website/full_javadoc/compbio/ws/server/IUPredWS.html

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   7 IUPredWS\r
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  10 <META NAME="date" CONTENT="2011-08-12">\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  81 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.ws.server</FONT>\r
  92 <BR>\r
  93 Class IUPredWS</H2>\r
  94 <PRE>\r
  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>\r
  96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">compbio.ws.server.GenericMetadataService</A>\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">compbio.ws.server.SequenceAnnotationService</A>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;\r
  98           <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.IUPredWS</B>\r
  99 </PRE>\r
 100 <DL>\r
 101 <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>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;, <A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</DD>\r
 102 </DL>\r
 103 <HR>\r
 104 <DL>\r
 105 <DT><PRE>public class <B>IUPredWS</B><DT>extends <A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;<DT>implements <A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</DL>\r
 106 </PRE>\r
 107 \r
 108 <P>\r
 109 <HR>\r
 110 \r
 111 <P>\r
 112 <!-- =========== FIELD SUMMARY =========== -->\r
 113 \r
 114 <A NAME="field_summary"><!-- --></A>\r
 115 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 116 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 117 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 118 <B>Field Summary</B></FONT></TH>\r
 119 </TR>\r
 120 </TABLE>\r
 121 &nbsp;<A NAME="fields_inherited_from_class_compbio.data.msa.JABAService"><!-- --></A>\r
 122 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 123 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 124 <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>\r
 125 </TR>\r
 126 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 127 <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>\r
 128 </TR>\r
 129 </TABLE>\r
 130 &nbsp;\r
 131 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 132 \r
 133 <A NAME="constructor_summary"><!-- --></A>\r
 134 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 135 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 136 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 137 <B>Constructor Summary</B></FONT></TH>\r
 138 </TR>\r
 139 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 140 <TD><CODE><B><A HREF="../../../compbio/ws/server/IUPredWS.html#IUPredWS()">IUPredWS</A></B>()</CODE>\r
 141 \r
 142 <BR>\r
 143 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 144 </TR>\r
 145 </TABLE>\r
 146 &nbsp;\r
 147 <!-- ========== METHOD SUMMARY =========== -->\r
 148 \r
 149 <A NAME="method_summary"><!-- --></A>\r
 150 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 151 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 152 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 153 <B>Method Summary</B></FONT></TH>\r
 154 </TR>\r
 155 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 156 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 157 <CODE>&nbsp;<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>\r
 158 <TD><CODE><B><A HREF="../../../compbio/ws/server/IUPredWS.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 159               <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;&nbsp;preset)</CODE>\r
 160 \r
 161 <BR>\r
 162 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to the preset settings.</TD>\r
 163 </TR>\r
 164 </TABLE>\r
 165 &nbsp;<A NAME="methods_inherited_from_class_compbio.ws.server.SequenceAnnotationService"><!-- --></A>\r
 166 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 167 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 168 <TH ALIGN="left"><B>Methods inherited from class compbio.ws.server.<A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A></B></TH>\r
 169 </TR>\r
 170 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 171 <TD><CODE><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#analize(java.util.List)">analize</A>, <A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#customAnalize(java.util.List, java.util.List)">customAnalize</A>, <A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#getAnnotation(java.lang.String)">getAnnotation</A></CODE></TD>\r
 172 </TR>\r
 173 </TABLE>\r
 174 &nbsp;<A NAME="methods_inherited_from_class_compbio.ws.server.GenericMetadataService"><!-- --></A>\r
 175 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 176 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 177 <TH ALIGN="left"><B>Methods inherited from class compbio.ws.server.<A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A></B></TH>\r
 178 </TR>\r
 179 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 180 <TD><CODE><A HREF="../../../compbio/ws/server/GenericMetadataService.html#cancelJob(java.lang.String)">cancelJob</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#getJobStatus(java.lang.String)">getJobStatus</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#getPresets()">getPresets</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#getRunnerOptions()">getRunnerOptions</A>, <A HREF="../../../compbio/ws/server/GenericMetadataService.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE></TD>\r
 181 </TR>\r
 182 </TABLE>\r
 183 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 184 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 185 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 186 <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>\r
 187 </TR>\r
 188 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 189 <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>\r
 190 </TR>\r
 191 </TABLE>\r
 192 &nbsp;<A NAME="methods_inherited_from_class_compbio.data.msa.SequenceAnnotation"><!-- --></A>\r
