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79 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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81 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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91 compbio.ws.server</FONT>
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95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.MafftWS</B>
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99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>>, <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></DD>
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103 <DT><PRE>public class <B>MafftWS</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A><DT>implements <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></DL>
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110 <!-- =========== FIELD SUMMARY =========== -->
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112 <A NAME="field_summary"><!-- --></A>
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113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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114 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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115 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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116 <B>Field Summary</B></FONT></TH>
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119 <A NAME="fields_inherited_from_class_compbio.data.msa.JABAService"><!-- --></A>
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120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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121 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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122 <TH ALIGN="left"><B>Fields inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></B></TH>
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124 <TR BGCOLOR="white" CLASS="TableRowColor">
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125 <TD><CODE><A HREF="../../../compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</A>, <A HREF="../../../compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</A></CODE></TD>
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129 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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131 <A NAME="constructor_summary"><!-- --></A>
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132 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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133 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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134 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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135 <B>Constructor Summary</B></FONT></TH>
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137 <TR BGCOLOR="white" CLASS="TableRowColor">
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138 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#MafftWS()">MafftWS</A></B>()</CODE>
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141 </TD>
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145 <!-- ========== METHOD SUMMARY =========== -->
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147 <A NAME="method_summary"><!-- --></A>
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148 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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149 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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150 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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151 <B>Method Summary</B></FONT></TH>
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153 <TR BGCOLOR="white" CLASS="TableRowColor">
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154 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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155 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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156 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#align(java.util.List)">align</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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159 Align a list of sequences with default settings.</TD>
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161 <TR BGCOLOR="white" CLASS="TableRowColor">
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162 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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163 <CODE> boolean</CODE></FONT></TD>
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164 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#cancelJob(java.lang.String)">cancelJob</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>
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167 Stop running the job <code>jobId</code> but leave its output untouched</TD>
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169 <TR BGCOLOR="white" CLASS="TableRowColor">
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170 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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171 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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172 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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173 <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>>> options)</CODE>
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176 Align a list of sequences with options.</TD>
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178 <TR BGCOLOR="white" CLASS="TableRowColor">
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179 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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180 <CODE> <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>
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181 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>
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184 Return the status of the job.</TD>
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186 <TR BGCOLOR="white" CLASS="TableRowColor">
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187 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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188 <CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></FONT></TD>
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189 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getLimit(java.lang.String)">getLimit</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</CODE>
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192 Get a Limit for a preset.</TD>
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194 <TR BGCOLOR="white" CLASS="TableRowColor">
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195 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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196 <CODE> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></FONT></TD>
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197 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getLimits()">getLimits</A></B>()</CODE>
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200 List Limits supported by a web service.</TD>
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202 <TR BGCOLOR="white" CLASS="TableRowColor">
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203 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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204 <CODE> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></FONT></TD>
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205 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getPresets()">getPresets</A></B>()</CODE>
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208 Get presets supported by a web service</TD>
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210 <TR BGCOLOR="white" CLASS="TableRowColor">
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211 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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212 <CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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213 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>
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216 Return the result of the job.</TD>
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218 <TR BGCOLOR="white" CLASS="TableRowColor">
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219 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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220 <CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></FONT></TD>
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221 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>
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224 Get options supported by a web service</TD>
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226 <TR BGCOLOR="white" CLASS="TableRowColor">
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227 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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228 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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229 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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230 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>> preset)</CODE>
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233 Align a list of sequences with preset.</TD>
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235 <TR BGCOLOR="white" CLASS="TableRowColor">
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236 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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237 <CODE> <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>
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238 <TD><CODE><B><A HREF="../../../compbio/ws/server/MafftWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId,
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239 long position)</CODE>
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242 Reads 1kb chunk from the statistics file which is specific to a given web
243 service from the <code>position</code>.</TD>
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246 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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247 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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248 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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249 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>
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251 <TR BGCOLOR="white" CLASS="TableRowColor">
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252 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>
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258 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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260 <A NAME="constructor_detail"><!-- --></A>
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261 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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262 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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263 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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264 <B>Constructor Detail</B></FONT></TH>
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268 <A NAME="MafftWS()"><!-- --></A><H3>
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271 public <B>MafftWS</B>()</PRE>
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275 <!-- ============ METHOD DETAIL ========== -->
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277 <A NAME="method_detail"><!-- --></A>
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278 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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279 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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280 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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281 <B>Method Detail</B></FONT></TH>
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285 <A NAME="align(java.util.List)"><!-- --></A><H3>
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288 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>align</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)
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289 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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291 <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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292 <DD>Align a list of sequences with default settings.
