowColor">
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210 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.data.msa"><B>ResultNotAvailableException</B></A></B>
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213 ResultNotAvailableException is thrown wherever the results of the calculation
214 cannot be obtained.</TD>
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216 <TR BGCOLOR="white" CLASS="TableRowColor">
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217 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.data.msa"><B>RunnerConfig</B></A></B>
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220 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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222 <TR BGCOLOR="white" CLASS="TableRowColor">
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223 <TD><B><A HREF="../../compbio/metadata/class-use/UnsupportedRuntimeException.html#compbio.data.msa"><B>UnsupportedRuntimeException</B></A></B>
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226 Indicates that the server could not execute native executables.</TD>
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228 <TR BGCOLOR="white" CLASS="TableRowColor">
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229 <TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.data.msa"><B>WrongParameterException</B></A></B>
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232 WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
233 does not match the actual runnable or then attempting to set the value of
234 <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>
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239 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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240 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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241 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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242 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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243 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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245 <TR BGCOLOR="white" CLASS="TableRowColor">
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246 <TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa.jaxws"><B>ChunkHolder</B></A></B>
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249 Represents a chunk of string data together with the position in a file from
250 where corresponding to of the data.</TD>
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252 <TR BGCOLOR="white" CLASS="TableRowColor">
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253 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa.jaxws"><B>JobStatus</B></A></B>
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256 The status of the job.</TD>
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258 <TR BGCOLOR="white" CLASS="TableRowColor">
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259 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.data.msa.jaxws"><B>Limit</B></A></B>
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262 A value object containing a maximum number of sequences and a maximum average
263 sequence length for a preset.</TD>
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265 <TR BGCOLOR="white" CLASS="TableRowColor">
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266 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.data.msa.jaxws"><B>LimitsManager</B></A></B>
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269 A collection of Limits</TD>
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271 <TR BGCOLOR="white" CLASS="TableRowColor">
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272 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.data.msa.jaxws"><B>Option</B></A></B>
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275 Command line option/flag or multiple exclusive options with no value.</TD>
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277 <TR BGCOLOR="white" CLASS="TableRowColor">
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278 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa.jaxws"><B>Preset</B></A></B>
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281 Collection of Options and Parameters with their values</TD>
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283 <TR BGCOLOR="white" CLASS="TableRowColor">
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284 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa.jaxws"><B>PresetManager</B></A></B>
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287 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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289 <TR BGCOLOR="white" CLASS="TableRowColor">
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290 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.data.msa.jaxws"><B>RunnerConfig</B></A></B>
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293 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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298 <A NAME="compbio.engine"><!-- --></A>
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299 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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300 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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301 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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302 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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304 <TR BGCOLOR="white" CLASS="TableRowColor">
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305 <TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.engine"><B>ChunkHolder</B></A></B>
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308 Represents a chunk of string data together with the position in a file from
309 where corresponding to of the data.</TD>
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311 <TR BGCOLOR="white" CLASS="TableRowColor">
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312 <TD><B><A HREF="../../compbio/metadata/class-use/JobExecutionException.html#compbio.engine"><B>JobExecutionException</B></A></B>
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315 JobExecutionException is thrown wherever the results of the calculation
316 cannot be obtained.</TD>
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318 <TR BGCOLOR="white" CLASS="TableRowColor">
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319 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine"><B>JobStatus</B></A></B>
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322 The status of the job.</TD>
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324 <TR BGCOLOR="white" CLASS="TableRowColor">
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325 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine"><B>JobSubmissionException</B></A></B>
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328 Exception for generic problems with JobSubmission it is often thrown as a
329 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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331 <TR BGCOLOR="white" CLASS="TableRowColor">
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332 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine"><B>ResultNotAvailableException</B></A></B>
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335 ResultNotAvailableException is thrown wherever the results of the calculation
336 cannot be obtained.</TD>
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341 <A NAME="compbio.engine.client"><!-- --></A>
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342 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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343 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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344 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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345 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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347 <TR BGCOLOR="white" CLASS="TableRowColor">
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348 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine.client"><B>JobStatus</B></A></B>
