1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
\r
5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->
\r
10 <META NAME="date" CONTENT="2010-02-17">
\r
12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">
\r
14 <SCRIPT type="text/javascript">
\r
15 function windowTitle()
\r
17 if (location.href.indexOf('is-external=true') == -1) {
\r
18 parent.document.title="C-Index";
\r
27 <BODY BGCOLOR="white" onload="windowTitle();">
\r
31 <!-- ========= START OF TOP NAVBAR ======= -->
\r
32 <A NAME="navbar_top"><!-- --></A>
\r
33 <A HREF="#skip-navbar_top" title="Skip navigation links"></A>
\r
34 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
\r
36 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
\r
37 <A NAME="navbar_top_firstrow"><!-- --></A>
\r
38 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
\r
39 <TR ALIGN="center" VALIGN="top">
\r
40 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
\r
41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
\r
42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
\r
43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
\r
44 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
\r
45 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
\r
46 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>
\r
47 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
\r
51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
\r
57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
58 <A HREF="index-2.html"><B>PREV LETTER</B></A>
\r
59 <A HREF="index-4.html"><B>NEXT LETTER</B></A></FONT></TD>
\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
61 <A HREF="../index.html?index-filesindex-3.html" target="_top"><B>FRAMES</B></A>
\r
62 <A HREF="index-3.html" target="_top"><B>NO FRAMES</B></A>
\r
63 <SCRIPT type="text/javascript">
\r
66 document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
\r
71 <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
\r
78 <A NAME="skip-navbar_top"></A>
\r
79 <!-- ========= END OF TOP NAVBAR ========= -->
\r
81 <A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>
\r
82 <A NAME="_C_"><!-- --></A><H2>
\r
85 <DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#call()"><B>call()</B></A> -
\r
86 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>
\r
87 <DD>It is vital that output and error streams are captured immediately for
88 this call() to succeed.
\r
89 <DT><A HREF="../compbio/engine/local/LocalExecutorService.html#canAcceptMoreWork()"><B>canAcceptMoreWork()</B></A> -
\r
90 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>
\r
91 <DD>If the Executor queue is empty
\r
92 <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><B>CancelJob</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#CancelJob()"><B>CancelJob()</B></A> -
\r
93 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>
\r
95 <DT><A HREF="../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> -
\r
96 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>
\r
97 <DD>Stop running job but leave its output untouched
\r
98 <DT><A HREF="../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> -
\r
99 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>
\r
100 <DD>Stop running job.
\r
101 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> -
\r
102 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>
\r
104 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#cancelJob(java.lang.String, compbio.engine.cluster.drmaa.ClusterSession)"><B>cancelJob(String, ClusterSession)</B></A> -
\r
105 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>
\r
107 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#cancelJob()"><B>cancelJob()</B></A> -
\r
108 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
110 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> -
\r
111 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>
\r
113 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#cancelJob(java.util.concurrent.Future, java.lang.String)"><B>cancelJob(Future<ConfiguredExecutable<?>>, String)</B></A> -
\r
114 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>
\r
116 <DT><A HREF="../compbio/engine/local/LocalRunner.html#cancelJob()"><B>cancelJob()</B></A> -
\r
117 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>
\r
119 <DT><A HREF="../compbio/engine/SyncExecutor.html#cancelJob()"><B>cancelJob()</B></A> -
\r
120 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>
\r
121 <DD>Stops running job.
\r
122 <DT><A HREF="../compbio/ws/server/ClustalWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> -
\r
123 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>
\r
125 <DT><A HREF="../compbio/ws/server/MafftWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> -
\r
126 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>
\r
128 <DT><A HREF="../compbio/ws/server/MuscleWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> -
\r
129 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>
\r
131 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> -
\r
132 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>
\r
134 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> -
\r
135 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>
\r
137 <DT><A HREF="../compbio/ws/server/WSUtil.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> -
\r
138 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>
\r
140 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><B>CancelJobResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#CancelJobResponse()"><B>CancelJobResponse()</B></A> -
\r
141 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>
\r
143 <DT><A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Represents a chunk of string data together with the position in a file from
144 where corresponding to of the data.<DT><A HREF="../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)"><B>ChunkHolder(String, long)</B></A> -
\r
145 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>
\r
147 <DT><A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine"><B>Cleaner</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD> <DT><A HREF="../compbio/engine/Cleaner.html#Cleaner()"><B>Cleaner()</B></A> -
\r
148 Constructor for class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>
\r
150 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)"><B>cleanSequence(String)</B></A> -
\r
151 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
\r
152 <DD>Removes all whitespace chars in the sequence string
\r
153 <DT><A HREF="../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> -
\r
154 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>
\r
155 <DD>Remove all files and a job directory for a jobid.
