website/full_javadoc/index-files/index-5.html

   1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
   2 <!--NewPage-->\r
   3 <HTML>\r
   4 <HEAD>\r
   5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
   6 <TITLE>\r
   7 E-Index\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2010-02-17">\r
  11 \r
  12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
  13 \r
  14 <SCRIPT type="text/javascript">\r
  15 function windowTitle()\r
  16 {\r
  17     if (location.href.indexOf('is-external=true') == -1) {\r
  18         parent.document.title="E-Index";\r
  19     }\r
  20 }\r
  21 </SCRIPT>\r
  22 <NOSCRIPT>\r
  23 </NOSCRIPT>\r
  24 \r
  25 </HEAD>\r
  26 \r
  27 <BODY BGCOLOR="white" onload="windowTitle();">\r
  28 <HR>\r
  29 \r
  30 \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
  35 <TR>\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>&nbsp;</TD>\r
  41   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
  42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
  44   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
  45   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
  46   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
  47   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
  48   </TR>\r
  49 </TABLE>\r
  50 </TD>\r
  51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
  52 </EM>\r
  53 </TD>\r
  54 </TR>\r
  55 \r
  56 <TR>\r
  57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  58 &nbsp;<A HREF="index-4.html"><B>PREV LETTER</B></A>&nbsp;\r
  59 &nbsp;<A HREF="index-6.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-5.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="index-5.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
  63 &nbsp;<SCRIPT type="text/javascript">\r
  64   <!--\r
  65   if(window==top) {\r
  66     document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
  67   }\r
  68   //-->\r
  69 </SCRIPT>\r
  70 <NOSCRIPT>\r
  71   <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
  72 </NOSCRIPT>\r
  73 \r
  74 \r
  75 </FONT></TD>\r
  76 </TR>\r
  77 </TABLE>\r
  78 <A NAME="skip-navbar_top"></A>\r
  79 <!-- ========= END OF TOP NAVBAR ========= -->\r
  80 \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="_E_"><!-- --></A><H2>\r
  83 <B>E</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl"><B>Environment</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>This is utility class to encapsulate environmental variables like directory paths<DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>EnvVariableProcessor</B></A> - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html#EnvVariableProcessor()"><B>EnvVariableProcessor()</B></A> - \r
  86 Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/data/sequence/Alignment.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
  89 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
  90 <DD>Please note that this implementation does not take the order of sequences
  91  into account!\r
  92 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
  93 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
  94 <DD>&nbsp;\r
  95 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
  96 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
  97 <DD>&nbsp;\r
  98 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
  99 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 100 <DD>&nbsp;\r
 101 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 102 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 103 <DD>&nbsp;\r
 104 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 105 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 106 <DD>&nbsp;\r
 107 <DT><A HREF="../compbio/engine/ClusterJobId.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 108 Method in class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
 109 <DD>&nbsp;\r
 110 <DT><A HREF="../compbio/engine/conf/_Key.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 111 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
 112 <DD>&nbsp;\r
 113 <DT><A HREF="../compbio/engine/FilePuller.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 114 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 115 <DD>&nbsp;\r
 116 <DT><A HREF="../compbio/engine/Job.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 117 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 118 <DD>&nbsp;\r
 119 <DT><A HREF="../compbio/metadata/ChunkHolder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 120 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
 121 <DD>&nbsp;\r
 122 <DT><A HREF="../compbio/metadata/Limit.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 123 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 124 <DD>&nbsp;\r
 125 <DT><A HREF="../compbio/metadata/Option.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 126 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 127 <DD>&nbsp;\r
 128 <DT><A HREF="../compbio/metadata/Parameter.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 129 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 130 <DD>&nbsp;\r
 131 <DT><A HREF="../compbio/metadata/Preset.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 132 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 133 <DD>&nbsp;\r
 134 <DT><A HREF="../compbio/metadata/RunnerConfig.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 135 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 136 <DD>&nbsp;\r
 137 <DT><A HREF="../compbio/metadata/ValueConstrain.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 138 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 139 <DD>&nbsp;\r
 140 <DT><A HREF="../compbio/pipeline/_jpred/PScore.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
 141 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>\r
 142 <DD>&nbsp;\r
 143 <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
 144 Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
 145 <DD>&nbsp;\r
 146 <DT><A HREF="../compbio/engine/local/_TrackingExecutor.html#execute(java.lang.Runnable)"><B>execute(Runnable)</B></A> - \r
 147 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
 148 <DD>&nbsp;\r
 149 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()"><B>executeJob()</B></A> - \r
 150 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
 151 <DD>&nbsp;\r
 152 <DT><A HREF="../compbio/engine/local/LocalRunner.html#executeJob()"><B>executeJob()</B></A> - \r
 153 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
 154 <DD>&nbsp;\r
 155 <DT><A HREF="../compbio/engine/SyncExecutor.html#executeJob()"><B>executeJob()</B></A> - \r
 156 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 157 <DD>Execute the job\r
 158 </DL>\r
 159 <HR>\r
 160 \r
 161 \r
 162 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 163 <A NAME="navbar_bottom"><!-- --></A>\r
 164 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 165 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 166 <TR>\r
 167 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 168 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 169 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 170   <TR ALIGN="center" VALIGN="top">\r
 171   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 172   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
 173   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
 174   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
 175   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 176   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 177   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
 178   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 179   </TR>\r
 180 </TABLE>\r
 181 </TD>\r
 182 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 183 </EM>\r
 184 </TD>\r
 185 </TR>\r
 186 \r
 187 <TR>\r
 188 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 189 &nbsp;<A HREF="index-4.html"><B>PREV LETTER</B></A>&nbsp;\r
 190 &nbsp;<A HREF="index-6.html"><B>NEXT LETTER</B></A></FONT></TD>\r
 191 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 192   <A HREF="../index.html?index-filesindex-5.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 193 &nbsp;<A HREF="index-5.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 194 &nbsp;<SCRIPT type="text/javascript">\r
 195   <!--\r
 196   if(window==top) {\r
 197     document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
 198   }\r
 199   //-->\r
 200 </SCRIPT>\r
 201 <NOSCRIPT>\r
 202   <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
 203 </NOSCRIPT>\r
 204 \r
 205 \r
 206 </FONT></TD>\r
 207 </TR>\r
 208 </TABLE>\r
 209 <A NAME="skip-navbar_bottom"></A>\r
 210 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 211 \r
 212 <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
 213 \r
 214 </BODY>\r
 215 </HTML>\r