 193 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 194 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 195 <TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A></B></TH>\r
 196 </TR>\r
 197 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 198 <TD><CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#analize(java.util.List)">analize</A>, <A HREF="../../../compbio/data/msa/SequenceAnnotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</A>, <A HREF="../../../compbio/data/msa/SequenceAnnotation.html#getAnnotation(java.lang.String)">getAnnotation</A></CODE></TD>\r
 199 </TR>\r
 200 </TABLE>\r
 201 &nbsp;<A NAME="methods_inherited_from_class_compbio.data.msa.JManagement"><!-- --></A>\r
 202 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 203 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 204 <TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A></B></TH>\r
 205 </TR>\r
 206 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 207 <TD><CODE><A HREF="../../../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)">cancelJob</A>, <A HREF="../../../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)">getJobStatus</A>, <A HREF="../../../compbio/data/msa/JManagement.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE></TD>\r
 208 </TR>\r
 209 </TABLE>\r
 210 &nbsp;<A NAME="methods_inherited_from_class_compbio.data.msa.Metadata"><!-- --></A>\r
 211 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 212 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 213 <TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A></B></TH>\r
 214 </TR>\r
 215 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 216 <TD><CODE><A HREF="../../../compbio/data/msa/Metadata.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getPresets()">getPresets</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">getRunnerOptions</A></CODE></TD>\r
 217 </TR>\r
 218 </TABLE>\r
 219 &nbsp;\r
 220 <P>\r
 221 \r
 222 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 223 \r
 224 <A NAME="constructor_detail"><!-- --></A>\r
 225 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 226 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 227 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 228 <B>Constructor Detail</B></FONT></TH>\r
 229 </TR>\r
 230 </TABLE>\r
 231 \r
 232 <A NAME="IUPredWS()"><!-- --></A><H3>\r
 233 IUPredWS</H3>\r
 234 <PRE>\r
 235 public <B>IUPredWS</B>()</PRE>\r
 236 <DL>\r
 237 </DL>\r
 238 \r
 239 <!-- ============ METHOD DETAIL ========== -->\r
 240 \r
 241 <A NAME="method_detail"><!-- --></A>\r
 242 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 243 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 244 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 245 <B>Method Detail</B></FONT></TH>\r
 246 </TR>\r
 247 </TABLE>\r
 248 \r
 249 <A NAME="presetAnalize(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
 250 presetAnalize</H3>\r
 251 <PRE>\r
 252 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>presetAnalize</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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 253                             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;&nbsp;preset)\r
 254                      throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
 255                             <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
 256                             <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
 257                             <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
 258 <DL>\r
 259 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">SequenceAnnotation</A></CODE></B></DD>\r
 260 <DD>Analyse the sequences according to the preset settings. The actual
 261  analysis algorithm is defined by the type T.
 262
 263  Limit for a presetName is used whether the calculation will be permitted
 264  or denied. If no Limit was defined for a presetName, than default limit
 265  is used.\r
 266 <P>\r
 267 <DD><DL>\r
 268 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></CODE> in class <CODE><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>&lt;<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>&gt;</CODE></DL>\r
 269 </DD>\r
 270 <DD><DL>\r
 271 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
 272             any sequence validity checks. Nor does it checks whether the
 273             sequences names are unique. It is responsibility of the caller
 274             to validate this information<DD><CODE>preset</CODE> - A list of Options\r
 275 <DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
 276 <DT><B>Throws:</B>\r
 277 <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
 278              given web service, e.g. JABAWS is deployed on Windows and
 279              Mafft service is called\r
 280 <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
 281              exceeds what is defined by the limit\r
 282 <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
 283              following reasons: 1) The number of sequences in the
 284              submission or their average length is greater then defined by
 285              the default Limit. 2) Any problems on the server side e.g. it
 286              is misconfigured or malfunction, is reported via this
 287              exception. In the first case the information on the limit
 288              could be obtained from an exception.\r
 289 <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
 290              supported, 2) The value of the option is defined outside the
 291              boundaries. In both cases exception object contain the
 292              information on the violating Option.</DL>\r
 293 </DD>\r
 294 </DL>\r
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