294 Any dataset containing a greater number of sequences or when the average
295 length of the sequences are greater then defined in the default Limit,
296 will not be accepted for an alignment operation and
297 JobSubmissionException will be thrown.
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300 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
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303 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
304 any sequence validity checks. Nor does it checks whether the
305 sequences names are unique. It is responsibility of the caller
306 to make sure of this
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307 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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309 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
310 following reasons: 1) The number of sequences in the
311 submission or their average length is greater then defined by
312 the default Limit. 2) Any problems on the server side e.g. it
313 is misconfigured or malfunction, is reported via this
314 exception. In the first case the information on the limit
315 could be obtained from an exception.
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316 <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
317 given web service, e.g. JABAWS is deployed on Windows and
318 Mafft service is called
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319 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or their average
320 length exceeds what is defined by the limit</DL>
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325 <A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>
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328 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>customAlign</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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329 <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>>> options)
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330 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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331 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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333 <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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334 <DD>Align a list of sequences with options.
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337 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
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340 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
341 any sequence validity checks. Nor does it checks whether the
342 sequences names are unique. It is responsibility of the caller
343 to validate this information<DD><CODE>options</CODE> - A list of Options
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344 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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346 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
347 following reasons: 1) The number of sequences in the
348 submission or their average length is greater then defined by
349 the default Limit. 2) Any problems on the server side e.g. it
350 is misconfigured or malfunction, is reported via this
351 exception. In the first case the information on the limit
352 could be obtained from an exception.
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353 <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
354 given web service, e.g. JABAWS is deployed on Windows and
355 Mafft service is called
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356 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or their average
357 length exceeds what is defined by the limit
\r
358 <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
359 supported, 2) The value of the option is defined outside the
360 boundaries. In both cases exception object contain the
361 information on the violating Option.<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
362 permitted or denied</CODE></A></DL>
\r
367 <A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>
\r
370 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>presetAlign</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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371 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>> preset)
\r
372 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
\r
373 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
\r
375 <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>
\r
376 <DD>Align a list of sequences with preset.
378 Limit for a presetName is used whether the calculation will be permitted
379 or denied. If no Limit was defined for a presetName, than default limit
383 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
\r
386 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
387 any sequence validity checks. Nor does it checks whether the
388 sequences names are unique. It is responsibility of the caller
389 to validate this information<DD><CODE>preset</CODE> - A list of Options
\r
390 <DT><B>Returns:</B><DD>String - jobId - unique identifier for the job
\r
392 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
393 following reasons: 1) The number of sequences in the
394 submission or their average length is greater then defined by
395 the default Limit. 2) Any problems on the server side e.g. it
396 is misconfigured or malfunction, is reported via this
397 exception. In the first case the information on the limit
398 could be obtained from an exception.
\r
399 <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
400 given web service, e.g. JABAWS is deployed on Windows and
401 Mafft service is called
\r
402 <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
403 exceeds what is defined by the limit
\r
404 <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
405 supported, 2) The value of the option is defined outside the
406 boundaries. In both cases exception object contain the
407 information on the violating Option.<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></DL>
\r
412 <A NAME="getResult(java.lang.String)"><!-- --></A><H3>
\r
415 public <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)
\r
416 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
\r
418 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">MsaWS</A></CODE></B></DD>
\r
419 <DD>Return the result of the job. This method waits for the job
420 <code>jobId</code> to complete before return.
