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

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   7 SequenceAnnotationService\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
  80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
  81 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  89 <H2>\r
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  91 compbio.ws.server</FONT>\r
  92 <BR>\r
  93 Class SequenceAnnotationService&lt;T&gt;</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 "><B>compbio.ws.server.SequenceAnnotationService&lt;T&gt;</B>\r
  98 </PRE>\r
  99 <DL>\r
 100 <DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - </DL>\r
 101 <DL>\r
 102 <DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</A>, <A HREF="../../../compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server">DisemblWS</A>, <A HREF="../../../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</A>, <A HREF="../../../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server">IUPredWS</A>, <A HREF="../../../compbio/ws/server/JronnWS.html" title="class in compbio.ws.server">JronnWS</A></DD>\r
 103 </DL>\r
 104 <HR>\r
 105 <DL>\r
 106 <DT><PRE>public abstract class <B>SequenceAnnotationService&lt;T&gt;</B><DT>extends <A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A></DL>\r
 107 </PRE>\r
 108 \r
 109 <P>\r
 110 Common methods for all SequenceAnnotation web services\r
 111 <P>\r
 112 \r
 113 <P>\r
 114 <DL>\r
 115 <DT><B>Since:</B></DT>\r
 116   <DD>2.0</DD>\r
 117 <DT><B>Version:</B></DT>\r
 118   <DD>1.0 June 2011</DD>\r
 119 <DT><B>Author:</B></DT>\r
 120   <DD>pvtroshin</DD>\r
 121 </DL>\r
 122 <HR>\r
 123 \r
 124 <P>\r
 125 \r
 126 <!-- ========== METHOD SUMMARY =========== -->\r
 127 \r
 128 <A NAME="method_summary"><!-- --></A>\r
 129 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 130 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 131 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 132 <B>Method Summary</B></FONT></TH>\r
 133 </TR>\r
 134 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 135 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 136 <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
 137 <TD><CODE><B><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#analize(java.util.List)">analize</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)</CODE>\r
 138 \r
 139 <BR>\r
 140 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 141 </TR>\r
 142 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 143 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 144 <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
 145 <TD><CODE><B><A HREF="../../../compbio/ws/server/SequenceAnnotationService.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
 146               <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/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>&gt;&gt;&nbsp;options)</CODE>\r
 147 \r
 148 <BR>\r
 149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 150 </TR>\r
 151 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 152 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 153 <CODE>&nbsp;<A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
 154 <TD><CODE><B><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#getAnnotation(java.lang.String)">getAnnotation</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>&nbsp;jobId)</CODE>\r
 155 \r
 156 <BR>\r
 157 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 158 </TR>\r
 159 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 160 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 161 <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
 162 <TD><CODE><B><A HREF="../../../compbio/ws/server/SequenceAnnotationService.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
 163               <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>&gt;&nbsp;preset)</CODE>\r
 164 \r
 165 <BR>\r
 166 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 167 </TR>\r
 168 </TABLE>\r
 169 &nbsp;<A NAME="methods_inherited_from_class_compbio.ws.server.GenericMetadataService"><!-- --></A>\r
 170 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 171 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 172 <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
 173 </TR>\r
 174 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 175 <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
 176 </TR>\r
 177 </TABLE>\r
 178 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 179 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 180 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 181 <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
 182 </TR>\r
 183 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 184 <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
 185 </TR>\r
 186 </TABLE>\r
 187 &nbsp;\r
 188 <P>\r
 189 \r
 190 <!-- ============ METHOD DETAIL ========== -->\r
 191 \r
 192 <A NAME="method_detail"><!-- --></A>\r
 193 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 194 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 195 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 196 <B>Method Detail</B></FONT></TH>\r
 197 </TR>\r
 198 </TABLE>\r
 199 \r
 200 <A NAME="getAnnotation(java.lang.String)"><!-- --></A><H3>\r
 201 getAnnotation</H3>\r
 202 <PRE>\r
 203 public <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>getAnnotation</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>&nbsp;jobId)\r
 204                            throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 205 <DL>\r
 206 <DD><DL>\r
 207 \r
 208 <DT><B>Throws:</B>\r
 209 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 210 </DD>\r
 211 </DL>\r
 212 <HR>\r
 213 \r
 214 <A NAME="analize(java.util.List)"><!-- --></A><H3>\r
 215 analize</H3>\r
 216 <PRE>\r
 217 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>analize</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
 218                throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
 219                       <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
 220                       <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 221 <DL>\r
 222 <DD><DL>\r
 223 \r
 224 <DT><B>Throws:</B>\r
 225 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE>\r
 226 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE>\r
 227 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
 228 </DD>\r
 229 </DL>\r
 230 <HR>\r
 231 \r
 232 <A NAME="customAnalize(java.util.List, java.util.List)"><!-- --></A><H3>\r
 233 customAnalize</H3>\r
 234 <PRE>\r
 235 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
 236                             <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/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>&gt;&gt;&nbsp;options)\r
 237                      throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
 238                             <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
 239                             <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
 240                             <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
 241 <DL>\r
 242 <DD><DL>\r
 243 \r
 244 <DT><B>Throws:</B>\r
 245 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE>\r
 246 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE>\r
 247 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE>\r
 248 <DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE></DL>\r
 249 </DD>\r
 250 </DL>\r
 251 <HR>\r
 252 \r
 253 <A NAME="presetAnalize(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
 254 presetAnalize</H3>\r
 255 <PRE>\r
 256 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
 257                             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>&gt;&nbsp;preset)\r
 258                      throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
 259                             <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
 260                             <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
 261                             <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
 262 <DL>\r
 263 <DD><DL>\r
 264 \r
 265 <DT><B>Throws:</B>\r
 266 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE>\r
 267 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE>\r
 268 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE>\r
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