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351 The status of the job.</TD>
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353 <TR BGCOLOR="white" CLASS="TableRowColor">
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354 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine.client"><B>JobSubmissionException</B></A></B>
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357 Exception for generic problems with JobSubmission it is often thrown as a
358 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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360 <TR BGCOLOR="white" CLASS="TableRowColor">
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361 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.engine.client"><B>Limit</B></A></B>
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364 A value object containing a maximum number of sequences and a maximum average
365 sequence length for a preset.</TD>
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367 <TR BGCOLOR="white" CLASS="TableRowColor">
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368 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.engine.client"><B>LimitsManager</B></A></B>
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371 A collection of Limits</TD>
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373 <TR BGCOLOR="white" CLASS="TableRowColor">
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374 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.engine.client"><B>Option</B></A></B>
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377 Command line option/flag or multiple exclusive options with no value.</TD>
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379 <TR BGCOLOR="white" CLASS="TableRowColor">
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380 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.engine.client"><B>PresetManager</B></A></B>
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383 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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385 <TR BGCOLOR="white" CLASS="TableRowColor">
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386 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine.client"><B>ResultNotAvailableException</B></A></B>
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389 ResultNotAvailableException is thrown wherever the results of the calculation
390 cannot be obtained.</TD>
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392 <TR BGCOLOR="white" CLASS="TableRowColor">
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393 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.engine.client"><B>RunnerConfig</B></A></B>
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396 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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398 <TR BGCOLOR="white" CLASS="TableRowColor">
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399 <TD><B><A HREF="../../compbio/metadata/class-use/UnsupportedRuntimeException.html#compbio.engine.client"><B>UnsupportedRuntimeException</B></A></B>
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402 Indicates that the server could not execute native executables.</TD>
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407 <A NAME="compbio.engine.cluster.drmaa"><!-- --></A>
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408 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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409 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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410 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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411 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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413 <TR BGCOLOR="white" CLASS="TableRowColor">
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414 <TD><B><A HREF="../../compbio/metadata/class-use/JobExecutionException.html#compbio.engine.cluster.drmaa"><B>JobExecutionException</B></A></B>
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417 JobExecutionException is thrown wherever the results of the calculation
418 cannot be obtained.</TD>
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420 <TR BGCOLOR="white" CLASS="TableRowColor">
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421 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine.cluster.drmaa"><B>JobStatus</B></A></B>
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424 The status of the job.</TD>
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426 <TR BGCOLOR="white" CLASS="TableRowColor">
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427 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine.cluster.drmaa"><B>JobSubmissionException</B></A></B>
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430 Exception for generic problems with JobSubmission it is often thrown as a
431 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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433 <TR BGCOLOR="white" CLASS="TableRowColor">
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434 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine.cluster.drmaa"><B>ResultNotAvailableException</B></A></B>
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437 ResultNotAvailableException is thrown wherever the results of the calculation
438 cannot be obtained.</TD>
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443 <A NAME="compbio.engine.local"><!-- --></A>
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444 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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445 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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446 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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447 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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449 <TR BGCOLOR="white" CLASS="TableRowColor">
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450 <TD><B><A HREF="../../compbio/metadata/class-use/JobExecutionException.html#compbio.engine.local"><B>JobExecutionException</B></A></B>
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453 JobExecutionException is thrown wherever the results of the calculation
454 cannot be obtained.</TD>
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456 <TR BGCOLOR="white" CLASS="TableRowColor">
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457 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.engine.local"><B>JobStatus</B></A></B>
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460 The status of the job.</TD>
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462 <TR BGCOLOR="white" CLASS="TableRowColor">
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463 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.engine.local"><B>JobSubmissionException</B></A></B>
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466 Exception for generic problems with JobSubmission it is often thrown as a
467 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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469 <TR BGCOLOR="white" CLASS="TableRowColor">
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470 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.engine.local"><B>ResultNotAvailableException</B></A></B>
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473 ResultNotAvailableException is thrown wherever the results of the calculation
474 cannot be obtained.</TD>
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479 <A NAME="compbio.metadata"><!-- --></A>
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480 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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481 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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482 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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483 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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485 <TR BGCOLOR="white" CLASS="TableRowColor">
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486 <TD><B><A HREF="../../compbio/metadata/class-use/Argument.html#compbio.metadata"><B>Argument</B></A></B>
