git://source.jalview.org / jabaws.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
remove old datamodel javadoc
[jabaws.git] / website / full_javadoc / index-files / index-5.html
diff --git a/website/full_javadoc/index-files/index-5.html b/website/full_javadoc/index-files/index-5.html
index 46a4b47..694143c 100644 (file)
--- a/website/full_javadoc/index-files/index-5.html
+++ b/website/full_javadoc/index-files/index-5.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
 <TITLE>\r
 E-Index\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-08-12">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -95,6 +95,18 @@ Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignmen
 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Range.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Score.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 <DD>&nbsp;\r
@@ -109,7 +121,7 @@ Method in class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" tit
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/conf/_Key.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/engine/FilePuller.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 <DD>&nbsp;\r
@@ -137,15 +149,24 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html"
 <DT><A HREF="../compbio/metadata/ValueConstrain.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/pipeline/_jpred/Hit.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Hit.html" title="class in compbio.pipeline._jpred">Hit</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/pipeline/_jpred/PScore.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/collector/JobStat.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#ERROR"><B>ERROR</B></A> - \r
+Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><B>Executable</B></A>&lt;<A HREF="../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>Interface to a native executable.<DT><A HREF="../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><B>Executable.ExecProvider</B></A> - Enum in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local"><B>ExecutableWrapper</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)"><B>ExecutableWrapper(ConfiguredExecutable&lt;?&gt;, String)</B></A> - \r
 Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#execute(java.lang.Runnable)"><B>execute(Runnable)</B></A> - \r
-Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
-<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()"><B>executeJob()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
 <DD>&nbsp;\r
@@ -155,6 +176,30 @@ Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunne
 <DT><A HREF="../compbio/engine/SyncExecutor.html#executeJob()"><B>executeJob()</B></A> - \r
 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 <DD>Execute the job\r
+<DT><A HREF="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector"><B>ExecutionStatCollector</B></A> - Class in <A HREF="../compbio/stat/collector/package-summary.html">compbio.stat.collector</A><DD>Number of runs of each WS = number of folders with name
+ 
+ Number of successful runs = all runs with no result file
+ 
+ Per period of time = limit per file creating time Runtime (avg/max) =
+ 
+ started time - finished time
+ 
+ Task & result size = result.size
+ 
+ Abandoned runs - not collected runs
+ 
+ Cancelled runs - cancelled
+ 
+ Cluster vs local runs
+ 
+ Reasons for failure = look in the err out?
+ 
+ 
+ Metadata required:
+ 
+ work directory for local and cluster tasks = from Helper or cmd parameter.<DT><A HREF="../compbio/stat/collector/ExecutionStatCollector.html#ExecutionStatCollector(java.lang.String, int)"><B>ExecutionStatCollector(String, int)</B></A> - \r
+Constructor for class compbio.stat.collector.<A HREF="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</A>\r
+<DD>List subdirectories in the job directory\r
 </DL>\r
 <HR>\r
 \r