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7 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.metadata"><B>compbio.metadata</B></A></TD>
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98 <TD>A meta-data model for multiple sequence alignment web services
99 Classes in this package have no dependencies to other sources in the project. </TD>
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104 <A NAME="compbio.data.msa"><!-- --></A>
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105 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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106 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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107 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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108 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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110 <TR BGCOLOR="white" CLASS="TableRowColor">
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111 <TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa"><B>ChunkHolder</B></A></B>
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114 Represents a chunk of a string data together with the position in a file for
115 the next read operation.</TD>
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117 <TR BGCOLOR="white" CLASS="TableRowColor">
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118 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa"><B>JobStatus</B></A></B>
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121 The status of the job.</TD>
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123 <TR BGCOLOR="white" CLASS="TableRowColor">
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124 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.data.msa"><B>JobSubmissionException</B></A></B>
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127 Exception for generic problems with JobSubmission it is often thrown as a
128 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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130 <TR BGCOLOR="white" CLASS="TableRowColor">
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131 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.data.msa"><B>Limit</B></A></B>
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134 A value object containing a maximum number of sequences and a maximum average
135 sequence length for a preset.</TD>
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137 <TR BGCOLOR="white" CLASS="TableRowColor">
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138 <TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.data.msa"><B>LimitExceededException</B></A></B>
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141 This exception is thrown if the task larger in size that the limit that
142 applies to the calculation.</TD>
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144 <TR BGCOLOR="white" CLASS="TableRowColor">
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145 <TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.data.msa"><B>LimitsManager</B></A></B>
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148 A collection of Limits</TD>
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150 <TR BGCOLOR="white" CLASS="TableRowColor">
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151 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.data.msa"><B>Option</B></A></B>
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154 Command line option/flag or multiple exclusive options with no value.</TD>
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156 <TR BGCOLOR="white" CLASS="TableRowColor">
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157 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa"><B>Preset</B></A></B>
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160 Collection of Options and Parameters with their values</TD>
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162 <TR BGCOLOR="white" CLASS="TableRowColor">
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163 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa"><B>PresetManager</B></A></B>
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166 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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168 <TR BGCOLOR="white" CLASS="TableRowColor">
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169 <TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.data.msa"><B>ResultNotAvailableException</B></A></B>
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172 ResultNotAvailableException is thrown wherever the results of the calculation
173 cannot be obtained.</TD>
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175 <TR BGCOLOR="white" CLASS="TableRowColor">
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176 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.data.msa"><B>RunnerConfig</B></A></B>
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179 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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181 <TR BGCOLOR="white" CLASS="TableRowColor">
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182 <TD><B><A HREF="../../compbio/metadata/class-use/UnsupportedRuntimeException.html#compbio.data.msa"><B>UnsupportedRuntimeException</B></A></B>
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185 Indicates that the server could not execute native executables.</TD>
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187 <TR BGCOLOR="white" CLASS="TableRowColor">
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188 <TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.data.msa"><B>WrongParameterException</B></A></B>
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191 WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
192 does not match the actual runnable or then attempting to set the value of
193 <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>
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198 <A NAME="compbio.metadata"><!-- --></A>
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199 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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201 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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202 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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204 <TR BGCOLOR="white" CLASS="TableRowColor">
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205 <TD><B><A HREF="../../compbio/metadata/class-use/Argument.html#compbio.metadata"><B>Argument</B></A></B>
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208 An unmodifiable view for the options and parameters, with one exception - it
209 allows to set a value</TD>
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211 <TR BGCOLOR="white" CLASS="TableRowColor">
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212 <TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.metadata"><B>JobStatus</B></A></B>
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215 The status of the job.</TD>
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217 <TR BGCOLOR="white" CLASS="TableRowColor">
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218 <TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.metadata"><B>JobSubmissionException</B></A></B>
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221 Exception for generic problems with JobSubmission it is often thrown as a
222 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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224 <TR BGCOLOR="white" CLASS="TableRowColor">
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225 <TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.metadata"><B>Limit</B></A></B>
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228 A value object containing a maximum number of sequences and a maximum average
229 sequence length for a preset.</TD>
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231 <TR BGCOLOR="white" CLASS="TableRowColor">
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232 <TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.metadata"><B>LimitExceededException</B></A></B>
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235 This exception is thrown if the task larger in size that the limit that
236 applies to the calculation.</TD>
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238 <TR BGCOLOR="white" CLASS="TableRowColor">
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239 <TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.metadata"><B>Option</B></A></B>
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242 Command line option/flag or multiple exclusive options with no value.</TD>
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244 <TR BGCOLOR="white" CLASS="TableRowColor">
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245 <TD><B><A HREF="../../compbio/metadata/class-use/Parameter.html#compbio.metadata"><B>Parameter</B></A></B>
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248 A single value containing an option supported by the web service e.g.</TD>
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250 <TR BGCOLOR="white" CLASS="TableRowColor">
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251 <TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.metadata"><B>Preset</B></A></B>
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254 Collection of Options and Parameters with their values</TD>
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256 <TR BGCOLOR="white" CLASS="TableRowColor">
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257 <TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.metadata"><B>PresetManager</B></A></B>
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260 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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262 <TR BGCOLOR="white" CLASS="TableRowColor">
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263 <TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.metadata"><B>RunnerConfig</B></A></B>
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266 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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268 <TR BGCOLOR="white" CLASS="TableRowColor">
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269 <TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.html#compbio.metadata"><B>ValueConstrain</B></A></B>
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272 The type and the lower and upper boundaries for numerical 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/ValueConstrain.Type.html#compbio.metadata"><B>ValueConstrain.Type</B></A></B>
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278 </TD>
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280 <TR BGCOLOR="white" CLASS="TableRowColor">
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281 <TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.metadata"><B>WrongParameterException</B></A></B>
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284 WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
285 does not match the actual runnable or then attempting to set the value of
286 <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>
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