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remove old datamodel javadoc
[jabaws.git] / website / full_javadoc / index-files / index-12.html
diff --git a/website/full_javadoc/index-files/index-12.html b/website/full_javadoc/index-files/index-12.html
index 570fd96..4afad04 100644 (file)
--- a/website/full_javadoc/index-files/index-12.html
+++ b/website/full_javadoc/index-files/index-12.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
 L-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
@@ -85,12 +85,12 @@ function windowTitle()
 <DT><A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>Limit</B></A>&lt;<A HREF="../compbio/metadata/Limit.html" title="type parameter in Limit">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A value object containing a maximum number of sequences and a maximum average
  sequence length for a preset.<DT><A HREF="../compbio/metadata/Limit.html#Limit(int, int, java.lang.String)"><B>Limit(int, int, String)</B></A> - \r
 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>&nbsp;\r
+<DD>Instantiate the limit\r
 <DT><A HREF="../compbio/metadata/Limit.html#Limit(int, int, java.lang.String, boolean)"><B>Limit(int, int, String, boolean)</B></A> - \r
 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>LimitExceededException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Thrown if the task larger in size that the limit that applies to the
- calculation.<DT><A HREF="../compbio/metadata/LimitExceededException.html#LimitExceededException(java.lang.String)"><B>LimitExceededException(String)</B></A> - \r
+<DT><A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>LimitExceededException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>This exception is thrown if the task larger in size that the limit that
+ applies to the calculation.<DT><A HREF="../compbio/metadata/LimitExceededException.html#LimitExceededException(java.lang.String)"><B>LimitExceededException(String)</B></A> - \r
 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>LimitExceededExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#LimitExceededExceptionBean()"><B>LimitExceededExceptionBean()</B></A> - \r
@@ -102,7 +102,7 @@ Constructor for class compbio.metadata.<A HREF="../compbio/metadata/LimitsManage
 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#load(java.io.InputStream)"><B>load(InputStream)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><B>LoadBalancer</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/Util.html#loadExecutable(java.lang.String)"><B>loadExecutable(String)</B></A> - \r
+<DT><A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><B>LoadBalancer</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>This class decides where to execute the job.<DT><A HREF="../compbio/engine/client/Util.html#loadExecutable(java.lang.String)"><B>loadExecutable(String)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
@@ -125,7 +125,7 @@ Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.h
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET"><B>LOCAL_ENGINE_LIMIT_PRESET</B></A> - \r
 Static variable in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
 <DD>&nbsp;\r
@@ -138,14 +138,23 @@ Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/Loca
 <DT><A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local"><B>LocalExecutorService</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local"><B>LocalRunner</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/LocalRunner.html#LocalRunner(compbio.engine.client.ConfiguredExecutable)"><B>LocalRunner(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String)"><B>log(Logger, WebServiceContext, String)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/WSUtil.html#log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, java.lang.String)"><B>log(Logger, WebServiceContext, String, String)</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html#LONG_TIME_LIMIT"><B>LONG_TIME_LIMIT</B></A> - \r
-Static variable in class compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee">_QueueConstraints</A>\r
+<DT><A HREF="../compbio/runner/Util.html#log"><B>log</B></A> - \r
+Static variable in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/_WSLogger.html#log(compbio.util.Timer, java.lang.String)"><B>log(Timer, String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/ws/server/_WSLogger.html#log(compbio.util.Timer, java.lang.String, java.lang.String)"><B>log(Timer, String, String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/ws/server/_WSLogger.html#logAll(compbio.util.Timer, java.lang.String)"><B>logAll(Timer, String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/ws/server/_WSLogger.html#logFine(compbio.util.Timer, java.lang.String)"><B>logFine(Timer, String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/Disembl.html#LOOPS_EXPECTATION_THRESHOLD"><B>LOOPS_EXPECTATION_THRESHOLD</B></A> - \r
+Variable in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
 <DD>&nbsp;\r
 </DL>\r
 <HR>\r