\r
156 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> -
\r
157 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>
\r
159 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#cleanup()"><B>cleanup()</B></A> -
\r
160 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
162 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> -
\r
163 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>
\r
165 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#cleanup(compbio.engine.client.ConfiguredExecutable)"><B>cleanup(ConfiguredExecutable<?>)</B></A> -
\r
166 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>
\r
168 <DT><A HREF="../compbio/engine/local/LocalRunner.html#cleanup()"><B>cleanup()</B></A> -
\r
169 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>
\r
171 <DT><A HREF="../compbio/engine/SyncExecutor.html#cleanup()"><B>cleanup()</B></A> -
\r
172 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>
\r
173 <DD>Clean up after the job
\r
174 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#close()"><B>close()</B></A> -
\r
175 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>
\r
177 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>ClustalAlignmentUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Tools to read and write clustal formated files<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()"><B>ClustalAlignmentUtil()</B></A> -
\r
178 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>
\r
180 <DT><A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>ClustalW</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD> <DT><A HREF="../compbio/runner/msa/ClustalW.html#ClustalW()"><B>ClustalW()</B></A> -
\r
181 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>
\r
183 <DT><A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>ClustalWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD> <DT><A HREF="../compbio/ws/server/ClustalWS.html#ClustalWS()"><B>ClustalWS()</B></A> -
\r
184 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>
\r
186 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#CLUSTER_STAT_IN_SEC"><B>CLUSTER_STAT_IN_SEC</B></A> -
\r
187 Static variable in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>
\r
189 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX"><B>CLUSTER_TASK_ID_PREFIX</B></A> -
\r
190 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>
\r
192 <DT><A HREF="../compbio/engine/Configurator.html#CLUSTER_WORK_DIRECTORY"><B>CLUSTER_WORK_DIRECTORY</B></A> -
\r
193 Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>
\r
195 <DT><A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine"><B>ClusterJobId</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD> <DT><A HREF="../compbio/engine/ClusterJobId.html#ClusterJobId(java.lang.String)"><B>ClusterJobId(String)</B></A> -
\r
196 Constructor for class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>
\r
198 <DT><A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client"><B>ClusterNativeSpecExecutable</B></A><<A HREF="../compbio/engine/client/ClusterNativeSpecExecutable.html" title="type parameter in ClusterNativeSpecExecutable">T</A>> - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD> <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterSession</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD> <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterUtil</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD> <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#ClusterUtil()"><B>ClusterUtil()</B></A> -
\r
199 Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>
\r
201 <DT><A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>CommandBuilder</B></A><<A HREF="../compbio/engine/client/CommandBuilder.html" title="type parameter in CommandBuilder">T</A>> - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD> <DT><A HREF="../compbio/engine/client/CommandBuilder.html#CommandBuilder(java.lang.String)"><B>CommandBuilder(String)</B></A> -
\r
202 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>
\r
204 <DT><A HREF="../compbio/engine/FilePuller.html#compareTo(java.util.concurrent.Delayed)"><B>compareTo(Delayed)</B></A> -
\r
205 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>
\r
207 <DT><A HREF="../compbio/data/_structure/package-summary.html"><B>compbio.data._structure</B></A> - package compbio.data._structure<DD> <DT><A HREF="../compbio/data/msa/package-summary.html"><B>compbio.data.msa</B></A> - package compbio.data.msa<DD> <DT><A HREF="../compbio/data/msa/jaxws/package-summary.html"><B>compbio.data.msa.jaxws</B></A> - package compbio.data.msa.jaxws<DD> <DT><A HREF="../compbio/pipeline/_jpred/package-summary.html"><B>compbio.pipeline._jpred</B></A> - package compbio.pipeline._jpred<DD> <DT><A HREF="../compbio/runner/_jpred/package-summary.html"><B>compbio.runner._jpred</B></A> - package compbio.runner._jpred<DD> <DT><A HREF="../compbio/runner/psiblast/package-summary.html"><B>compbio.runner.psiblast</B></A> - package compbio.runner.psiblast<DD> <DT><A HREF="../compbio/ws/client/package-summary.html"><B>compbio.ws.client</B></A> - package compbio.ws.client<DD> <DT><A HREF="../compbio/ws/server/package-summary.html"><B>compbio.ws.server</B></A> - package compbio.ws.server<DD> <DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#confDir"><B>confDir</B></A> -
\r
208 Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>
\r
