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79 SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.ws.server</FONT>
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93 Class _MsaService<T></H2>
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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>
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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>
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97 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server._MsaService<T></B>
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100 <DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - </DL>
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103 <DT><PRE>public abstract class <B>_MsaService<T></B><DT>extends <A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A></DL>
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107 TODO to complete after the approach is tested with SequenceAnnotation!
109 Common methods for all SequenceAnnotation web services
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114 <DT><B>Since:</B></DT>
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116 <DT><B>Version:</B></DT>
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117 <DD>1.0 June 2011</DD>
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118 <DT><B>Author:</B></DT>
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125 <!-- ========== METHOD SUMMARY =========== -->
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131 <B>Method Summary</B></FONT></TH>
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133 <TR BGCOLOR="white" CLASS="TableRowColor">
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134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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135 <CODE> <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>
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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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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139 </TD>
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141 <TR BGCOLOR="white" CLASS="TableRowColor">
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142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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143 <CODE> <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>
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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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>>> options)</CODE>
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148 </TD>
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150 <TR BGCOLOR="white" CLASS="TableRowColor">
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151 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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152 <CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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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> jobId)</CODE>
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156 </TD>
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158 <TR BGCOLOR="white" CLASS="TableRowColor">
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159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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160 <CODE> <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>
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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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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162 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>> preset)</CODE>
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165 </TD>
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167 <TR BGCOLOR="white" CLASS="TableRowColor">
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168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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169 <CODE> <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>
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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> jobId,
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171 long position)</CODE>
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174 Assume statistics is not supported</TD>
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177 <A NAME="methods_inherited_from_class_compbio.ws.server.GenericMetadataService"><!-- --></A>
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178 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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179 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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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>
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182 <TR BGCOLOR="white" CLASS="TableRowColor">
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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>
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186 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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187 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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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>
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204 <B>Method Detail</B></FONT></TH>
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208 <A NAME="align(java.util.List)"><!-- --></A><H3>
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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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)
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212 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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217 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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222 <A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>
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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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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226 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>> preset)
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227 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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228 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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233 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE>
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234 <DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE></DL>
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239 <A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>
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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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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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><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>>> options)
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244 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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245 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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250 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE>
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251 <DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE></DL>
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256 <A NAME="getResult(java.lang.String)"><!-- --></A><H3>
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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> jobId)
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260 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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265 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
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270 <A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>
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271 pullExecStatistics</H3>
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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> jobId,
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274 long position)</PRE>
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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>
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277 <DD>Assume statistics is not supported
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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>
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284 <DT><B>Returns:</B><DD>ChunkHolder</DL>
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