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489 An unmodifiable view for the options and parameters, with one exception - it
490 allows to set a value</TD>
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492 <TR BGCOLOR="white" CLASS="TableRowColor">
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493 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.metadata"><B>JobStatus</B></A></B>
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496 The status of the job.</TD>
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498 <TR BGCOLOR="white" CLASS="TableRowColor">
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499 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.metadata"><B>JobSubmissionException</B></A></B>
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502 Exception for generic problems with JobSubmission it is often thrown as a
503 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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505 <TR BGCOLOR="white" CLASS="TableRowColor">
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506 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.metadata"><B>Limit</B></A></B>
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509 A value object containing a maximum number of sequences and a maximum average
510 sequence length for a preset.</TD>
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512 <TR BGCOLOR="white" CLASS="TableRowColor">
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513 <TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.metadata"><B>LimitExceededException</B></A></B>
\r
516 Thrown if the task larger in size that the limit that applies to the
519 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
520 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.metadata"><B>Option</B></A></B>
\r
523 Command line option/flag or multiple exclusive options with no value.</TD>
\r
525 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
526 <TD><B><A HREF="../../compbio/metadata/class-use/Parameter.html#compbio.metadata"><B>Parameter</B></A></B>
\r
529 A single value containing option supported by the web service e.g.</TD>
\r
531 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
532 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.metadata"><B>Preset</B></A></B>
\r
535 Collection of Options and Parameters with their values</TD>
\r
537 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
538 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.metadata"><B>PresetManager</B></A></B>
\r
541 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
543 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
544 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.metadata"><B>RunnerConfig</B></A></B>
\r
547 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
549 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
550 <TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.html#compbio.metadata"><B>ValueConstrain</B></A></B>
\r
553 The type and the lower and upper boundaries for numerical value.</TD>
\r
555 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
556 <TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.Type.html#compbio.metadata"><B>ValueConstrain.Type</B></A></B>
\r
559 </TD>
\r
561 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
562 <TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.metadata"><B>WrongParameterException</B></A></B>
\r
565 WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
566 does not match the actual runnable or then attempting to set the value of
567 <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>
\r
572 <A NAME="compbio.runner"><!-- --></A>
\r
573 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
574 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
575 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
576 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
578 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
579 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner"><B>Limit</B></A></B>
\r
582 A value object containing a maximum number of sequences and a maximum average
583 sequence length for a preset.</TD>
\r
585 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
586 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner"><B>LimitsManager</B></A></B>
\r
589 A collection of Limits</TD>
\r
591 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
592 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.runner"><B>Option</B></A></B>
\r
595 Command line option/flag or multiple exclusive options with no value.</TD>
\r
597 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
598 <TD><B><A HREF="../../compbio/metadata/class-use/Parameter.html#compbio.runner"><B>Parameter</B></A></B>
\r
601 A single value containing option supported by the web service e.g.</TD>
\r
603 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
604 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.runner"><B>PresetManager</B></A></B>
\r
607 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
609 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
610 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.runner"><B>RunnerConfig</B></A></B>
\r
613 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
618 <A NAME="compbio.runner._impl"><!-- --></A>
\r
619 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
620 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
621 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
622 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
624 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
625 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner._impl"><B>Limit</B></A></B>
\r
628 A value object containing a maximum number of sequences and a maximum average
629 sequence length for a preset.</TD>
\r
631 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
632 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner._impl"><B>LimitsManager</B></A></B>
\r
635 A collection of Limits</TD>
\r
640 <A NAME="compbio.runner.msa"><!-- --></A>
\r
641 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
642 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
643 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
644 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
646 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
647 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner.msa"><B>Limit</B></A></B>
\r
650 A value object containing a maximum number of sequences and a maximum average
651 sequence length for a preset.</TD>
\r
653 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
654 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner.msa"><B>LimitsManager</B></A></B>
\r
657 A collection of Limits</TD>
\r
659 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
660 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.msa"><B>ResultNotAvailableException</B></A></B>
\r
663 ResultNotAvailableException is thrown wherever the results of the calculation
664 cannot be obtained.</TD>
\r
669 <A NAME="compbio.runner.psiblast"><!-- --></A>
\r
670 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
671 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
672 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
673 Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>
\r
675 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
676 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner.psiblast"><B>Limit</B></A></B>
\r
679 A value object containing a maximum number of sequences and a maximum average
680 sequence length for a preset.</TD>
\r
682 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
683 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner.psiblast"><B>LimitsManager</B></A></B>
\r
686 A collection of Limits</TD>
\r
688 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
689 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.psiblast"><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 string data together with the position in a file from
709 where corresponding to of the data.</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 Thrown if the task larger in size that the limit that applies to the
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/WrongParameterException.html#compbio.ws.server"><B>WrongParameterException</B></A></B>
\r
779 WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
780 does not match the actual runnable or then attempting to set the value of
781 <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>
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