210 <DT><A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><B>ConfExecutable</B></A><<A HREF="../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>> - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD> <DT><A HREF="../compbio/engine/client/ConfExecutable.html#ConfExecutable(compbio.engine.client.Executable, java.lang.String)"><B>ConfExecutable(Executable<T>, String)</B></A> -
\r
211 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>
\r
213 <DT><A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine"><B>Configurator</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD> <DT><A HREF="../compbio/engine/Configurator.html#Configurator()"><B>Configurator()</B></A> -
\r
214 Constructor for class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>
\r
216 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><B>ConfiguredExecutable</B></A><<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>> - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD> <DT><A HREF="../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)"><B>configureExecutable(Executable<T>)</B></A> -
\r
217 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>
\r
219 <DT><A HREF="../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)"><B>configureExecutable(Executable<T>, List<FastaSequence>)</B></A> -
\r
220 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>
\r
222 <DT><A HREF="../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)"><B>configureExecutable(Executable<T>, Executable.ExecProvider)</B></A> -
\r
223 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>
\r
225 <DT><A HREF="../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Jws2Client.Services)"><B>connect(String, Jws2Client.Services)</B></A> -
\r
226 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>
\r
227 <DD>Connects to a web service by the host and the service name
\r
228 <DT><A HREF="../compbio/engine/client/Util.html#convertToAbsolute(java.lang.String)"><B>convertToAbsolute(String)</B></A> -
\r
229 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>
\r
231 <DT><A HREF="../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><B>copyAndValidateRConfig(RunnerConfig<?>)</B></A> -
\r
232 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
\r
234 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)"><B>countMatchesInSequence(String, String)</B></A> -
\r
235 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>
\r
237 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws"><B>CustomAlign</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#CustomAlign()"><B>CustomAlign()</B></A> -
\r
238 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>
\r
240 <DT><A HREF="../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List<FastaSequence>, List<Option<T>>)</B></A> -
\r
241 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>
\r
242 <DD>Align a list of sequences with options.
\r
243 <DT><A HREF="../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List<FastaSequence>, List<Option<ClustalW>>)</B></A> -
\r
244 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>
\r
246 <DT><A HREF="../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List<FastaSequence>, List<Option<Mafft>>)</B></A> -
\r
247 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>
\r
249 <DT><A HREF="../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List<FastaSequence>, List<Option<Muscle>>)</B></A> -
\r
250 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>
\r
252 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List<FastaSequence>, List<Option<Probcons>>)</B></A> -
\r
253 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>
\r
255 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List<FastaSequence>, List<Option<Tcoffee>>)</B></A> -
\r
256 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>
\r
258 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>CustomAlignResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#CustomAlignResponse()"><B>CustomAlignResponse()</B></A> -
\r
259 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>
\r
265 <!-- ======= START OF BOTTOM NAVBAR ====== -->
\r
266 <A NAME="navbar_bottom"><!-- --></A>
\r
267 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
\r
268 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
\r
270 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
\r
271 <A NAME="navbar_bottom_firstrow"><!-- --></A>
\r
272 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
\r
273 <TR ALIGN="center" VALIGN="top">
\r
274 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
\r
275 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
\r
276 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
\r
277 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
\r
278 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
\r
279 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
\r
280 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>
\r
281 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
\r
285 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
\r
291 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
292 <A HREF="index-2.html"><B>PREV LETTER</B></A>
\r
293 <A HREF="index-4.html"><B>NEXT LETTER</B></A></FONT></TD>
\r
294 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
295 <A HREF="../index.html?index-filesindex-3.html" target="_top"><B>FRAMES</B></A>
\r
296 <A HREF="index-3.html" target="_top"><B>NO FRAMES</B></A>
\r
297 <SCRIPT type="text/javascript">
\r
300 document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
\r
305 <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
\r
312 <A NAME="skip-navbar_bottom"></A>
\r
313 <!-- ======== END OF BOTTOM NAVBAR ======= -->
\r
315 <A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>
\r