\r
423 <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/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
\r
426 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier
\r
427 <DT><B>Returns:</B><DD>Alignment
\r
429 <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
430 successful or the result of the execution could not be found.
431 (e.g. removed). Exception could also be thrown due to the
432 lower level problems on the server i.e. IOException,
433 FileNotFoundException problems as well as
434 UnknownFileFormatException.</DL>
\r
439 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
\r
442 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>> <B>getLimit</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</PRE>
\r
444 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/Metadata.html#getLimit(java.lang.String)">Metadata</A></CODE></B></DD>
\r
445 <DD>Get a Limit for a preset.
\r
448 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/Metadata.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
\r
451 <DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
452 default preset is returned. If no limit for a particular
453 preset is defined then the default preset is returned
\r
454 <DT><B>Returns:</B><DD>Limit</DL>
\r
459 <A NAME="getLimits()"><!-- --></A><H3>
\r
462 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>> <B>getLimits</B>()</PRE>
\r
464 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/Metadata.html#getLimits()">Metadata</A></CODE></B></DD>
\r
465 <DD>List Limits supported by a web service.
\r
468 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/Metadata.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
\r
472 <DT><B>Returns:</B><DD>LimitManager</DL>
\r
477 <A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>
\r
478 pullExecStatistics</H3>
\r
480 public <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId,
\r
481 long position)</PRE>
\r
483 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/JManagement.html#pullExecStatistics(java.lang.String, long)">JManagement</A></CODE></B></DD>
\r
484 <DD>Reads 1kb chunk from the statistics file which is specific to a given web
485 service from the <code>position</code>. If in time of a request less then
486 1kb data is available from the position to the end of the file, then it
487 returns all the data available from the position to the end of the file.
\r
490 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/JManagement.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A></CODE></DL>
\r
493 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read
\r
494 <DT><B>Returns:</B><DD>ChunkHolder - which contains a chunk of data and a next position
495 within the file from which no data has been read<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><CODE>ChunkHolder</CODE></A></DL>
\r
500 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>
\r
503 public boolean <B>cancelJob</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</PRE>
\r
505 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)">JManagement</A></CODE></B></DD>
\r
506 <DD>Stop running the job <code>jobId</code> but leave its output untouched
\r
509 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)">cancelJob</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A></CODE></DL>
\r
513 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>
\r
518 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>
\r
521 public <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</PRE>
\r
523 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)">JManagement</A></CODE></B></DD>
\r
524 <DD>Return the status of the job.
\r
527 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A></CODE></DL>
\r
530 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier
\r
531 <DT><B>Returns:</B><DD>JobStatus - status of the job<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><CODE>JobStatus</CODE></A></DL>
\r
536 <A NAME="getPresets()"><!-- --></A><H3>
\r
539 public <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>> <B>getPresets</B>()</PRE>
\r
541 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/Metadata.html#getPresets()">Metadata</A></CODE></B></DD>
\r
542 <DD>Get presets supported by a web service
\r
545 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/Metadata.html#getPresets()">getPresets</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
\r
549 <DT><B>Returns:</B><DD>PresetManager the object contains information about presets
550 supported by a web service</DL>
\r
555 <A NAME="getRunnerOptions()"><!-- --></A><H3>
\r
556 getRunnerOptions</H3>
\r
558 public <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>> <B>getRunnerOptions</B>()</PRE>
\r
560 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">Metadata</A></CODE></B></DD>
\r
561 <DD>Get options supported by a web service
\r
564 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">getRunnerOptions</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></DL>
\r
568 <DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
572 <!-- ========= END OF CLASS DATA ========= -->
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577 <A NAME="navbar_bottom"><!-- --></A>
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