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83 Package compbio.metadata
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85 A meta-data model for multiple sequence alignment web services
86 Classes in this package have no dependencies to other sources in the project.
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90 <A HREF="#package_description"><B>Description</B></A>
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93 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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94 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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95 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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96 <B>Interface Summary</B></FONT></TH>
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98 <TR BGCOLOR="white" CLASS="TableRowColor">
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99 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument<T></A></B></TD>
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100 <TD>An unmodifiable view for the options and parameters, with one exception - it
101 allows to set a value</TD>
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108 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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109 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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110 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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111 <B>Class Summary</B></FONT></TH>
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113 <TR BGCOLOR="white" CLASS="TableRowColor">
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114 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></B></TD>
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115 <TD>Represents a chunk of a string data together with the position in a file for
116 the next read operation.</TD>
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118 <TR BGCOLOR="white" CLASS="TableRowColor">
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119 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit<T></A></B></TD>
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120 <TD>A value object containing a maximum number of sequences and a maximum average
121 sequence length for a preset.</TD>
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123 <TR BGCOLOR="white" CLASS="TableRowColor">
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124 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager<T></A></B></TD>
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125 <TD>A collection of Limits</TD>
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127 <TR BGCOLOR="white" CLASS="TableRowColor">
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128 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option<T></A></B></TD>
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129 <TD>Command line option/flag or multiple exclusive options with no value.</TD>
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131 <TR BGCOLOR="white" CLASS="TableRowColor">
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132 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter<T></A></B></TD>
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133 <TD>A single value containing an option supported by the web service e.g.</TD>
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135 <TR BGCOLOR="white" CLASS="TableRowColor">
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136 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset<T></A></B></TD>
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137 <TD>Collection of Options and Parameters with their values</TD>
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139 <TR BGCOLOR="white" CLASS="TableRowColor">
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140 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager<T></A></B></TD>
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141 <TD>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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143 <TR BGCOLOR="white" CLASS="TableRowColor">
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144 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig<T></A></B></TD>
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145 <TD>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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147 <TR BGCOLOR="white" CLASS="TableRowColor">
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148 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></B></TD>
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149 <TD>The type and the lower and upper boundaries for numerical value.</TD>
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156 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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157 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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158 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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159 <B>Enum Summary</B></FONT></TH>
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161 <TR BGCOLOR="white" CLASS="TableRowColor">
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162 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></B></TD>
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163 <TD>The status of the job.</TD>
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165 <TR BGCOLOR="white" CLASS="TableRowColor">
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166 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></B></TD>
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174 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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175 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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176 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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177 <B>Exception Summary</B></FONT></TH>
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179 <TR BGCOLOR="white" CLASS="TableRowColor">
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180 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></B></TD>
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181 <TD>JobExecutionException is thrown wherever the results of the calculation
182 cannot be obtained.</TD>
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184 <TR BGCOLOR="white" CLASS="TableRowColor">
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185 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></B></TD>
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186 <TD>Exception for generic problems with JobSubmission it is often thrown as a
187 wrapper for the lower level exceptions like IOException or DrmaaException.</TD>
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189 <TR BGCOLOR="white" CLASS="TableRowColor">
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190 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></B></TD>
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191 <TD>This exception is thrown if the task larger in size that the limit that
192 applies to the calculation.</TD>
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194 <TR BGCOLOR="white" CLASS="TableRowColor">
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195 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></B></TD>
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196 <TD>ResultNotAvailableException is thrown wherever the results of the calculation
197 cannot be obtained.</TD>
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199 <TR BGCOLOR="white" CLASS="TableRowColor">
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200 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></B></TD>
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201 <TD>Indicates that the server could not execute native executables.</TD>
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203 <TR BGCOLOR="white" CLASS="TableRowColor">
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204 <TD WIDTH="15%"><B><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></B></TD>
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205 <TD>WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
206 does not match the actual runnable or then attempting to set the value of
207 <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>
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213 <A NAME="package_description"><!-- --></A><H2>
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214 Package compbio.metadata Description
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218 A meta-data model for multiple sequence alignment web services
219 Classes in this package have no dependencies to other sources in the project.
220 They form a base layer of JAva Bioinformatics Analysis Web Services (JABAWS)
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225 <DT><B>Version:</B></DT>
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226 <DD>1.0 January 2010</DD>
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227 <DT><B>Author:</B></DT>
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228 <DD>Peter Troshin</DD>
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