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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.ws.server</FONT>
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93 Class ClustalWS</H2>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.ClustalWS</B>
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99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></DD>
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103 <DT><PRE>public class <B>ClustalWS</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></DL>
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111 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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113 <A NAME="constructor_summary"><!-- --></A>
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114 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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115 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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116 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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117 <B>Constructor Summary</B></FONT></TH>
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119 <TR BGCOLOR="white" CLASS="TableRowColor">
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120 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#ClustalWS()">ClustalWS</A></B>()</CODE>
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123 </TD>
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127 <!-- ========== METHOD SUMMARY =========== -->
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129 <A NAME="method_summary"><!-- --></A>
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130 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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131 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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132 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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133 <B>Method Summary</B></FONT></TH>
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135 <TR BGCOLOR="white" CLASS="TableRowColor">
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136 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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137 <CODE> java.lang.String</CODE></FONT></TD>
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138 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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141 Align a list of sequences with default settings.</TD>
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143 <TR BGCOLOR="white" CLASS="TableRowColor">
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144 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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145 <CODE> boolean</CODE></FONT></TD>
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146 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String jobId)</CODE>
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149 Stop running job but leave its output untouched</TD>
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151 <TR BGCOLOR="white" CLASS="TableRowColor">
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152 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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153 <CODE> java.lang.String</CODE></FONT></TD>
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154 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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155 java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>>> options)</CODE>
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158 Align a list of sequences with options.</TD>
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160 <TR BGCOLOR="white" CLASS="TableRowColor">
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161 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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162 <CODE> <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>
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163 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String jobId)</CODE>
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166 Return the status of the job.</TD>
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168 <TR BGCOLOR="white" CLASS="TableRowColor">
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169 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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170 <CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></FONT></TD>
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171 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String presetName)</CODE>
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174 Get a Limit for a preset.</TD>
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176 <TR BGCOLOR="white" CLASS="TableRowColor">
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177 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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178 <CODE> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></FONT></TD>
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179 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getLimits()">getLimits</A></B>()</CODE>
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182 List Limits supported by a web service.</TD>
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184 <TR BGCOLOR="white" CLASS="TableRowColor">
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185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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186 <CODE> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></FONT></TD>
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187 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getPresets()">getPresets</A></B>()</CODE>
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190 Get presets supported by a web service</TD>
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192 <TR BGCOLOR="white" CLASS="TableRowColor">
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193 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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194 <CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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195 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String jobId)</CODE>
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198 Return the result of the job.</TD>
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200 <TR BGCOLOR="white" CLASS="TableRowColor">
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201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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202 <CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></FONT></TD>
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203 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>
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206 Get options supported by a web service</TD>
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208 <TR BGCOLOR="white" CLASS="TableRowColor">
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209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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210 <CODE> java.lang.String</CODE></FONT></TD>
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211 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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212 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> preset)</CODE>
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215 Align a list of sequences with preset.</TD>
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217 <TR BGCOLOR="white" CLASS="TableRowColor">
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218 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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219 <CODE> <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>
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220 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String jobId,
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221 long position)</CODE>
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224 Reads 1kb chunk from the statistics file which is specific to a given web
225 service from the position.</TD>
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228 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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229 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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230 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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231 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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233 <TR BGCOLOR="white" CLASS="TableRowColor">
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234 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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240 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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242 <A NAME="constructor_detail"><!-- --></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="1"><FONT SIZE="+2">
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246 <B>Constructor Detail</B></FONT></TH>
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250 <A NAME="ClustalWS()"><!-- --></A><H3>
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253 public <B>ClustalWS</B>()</PRE>
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257 <!-- ============ METHOD DETAIL ========== -->
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259 <A NAME="method_detail"><!-- --></A>
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260 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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261 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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262 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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263 <B>Method Detail</B></FONT></TH>
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267 <A NAME="align(java.util.List)"><!-- --></A><H3>
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270 public java.lang.String <B>align</B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)
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271 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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273 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">MsaWS</A></CODE></B></DD>
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274 <DD>Align a list of sequences with default settings.
