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

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  58 &nbsp;<A HREF="../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\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 DisemblWS</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/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;\r
  98           <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.DisemblWS</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/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;, <A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</DD>\r
 102 </DL>\r
 103 <HR>\r
 104 <DL>\r
 105 <DT><PRE>public class <B>DisemblWS</B><DT>extends <A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</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/Disembl.html" title="class in compbio.runner.disorder">Disembl</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/DisemblWS.html#DisemblWS()">DisemblWS</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/DisemblWS.html#customAnalize(java.util.List, java.util.List)">customAnalize</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="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/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;&gt;&nbsp;options)</CODE>\r
 160 \r
 161 <BR>\r
 162 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to custom settings defined in options
 163  list.</TD>\r
 164 </TR>\r
 165 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 167 <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
 168 <TD><CODE><B><A HREF="../../../compbio/ws/server/DisemblWS.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
 169               <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;&nbsp;preset)</CODE>\r
 170 \r
 171 <BR>\r
 172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to the preset settings.</TD>\r
 173 </TR>\r
 174 </TABLE>\r
 175 &nbsp;<A NAME="methods_inherited_from_class_compbio.ws.server.SequenceAnnotationService"><!-- --></A>\r
 176 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 177 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 178 <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
 179 </TR>\r
 180 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 181 <TD><CODE><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#analize(java.util.List)">analize</A>, <A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#getAnnotation(java.lang.String)">getAnnotation</A></CODE></TD>\r
 182 </TR>\r
 183 </TABLE>\r
 184 &nbsp;<A NAME="methods_inherited_from_class_compbio.ws.server.GenericMetadataService"><!-- --></A>\r
 185 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 186 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 187 <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
 188 </TR>\r
 189 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 190 <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
 191 </TR>\r
 192 </TABLE>\r
 193 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 194 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 195 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 196 <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
 197 </TR>\r
 198 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 199 <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
 200 </TR>\r
 201 </TABLE>\r
 202 &nbsp;<A NAME="methods_inherited_from_class_compbio.data.msa.SequenceAnnotation"><!-- --></A>\r
 203 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 204 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 205 <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
 206 </TR>\r
 207 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 208 <TD><CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#analize(java.util.List)">analize</A>, <A HREF="../../../compbio/data/msa/SequenceAnnotation.html#getAnnotation(java.lang.String)">getAnnotation</A></CODE></TD>\r
 209 </TR>\r
 210 </TABLE>\r
 211 &nbsp;<A NAME="methods_inherited_from_class_compbio.data.msa.JManagement"><!-- --></A>\r
 212 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 213 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 214 <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
 215 </TR>\r
 216 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 217 <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
 218 </TR>\r
 219 </TABLE>\r
 220 &nbsp;<A NAME="methods_inherited_from_class_compbio.data.msa.Metadata"><!-- --></A>\r
 221 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 222 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 223 <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
 224 </TR>\r
 225 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 226 <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
 227 </TR>\r
 228 </TABLE>\r
 229 &nbsp;\r
 230 <P>\r
 231 \r
 232 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 233 \r
 234 <A NAME="constructor_detail"><!-- --></A>\r
 235 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 236 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 237 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 238 <B>Constructor Detail</B></FONT></TH>\r
 239 </TR>\r
 240 </TABLE>\r
 241 \r
 242 <A NAME="DisemblWS()"><!-- --></A><H3>\r
 243 DisemblWS</H3>\r
 244 <PRE>\r
 245 public <B>DisemblWS</B>()</PRE>\r
 246 <DL>\r
 247 </DL>\r
 248 \r
 249 <!-- ============ METHOD DETAIL ========== -->\r
 250 \r
 251 <A NAME="method_detail"><!-- --></A>\r
 252 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 253 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 254 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 255 <B>Method Detail</B></FONT></TH>\r
 256 </TR>\r
 257 </TABLE>\r
 258 \r
 259 <A NAME="customAnalize(java.util.List, java.util.List)"><!-- --></A><H3>\r
 260 customAnalize</H3>\r
 261 <PRE>\r
 262 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>customAnalize</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
