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15 function windowTitle()
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17 if (location.href.indexOf('is-external=true') == -1) {
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18 parent.document.title="ClustalOWS";
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27 <BODY BGCOLOR="white" onload="windowTitle();">
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40 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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42 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
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43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClustalOWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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58 <A HREF="../../../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>
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59 <A HREF="../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>
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62 <A HREF="ClustalOWS.html" target="_top"><B>NO FRAMES</B></A>
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66 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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71 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
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78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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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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80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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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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84 <A NAME="skip-navbar_top"></A>
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85 <!-- ========= END OF TOP NAVBAR ========= -->
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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.ws.server</FONT>
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93 Class ClustalOWS</H2>
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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.ClustalOWS</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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>>, <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></DD>
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103 <DT><PRE>public class <B>ClustalOWS</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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</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/ClustalOWS.html#ClustalOWS()">ClustalOWS</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/ClustalOWS.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/ClustalOWS.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/ClustalOWS.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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</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/ClustalOWS.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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></FONT></TD>
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189 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalOWS.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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></FONT></TD>
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197 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalOWS.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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></FONT></TD>
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205 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalOWS.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/ClustalOWS.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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></FONT></TD>
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221 <TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalOWS.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/ClustalOWS.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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</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/ClustalOWS.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="ClustalOWS()"><!-- --></A><H3>
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271 public <B>ClustalOWS</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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</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="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></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>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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329 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>> preset)
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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#presetAlign(java.util.List, compbio.metadata.Preset)">MsaWS</A></CODE></B></DD>
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334 <DD>Align a list of sequences with preset.
336 Limit for a presetName is used whether the calculation will be permitted
337 or denied. If no Limit was defined for a presetName, than default limit
341 <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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></DL>
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344 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
345 any sequence validity checks. Nor does it checks whether the
346 sequences names are unique. It is responsibility of the caller
347 to validate this information<DD><CODE>preset</CODE> - A list of Options
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348 <DT><B>Returns:</B><DD>String - jobId - unique identifier for the job
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350 <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
351 following reasons: 1) The number of sequences in the
352 submission or their average length is greater then defined by
353 the default Limit. 2) Any problems on the server side e.g. it
354 is misconfigured or malfunction, is reported via this
355 exception. In the first case the information on the limit
356 could be obtained from an exception.
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357 <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
358 given web service, e.g. JABAWS is deployed on Windows and
359 Mafft service is called
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360 <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
361 exceeds what is defined by the limit
\r
362 <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
363 supported, 2) The value of the option is defined outside the
364 boundaries. In both cases exception object contain the
365 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>
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370 <A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>
\r
373 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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374 <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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>>> options)
\r
375 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
\r
376 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
\r
378 <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>
\r
379 <DD>Align a list of sequences with options.
\r
382 <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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></DL>
\r
385 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
386 any sequence validity checks. Nor does it checks whether the
387 sequences names are unique. It is responsibility of the caller
388 to validate this information<DD><CODE>options</CODE> - A list of Options
\r
389 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
\r
391 <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
392 following reasons: 1) The number of sequences in the
393 submission or their average length is greater then defined by
394 the default Limit. 2) Any problems on the server side e.g. it
395 is misconfigured or malfunction, is reported via this
396 exception. In the first case the information on the limit
397 could be obtained from an exception.
\r
398 <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
399 given web service, e.g. JABAWS is deployed on Windows and
400 Mafft service is called
\r
401 <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
402 length exceeds what is defined by the limit
\r
403 <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
404 supported, 2) The value of the option is defined outside the
405 boundaries. In both cases exception object contain the
406 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
407 permitted or denied</CODE></A></DL>
\r
412 <A NAME="getRunnerOptions()"><!-- --></A><H3>
\r
413 getRunnerOptions</H3>
\r
415 public <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>> <B>getRunnerOptions</B>()</PRE>
\r
417 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">Metadata</A></CODE></B></DD>
\r
418 <DD>Get options supported by a web service
\r
421 <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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></DL>
\r
425 <DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
431 <A NAME="getResult(java.lang.String)"><!-- --></A><H3>
\r
434 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
435 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
\r
437 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">MsaWS</A></CODE></B></DD>
\r
438 <DD>Return the result of the job. This method waits for the job
439 <code>jobId</code> to complete before return.
\r
442 <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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></DL>
\r
445 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier
\r
446 <DT><B>Returns:</B><DD>Alignment
\r
448 <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
449 successful or the result of the execution could not be found.
450 (e.g. removed). Exception could also be thrown due to the
451 lower level problems on the server i.e. IOException,
452 FileNotFoundException problems as well as
453 UnknownFileFormatException.</DL>
\r
458 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
\r
461 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</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
463 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/Metadata.html#getLimit(java.lang.String)">Metadata</A></CODE></B></DD>
\r
464 <DD>Get a Limit for a preset.
\r
467 <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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></DL>
\r
470 <DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
471 default preset is returned. If no limit for a particular
472 preset is defined then the default preset is returned
\r
473 <DT><B>Returns:</B><DD>Limit</DL>
\r
478 <A NAME="getLimits()"><!-- --></A><H3>
\r
481 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>> <B>getLimits</B>()</PRE>
\r
483 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/Metadata.html#getLimits()">Metadata</A></CODE></B></DD>
\r
484 <DD>List Limits supported by a web service.
\r
487 <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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></DL>
\r
491 <DT><B>Returns:</B><DD>LimitManager</DL>
\r
496 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>
\r
499 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
501 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)">JManagement</A></CODE></B></DD>
\r
502 <DD>Stop running the job <code>jobId</code> but leave its output untouched
\r
505 <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
509 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>
\r
514 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>
\r
517 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
519 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)">JManagement</A></CODE></B></DD>
\r
520 <DD>Return the status of the job.
\r
523 <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
526 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier
\r
527 <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
532 <A NAME="getPresets()"><!-- --></A><H3>
\r
535 public <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>> <B>getPresets</B>()</PRE>
\r
537 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/Metadata.html#getPresets()">Metadata</A></CODE></B></DD>
\r
538 <DD>Get presets supported by a web service
\r
541 <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/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>></CODE></DL>
\r
545 <DT><B>Returns:</B><DD>PresetManager the object contains information about presets
546 supported by a web service</DL>
\r
551 <A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>
\r
552 pullExecStatistics</H3>
\r
554 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
555 long position)</PRE>
\r
557 <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
558 <DD>Reads 1kb chunk from the statistics file which is specific to a given web
559 service from the <code>position</code>. If in time of a request less then
560 1kb data is available from the position to the end of the file, then it
561 returns all the data available from the position to the end of the file.
\r
564 <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
567 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read
\r
568 <DT><B>Returns:</B><DD>ChunkHolder - which contains a chunk of data and a next position
569 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
572 <!-- ========= END OF CLASS DATA ========= -->
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