276 Any dataset containing a greater number of sequences or the average
277 length of the sequences are greater then defined in the default Limit
278 will not be accepted for an alignment operation and
279 JobSubmissionException will be thrown.
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282 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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285 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
286 any sequence validity checks. Nor does it checks whether the
287 sequences names are unique. It is responsibility of the caller
288 to validate this information
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289 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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291 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
292 given web service, e.g. JWS2 is deployed on Windows and Mafft
294 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
295 exceeds what is defined by the limit
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296 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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301 <A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>
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304 public java.lang.String <B>presetAlign</B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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305 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> preset)
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306 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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307 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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309 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">MsaWS</A></CODE></B></DD>
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310 <DD>Align a list of sequences with preset. @see Preset
312 Limit for a presetName is used whether the calculation will be permitted
313 or denied. If no Limit was defined for a presetName, than default limit
317 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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320 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
321 any sequence validity checks. Nor does it checks whether the
322 sequences names are unique. It is responsibility of the caller
323 to validate this information<DD><CODE>preset</CODE> - A list of Options
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324 <DT><B>Returns:</B><DD>String - jobId - unique identifier for the job
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326 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
327 given web service, e.g. JWS2 is deployed on Windows and Mafft
329 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
330 exceeds what is defined by the limit
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331 <DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
332 supported, 2) The value of the option is defined outside the
333 boundaries. In both cases exception object contain the
334 information on the violating Option.
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335 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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340 <A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>
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343 public java.lang.String <B>customAlign</B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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344 java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>>> options)
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345 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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346 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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348 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">MsaWS</A></CODE></B></DD>
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349 <DD>Align a list of sequences with options.
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352 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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355 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
356 any sequence validity checks. Nor does it checks whether the
357 sequences names are unique. It is responsibility of the caller
358 to validate this information<DD><CODE>options</CODE> - A list of Options
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359 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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361 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
362 given web service, e.g. JWS2 is deployed on Windows and Mafft
364 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
365 exceeds what is defined by the limit
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366 <DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
367 supported, 2) The value of the option is defined outside the
368 boundaries. In both cases exception object contain the
369 information on the violating Option.
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370 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Default Limit is used to decide whether the calculation will be
371 permitted or denied</CODE></A></DL>
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376 <A NAME="getRunnerOptions()"><!-- --></A><H3>
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377 getRunnerOptions</H3>
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379 public <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> <B>getRunnerOptions</B>()</PRE>
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381 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">MsaWS</A></CODE></B></DD>
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382 <DD>Get options supported by a web service
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385 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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389 <DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
395 <A NAME="getResult(java.lang.String)"><!-- --></A><H3>
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398 public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(java.lang.String jobId)
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399 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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401 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">MsaWS</A></CODE></B></DD>
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402 <DD>Return the result of the job.
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405 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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408 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier
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409 <DT><B>Returns:</B><DD>Alignment
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411 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - this exception is throw if the job execution was not
412 successful or the result of the execution could not be found.
413 (e.g. removed). Exception could also be thrown is dues to the
414 lower level problems on the server i.e. IOException,
415 FileNotFoundException problems as well as
416 UnknownFileFormatException.</DL>
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421 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
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424 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> <B>getLimit</B>(java.lang.String presetName)</PRE>
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426 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">MsaWS</A></CODE></B></DD>
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427 <DD>Get a Limit for a preset.
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430 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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433 <DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
434 default preset is returned. If no limit for a particular
435 preset is defined then the default preset is returned
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436 <DT><B>Returns:</B><DD>Limit</DL>
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441 <A NAME="getLimits()"><!-- --></A><H3>
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444 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> <B>getLimits</B>()</PRE>
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446 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">MsaWS</A></CODE></B></DD>
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447 <DD>List Limits supported by a web service.
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450 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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454 <DT><B>Returns:</B><DD>LimitManager</DL>
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459 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>
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462 public boolean <B>cancelJob</B>(java.lang.String jobId)</PRE>
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464 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">MsaWS</A></CODE></B></DD>
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465 <DD>Stop running job but leave its output untouched
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468 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">cancelJob</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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472 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>
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477 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>
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480 public <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String jobId)</PRE>
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482 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">MsaWS</A></CODE></B></DD>
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483 <DD>Return the status of the job. @see JobStatus
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486 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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489 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier
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490 <DT><B>Returns:</B><DD>JobStatus - status of the job</DL>
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495 <A NAME="getPresets()"><!-- --></A><H3>
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498 public <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> <B>getPresets</B>()</PRE>
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500 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">MsaWS</A></CODE></B></DD>
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501 <DD>Get presets supported by a web service
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504 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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508 <DT><B>Returns:</B><DD>PresetManager the object contains information about presets
509 supported by a web service</DL>
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514 <A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>
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515 pullExecStatistics</H3>
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517 public <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(java.lang.String jobId,
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518 long position)</PRE>
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520 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">MsaWS</A></CODE></B></DD>
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521 <DD>Reads 1kb chunk from the statistics file which is specific to a given web
522 service from the position. If in time of a request less then 1kb data is
523 available from the position to the end of the file, then it returns all
524 the data available from the position to the end of the file.
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527 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>
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530 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read
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531 <DT><B>Returns:</B><DD>ChunkHolder - @see ChunkHolder which contains a chuink of data
532 and a next position within the file from which no data has been
536 <!-- ========= END OF CLASS DATA ========= -->
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