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Re-formatting the file
[jabaws.git] / website / full_javadoc / index-files / index-19.html
diff --git a/website/full_javadoc/index-files/index-19.html b/website/full_javadoc/index-files/index-19.html
index 134ddda..80a3719 100644 (file)
--- a/website/full_javadoc/index-files/index-19.html
+++ b/website/full_javadoc/index-files/index-19.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 Wed Dec 07 12:30:43 GMT 2011 -->\r
 <TITLE>\r
 T-Index\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-12-07">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -85,12 +85,45 @@ function windowTitle()
 <DT><A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa"><B>Tcoffee</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/Tcoffee.html#Tcoffee()"><B>Tcoffee()</B></A> - \r
 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/Services.html#TCOFFEE_INFO"><B>TCOFFEE_INFO</B></A> - \r
+Static variable in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><B>TcoffeeWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#TcoffeeWS()"><B>TcoffeeWS()</B></A> - \r
 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#termSignal()"><B>termSignal()</B></A> - \r
 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/TestAllServices.html" title="class in compbio.data.msa.jaxws"><B>TestAllServices</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/TestAllServices.html#TestAllServices()"><B>TestAllServices()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServices.html" title="class in compbio.data.msa.jaxws">TestAllServices</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html#testAllServices()"><B>testAllServices()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
+<DD>Test all JABAWS services on the server\r
+<DT><A HREF="../compbio/ws/server/RegistryWS.html#testAllServices()"><B>testAllServices()</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
+<DD>TODO improve reporting.\r
+<DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws"><B>TestAllServicesResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html#TestAllServicesResponse()"><B>TestAllServicesResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws"><B>TestService</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/TestService.html#TestService()"><B>TestService()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html#testService(compbio.ws.client.Services)"><B>testService(Services)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
+<DD>Test a particular service\r
+<DT><A HREF="../compbio/ws/client/Jws2Client.html#testService(java.lang.String, compbio.ws.client.Services, java.io.PrintWriter)"><B>testService(String, Services, PrintWriter)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
+<DD>Asks registry to test the service on the host hostname\r
+<DT><A HREF="../compbio/ws/server/RegistryWS.html#testService(compbio.ws.client.Services)"><B>testService(Services)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws"><B>TestServiceResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html#TestServiceResponse()"><B>TestServiceResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Range.html#to"><B>to</B></A> - \r
+Variable 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/metadata/Option.html#toCommand(java.lang.String)"><B>toCommand(String)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 <DD>Convert the option to the command string.\r
@@ -103,6 +136,12 @@ Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignmen
 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#toString()"><B>toString()</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>Same as oneLineFasta\r
+<DT><A HREF="../compbio/data/sequence/Range.html#toString()"><B>toString()</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#toString()"><B>toString()</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/engine/client/CommandBuilder.html#toString()"><B>toString()</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
@@ -120,10 +159,10 @@ Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#toString()"><B>toString()</B></A> - \r
 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
-<DD>&nbsp;\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 <DT><A HREF="../compbio/engine/conf/_Key.html#toString()"><B>toString()</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#toString()"><B>toString()</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
@@ -157,9 +196,30 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html"
 <DT><A HREF="../compbio/metadata/ValueConstrain.html#toString()"><B>toString()</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#toString()"><B>toString()</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#toString()"><B>toString()</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#toString()"><B>toString()</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/collector/StatProcessor.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/ServiceTestResult.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/ServiceTestResult.html" title="class in compbio.stat.servlet">ServiceTestResult</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#toString()"><B>toString()</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/ws/client/Services.html#toString(java.util.Set)"><B>toString(Set&lt;Services&gt;)</B></A> - \r
+Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util"><B>Totals</B></A> - Class in <A HREF="../compbio/stat/servlet/util/package-summary.html">compbio.stat.servlet.util</A><DD>&nbsp;<DT><A HREF="../compbio/stat/servlet/util/Totals.html#Totals()"><B>Totals()</B></A> - \r
+Constructor for class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
+<DD>&nbsp;\r
 </DL>\r
 <HR>\r
 \r