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

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  10 <META NAME="date" CONTENT="2011-08-12">\r
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  18         parent.document.title="JronnWS";\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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  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.ws.server</FONT>\r
  92 <BR>\r
  93 Class JronnWS</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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>&gt;\r
  98           <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.JronnWS</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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>&gt;, <A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>&lt;<A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>&gt;</DD>\r
 102 </DL>\r
 103 <HR>\r
 104 <DL>\r
 105 <DT><PRE>public class <B>JronnWS</B><DT>extends <A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>&lt;<A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</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/Jronn.html" title="class in compbio.runner.disorder">Jronn</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/JronnWS.html#JronnWS()">JronnWS</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="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
 158 <TD><CODE><B><A HREF="../../../compbio/ws/server/JronnWS.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
 159                    long&nbsp;position)</CODE>\r
 160 \r
 161 <BR>\r
 162 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Assume statistics is not supported</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>, <A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</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></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>, <A HREF="../../../compbio/data/msa/SequenceAnnotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</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></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="JronnWS()"><!-- --></A><H3>\r
 233 JronnWS</H3>\r
 234 <PRE>\r
 235 public <B>JronnWS</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="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>\r
 250 pullExecStatistics</H3>\r
 251 <PRE>\r
 252 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
 253                                       long&nbsp;position)</PRE>\r
 254 <DL>\r
 255 <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
 256 <DD>Assume statistics is not supported\r
 257 <P>\r
 258 <DD><DL>\r
 259 <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><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
 260 </DD>\r
 261 <DD><DL>\r
 262 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read\r
 263 <DT><B>Returns:</B><DD>ChunkHolder<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><CODE>ChunkHolder</CODE></A></DL>\r
 264 </DD>\r
 265 </DL>\r
 266 <!-- ========= END OF CLASS DATA ========= -->\r
 267 <HR>\r
 268 \r
 269 \r
 270 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 271 <A NAME="navbar_bottom"><!-- --></A>\r
 272 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 273 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 274 <TR>\r
 275 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 276 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 277 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 278   <TR ALIGN="center" VALIGN="top">\r
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