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

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   7 _MsaService\r
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   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\r
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  18         parent.document.title="_MsaService";\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
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  81 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  88 <!-- ======== START OF CLASS DATA ======== -->\r
  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.ws.server</FONT>\r
  92 <BR>\r
  93 Class _MsaService&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._MsaService&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 <HR>\r
 102 <DL>\r
 103 <DT><PRE>public abstract class <B>_MsaService&lt;T&gt;</B><DT>extends <A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A></DL>\r
 104 </PRE>\r
 105 \r
 106 <P>\r
 107 TODO to complete after the approach is tested with SequenceAnnotation!
 108
 109  Common methods for all SequenceAnnotation web services\r
 110 <P>\r
 111 \r
 112 <P>\r
 113 <DL>\r
 114 <DT><B>Since:</B></DT>\r
 115   <DD>2.0</DD>\r
 116 <DT><B>Version:</B></DT>\r
 117   <DD>1.0 June 2011</DD>\r
 118 <DT><B>Author:</B></DT>\r
 119   <DD>pvtroshin</DD>\r
 120 </DL>\r
 121 <HR>\r
 122 \r
 123 <P>\r
 124 \r
 125 <!-- ========== METHOD SUMMARY =========== -->\r
 126 \r
 127 <A NAME="method_summary"><!-- --></A>\r
 128 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 129 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 130 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 131 <B>Method Summary</B></FONT></TH>\r
 132 </TR>\r
 133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 135 <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
 136 <TD><CODE><B><A HREF="../../../compbio/ws/server/_MsaService.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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 137 \r
 138 <BR>\r
 139 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 140 </TR>\r
 141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 143 <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
 144 <TD><CODE><B><A HREF="../../../compbio/ws/server/_MsaService.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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 145             <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/_MsaService.html" title="type parameter in _MsaService">T</A>&gt;&gt;&nbsp;options)</CODE>\r
 146 \r
 147 <BR>\r
 148 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 149 </TR>\r
 150 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 151 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 152 <CODE>&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 153 <TD><CODE><B><A HREF="../../../compbio/ws/server/_MsaService.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>&nbsp;jobId)</CODE>\r
 154 \r
 155 <BR>\r
 156 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 157 </TR>\r
 158 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 160 <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
 161 <TD><CODE><B><A HREF="../../../compbio/ws/server/_MsaService.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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 162             <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>&gt;&nbsp;preset)</CODE>\r
 163 \r
 164 <BR>\r
 165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 166 </TR>\r
 167 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 169 <CODE>&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
 170 <TD><CODE><B><A HREF="../../../compbio/ws/server/_MsaService.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>&nbsp;jobId,\r
 171                    long&nbsp;position)</CODE>\r
 172 \r
 173 <BR>\r
 174 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Assume statistics is not supported</TD>\r
 175 </TR>\r
 176 </TABLE>\r
 177 &nbsp;<A NAME="methods_inherited_from_class_compbio.ws.server.GenericMetadataService"><!-- --></A>\r
 178 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 179 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 180 <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
 181 </TR>\r
 182 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 183 <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></CODE></TD>\r
 184 </TR>\r
 185 </TABLE>\r
 186 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 187 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 188 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 189 <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
 190 </TR>\r
 191 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 192 <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
 193 </TR>\r
 194 </TABLE>\r
 195 &nbsp;\r
 196 <P>\r
 197 \r
 198 <!-- ============ METHOD DETAIL ========== -->\r
 199 \r
 200 <A NAME="method_detail"><!-- --></A>\r
 201 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 202 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 203 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 204 <B>Method Detail</B></FONT></TH>\r
 205 </TR>\r
 206 </TABLE>\r
 207 \r
 208 <A NAME="align(java.util.List)"><!-- --></A><H3>\r
 209 align</H3>\r
 210 <PRE>\r
 211 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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
 212              throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 213 <DL>\r
 214 <DD><DL>\r
 215 \r
 216 <DT><B>Throws:</B>\r
 217 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
 218 </DD>\r
 219 </DL>\r
 220 <HR>\r
 221 \r
 222 <A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
 223 presetAlign</H3>\r
 224 <PRE>\r
 225 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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 226                           <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>&gt;&nbsp;preset)\r
 227                    throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
 228                           <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
 229 <DL>\r
 230 <DD><DL>\r
 231 \r
 232 <DT><B>Throws:</B>\r
 233 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE>\r
 234 <DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE></DL>\r
 235 </DD>\r
 236 </DL>\r
 237 <HR>\r
 238 \r
 239 <A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>\r
 240 customAlign</H3>\r
 241 <PRE>\r
 242 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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 243                           <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/_MsaService.html" title="type parameter in _MsaService">T</A>&gt;&gt;&nbsp;options)\r
 244                    throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
 245                           <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
 246 <DL>\r
 247 <DD><DL>\r
 248 \r
 249 <DT><B>Throws:</B>\r
 250 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE>\r
 251 <DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE></DL>\r
 252 </DD>\r
 253 </DL>\r
 254 <HR>\r
 255 \r
 256 <A NAME="getResult(java.lang.String)"><!-- --></A><H3>\r
 257 getResult</H3>\r
 258 <PRE>\r
 259 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>&nbsp;jobId)\r
 260                     throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 261 <DL>\r
 262 <DD><DL>\r
 263 \r
 264 <DT><B>Throws:</B>\r
 265 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 266 </DD>\r
 267 </DL>\r
 268 <HR>\r
 269 \r
 270 <A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>\r
 271 pullExecStatistics</H3>\r
 272 <PRE>\r
 273 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>&nbsp;jobId,\r
 274                                       long&nbsp;position)</PRE>\r
 275 <DL>\r
 276 <DD><B>Description copied from class: <CODE><A HREF="../../../compbio/ws/server/GenericMetadataService.html#pullExecStatistics(java.lang.String, long)">GenericMetadataService</A></CODE></B></DD>\r
 277 <DD>Assume statistics is not supported\r
 278 <P>\r
 279 <DD><DL>\r
 280 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/ws/server/GenericMetadataService.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE> in class <CODE><A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A></CODE></DL>\r
 281 </DD>\r
 282 <DD><DL>\r
 283 \r
 284 <DT><B>Returns:</B><DD>ChunkHolder</DL>\r
 285 </DD>\r
 286 </DL>\r
 287 <!-- ========= END OF CLASS DATA ========= -->\r
 288 <HR>\r
 289 \r
 290 \r
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