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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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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.metadata"><B>compbio.metadata</B></A></TD>
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102 <TD>A meta-data model for multiple sequence alignment web services
103 Classes in this package have no dependencies to other sources in the project. </TD>
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108 <A NAME="compbio.data.msa"><!-- --></A>
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109 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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110 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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111 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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112 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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114 <TR BGCOLOR="white" CLASS="TableRowColor">
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115 <TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa"><B>ChunkHolder</B></A></B>
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118 Represents a chunk of a string data together with the position in a file for
119 the next read operation.</TD>
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121 <TR BGCOLOR="white" CLASS="TableRowColor">
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122 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa"><B>JobStatus</B></A></B>
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125 The status of the job.</TD>
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127 <TR BGCOLOR="white" CLASS="TableRowColor">
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128 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.data.msa"><B>JobSubmissionException</B></A></B>
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131 Exception for generic problems with JobSubmission it is often thrown as a
132 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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134 <TR BGCOLOR="white" CLASS="TableRowColor">
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135 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.data.msa"><B>Limit</B></A></B>
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138 A value object containing a maximum number of sequences and a maximum average
139 sequence length for a preset.</TD>
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141 <TR BGCOLOR="white" CLASS="TableRowColor">
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142 <TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.data.msa"><B>LimitExceededException</B></A></B>
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145 This exception is thrown if the task larger in size that the limit that
146 applies to the calculation.</TD>
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148 <TR BGCOLOR="white" CLASS="TableRowColor">
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149 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.data.msa"><B>LimitsManager</B></A></B>
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152 A collection of Limits</TD>
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154 <TR BGCOLOR="white" CLASS="TableRowColor">
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155 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.data.msa"><B>Option</B></A></B>
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158 Command line option/flag or multiple exclusive options with no value.</TD>
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160 <TR BGCOLOR="white" CLASS="TableRowColor">
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161 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa"><B>Preset</B></A></B>
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164 Collection of Options and Parameters with their values</TD>
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166 <TR BGCOLOR="white" CLASS="TableRowColor">
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167 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa"><B>PresetManager</B></A></B>
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170 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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172 <TR BGCOLOR="white" CLASS="TableRowColor">
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173 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.data.msa"><B>ResultNotAvailableException</B></A></B>
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176 ResultNotAvailableException is thrown wherever the results of the calculation
177 cannot be obtained.</TD>
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179 <TR BGCOLOR="white" CLASS="TableRowColor">
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180 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.data.msa"><B>RunnerConfig</B></A></B>
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183 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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185 <TR BGCOLOR="white" CLASS="TableRowColor">
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186 <TD><B><A HREF="../../compbio/metadata/class-use/UnsupportedRuntimeException.html#compbio.data.msa"><B>UnsupportedRuntimeException</B></A></B>
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189 Indicates that the server could not execute native executables.</TD>
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191 <TR BGCOLOR="white" CLASS="TableRowColor">
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192 <TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.data.msa"><B>WrongParameterException</B></A></B>
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195 WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
196 does not match the actual runnable or then attempting to set the value of
197 <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>
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202 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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203 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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204 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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205 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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206 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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208 <TR BGCOLOR="white" CLASS="TableRowColor">
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209 <TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa.jaxws"><B>ChunkHolder</B></A></B>
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212 Represents a chunk of a string data together with the position in a file for
213 the next read operation.</TD>
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215 <TR BGCOLOR="white" CLASS="TableRowColor">
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216 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa.jaxws"><B>JobStatus</B></A></B>
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219 The status of the job.</TD>
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221 <TR BGCOLOR="white" CLASS="TableRowColor">
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222 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.data.msa.jaxws"><B>Limit</B></A></B>
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225 A value object containing a maximum number of sequences and a maximum average
226 sequence length for a preset.</TD>
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228 <TR BGCOLOR="white" CLASS="TableRowColor">
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229 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.data.msa.jaxws"><B>LimitsManager</B></A></B>
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232 A collection of Limits</TD>
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234 <TR BGCOLOR="white" CLASS="TableRowColor">
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235 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.data.msa.jaxws"><B>Option</B></A></B>
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238 Command line option/flag or multiple exclusive options with no value.</TD>
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240 <TR BGCOLOR="white" CLASS="TableRowColor">
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241 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa.jaxws"><B>Preset</B></A></B>
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244 Collection of Options and Parameters with their values</TD>
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246 <TR BGCOLOR="white" CLASS="TableRowColor">
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247 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa.jaxws"><B>PresetManager</B></A></B>
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250 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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252 <TR BGCOLOR="white" CLASS="TableRowColor">
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253 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.data.msa.jaxws"><B>RunnerConfig</B></A></B>
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256 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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261 <A NAME="compbio.metadata"><!-- --></A>
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262 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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263 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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264 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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265 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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267 <TR BGCOLOR="white" CLASS="TableRowColor">
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268 <TD><B><A HREF="../../compbio/metadata/class-use/Argument.html#compbio.metadata"><B>Argument</B></A></B>
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271 An unmodifiable view for the options and parameters, with one exception - it
272 allows to set a value</TD>
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274 <TR BGCOLOR="white" CLASS="TableRowColor">
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275 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.metadata"><B>JobStatus</B></A></B>
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278 The status of the job.</TD>
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280 <TR BGCOLOR="white" CLASS="TableRowColor">
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281 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.metadata"><B>JobSubmissionException</B></A></B>
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284 Exception for generic problems with JobSubmission it is often thrown as a
285 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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287 <TR BGCOLOR="white" CLASS="TableRowColor">
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288 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.metadata"><B>Limit</B></A></B>
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291 A value object containing a maximum number of sequences and a maximum average
292 sequence length for a preset.</TD>
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294 <TR BGCOLOR="white" CLASS="TableRowColor">
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295 <TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.metadata"><B>LimitExceededException</B></A></B>
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298 This exception is thrown if the task larger in size that the limit that
299 applies to the calculation.</TD>
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301 <TR BGCOLOR="white" CLASS="TableRowColor">
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302 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.metadata"><B>Option</B></A></B>
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305 Command line option/flag or multiple exclusive options with no value.</TD>
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307 <TR BGCOLOR="white" CLASS="TableRowColor">
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308 <TD><B><A HREF="../../compbio/metadata/class-use/Parameter.html#compbio.metadata"><B>Parameter</B></A></B>
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311 A single value containing an option supported by the web service e.g.</TD>
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313 <TR BGCOLOR="white" CLASS="TableRowColor">
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314 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.metadata"><B>Preset</B></A></B>
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317 Collection of Options and Parameters with their values</TD>
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319 <TR BGCOLOR="white" CLASS="TableRowColor">
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320 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.metadata"><B>PresetManager</B></A></B>
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323 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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325 <TR BGCOLOR="white" CLASS="TableRowColor">
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326 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.metadata"><B>RunnerConfig</B></A></B>
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329 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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331 <TR BGCOLOR="white" CLASS="TableRowColor">
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332 <TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.html#compbio.metadata"><B>ValueConstrain</B></A></B>
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335 The type and the lower and upper boundaries for numerical value.</TD>
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337 <TR BGCOLOR="white" CLASS="TableRowColor">
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338 <TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.Type.html#compbio.metadata"><B>ValueConstrain.Type</B></A></B>
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341 </TD>
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343 <TR BGCOLOR="white" CLASS="TableRowColor">
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344 <TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.metadata"><B>WrongParameterException</B></A></B>
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347 WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
348 does not match the actual runnable or then attempting to set the value of
349 <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>
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