 263                             <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/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;&gt;&nbsp;options)\r
 264                      throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
 265                             <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
 266                             <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
 267                             <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
 268 <DL>\r
 269 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#customAnalize(java.util.List, java.util.List)">SequenceAnnotation</A></CODE></B></DD>\r
 270 <DD>Analyse the sequences according to custom settings defined in options
 271  list. The actual analysis algorithm is defined by the type T. Default
 272  Limit is used to decide whether the calculation will be permitted or
 273  denied\r
 274 <P>\r
 275 <DD><DL>\r
 276 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</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/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#customAnalize(java.util.List, java.util.List)">customAnalize</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/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</CODE></DL>\r
 277 </DD>\r
 278 <DD><DL>\r
 279 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
 280             any sequence validity checks. Nor does it checks whether the
 281             sequences names are unique. It is responsibility of the caller
 282             to validate this information<DD><CODE>options</CODE> - A list of Options\r
 283 <DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
 284 <DT><B>Throws:</B>\r
 285 <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
 286              given web service, e.g. JABAWS is deployed on Windows and
 287              Mafft service is called\r
 288 <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
 289              exceeds what is defined by the limit\r
 290 <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
 291              following reasons: 1) The number of sequences in the
 292              submission or their average length is greater then defined by
 293              the default Limit. 2) Any problems on the server side e.g. it
 294              is misconfigured or malfunction, is reported via this
 295              exception. In the first case the information on the limit
 296              could be obtained from an exception.\r
 297 <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
 298              supported, 2) The value of the option is defined outside the
 299              boundaries. In both cases exception object contain the
 300              information on the violating Option.<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A></DL>\r
 301 </DD>\r
 302 </DL>\r
 303 <HR>\r
 304 \r
 305 <A NAME="presetAnalize(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
 306 presetAnalize</H3>\r
 307 <PRE>\r
 308 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
 309                             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;&nbsp;preset)\r
 310                      throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
 311                             <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
 312                             <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
 313                             <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
 314 <DL>\r
 315 <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
 316 <DD>Analyse the sequences according to the preset settings. The actual
 317  analysis algorithm is defined by the type T.
 318
 319  Limit for a presetName is used whether the calculation will be permitted
 320  or denied. If no Limit was defined for a presetName, than default limit
 321  is used.\r
 322 <P>\r
 323 <DD><DL>\r
 324 <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/Disembl.html" title="class in compbio.runner.disorder">Disembl</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/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;</CODE></DL>\r
 325 </DD>\r
 326 <DD><DL>\r
 327 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
 328             any sequence validity checks. Nor does it checks whether the
 329             sequences names are unique. It is responsibility of the caller
 330             to validate this information<DD><CODE>preset</CODE> - A list of Options\r
 331 <DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
 332 <DT><B>Throws:</B>\r
 333 <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
 334              given web service, e.g. JABAWS is deployed on Windows and
 335              Mafft service is called\r
 336 <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
 337              exceeds what is defined by the limit\r
 338 <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
 339              following reasons: 1) The number of sequences in the
 340              submission or their average length is greater then defined by
 341              the default Limit. 2) Any problems on the server side e.g. it
 342              is misconfigured or malfunction, is reported via this
 343              exception. In the first case the information on the limit
 344              could be obtained from an exception.\r
 345 <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
 346              supported, 2) The value of the option is defined outside the
 347              boundaries. In both cases exception object contain the
 348              information on the violating Option.</DL>\r
 349 </DD>\r
 350 </DL>\r
 351 <!-- ========= END OF CLASS DATA ========= -->\r
 352 <HR>\r
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 364   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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 382 &nbsp;<A HREF="../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
 383 &nbsp;<A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
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