website/full_javadoc/index-files/index-15.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_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
   6 <TITLE>\r
   7 O-Index\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\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="O-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-14.html"><B>PREV LETTER</B></A>&nbsp;\r
  59 &nbsp;<A HREF="index-16.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-15.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="index-15.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="_O_"><!-- --></A><H2>\r
  83 <B>O</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><B>OB</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>TODO this needs fixing! Executable does not work<DT><A HREF="../compbio/runner/_impl/OB.html#OB()"><B>OB()</B></A> - \r
  86 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
  87 <DD>&nbsp;\r
  88 <DT><A HREF="../compbio/runner/_impl/OB.html#OB(java.lang.String)"><B>OB(String)</B></A> - \r
  89 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#openInputStream(java.lang.String)"><B>openInputStream(String)</B></A> - \r
  92 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
  93 <DD>Reads and parses Fasta or Clustal formatted file into a list of
  94  FastaSequence objects\r
  95 <DT><A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><B>Option</B></A>&lt;<A HREF="../compbio/metadata/Option.html" title="type parameter in Option">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Command line option/flag or multiple exclusive options with no value.<DT><A HREF="../compbio/metadata/Option.html#Option(java.lang.String, java.lang.String)"><B>Option(String, String)</B></A> - \r
  96 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
  97 <DD>&nbsp;\r
  98 <DT><A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><B>OptionCombinator</B></A> - Class in <A HREF="../compbio/runner/package-summary.html">compbio.runner</A><DD>This class solve the following problems.<DT><A HREF="../compbio/runner/OptionCombinator.html#OptionCombinator(compbio.metadata.RunnerConfig)"><B>OptionCombinator(RunnerConfig&lt;? extends Executable&lt;?&gt;&gt;)</B></A> - \r
  99 Constructor for class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 100 <DD>&nbsp;\r
 101 <DT><A HREF="../compbio/runner/OptionCombinator.html#optionsToCommandString(java.util.List)"><B>optionsToCommandString(List&lt;Option&lt;?&gt;&gt;)</B></A> - \r
 102 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 103 <DD>&nbsp;\r
 104 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#OUTPUT"><B>OUTPUT</B></A> - \r
 105 Static variable 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 </DL>\r
 108 <HR>\r
 109 \r
 110 \r
 111 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 112 <A NAME="navbar_bottom"><!-- --></A>\r
 113 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 114 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 115 <TR>\r
 116 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 117 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 118 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 119   <TR ALIGN="center" VALIGN="top">\r
 120   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 121   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
 122   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
 123   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
 124   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 125   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 126   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
 127   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 128   </TR>\r
 129 </TABLE>\r
 130 </TD>\r
 131 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 132 </EM>\r
 133 </TD>\r
 134 </TR>\r
 135 \r
 136 <TR>\r
 137 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 138 &nbsp;<A HREF="index-14.html"><B>PREV LETTER</B></A>&nbsp;\r
 139 &nbsp;<A HREF="index-16.html"><B>NEXT LETTER</B></A></FONT></TD>\r
 140 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 141   <A HREF="../index.html?index-filesindex-15.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 142 &nbsp;<A HREF="index-15.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 143 &nbsp;<SCRIPT type="text/javascript">\r
 144   <!--\r
 145   if(window==top) {\r
 146     document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
 147   }\r
 148   //-->\r
 149 </SCRIPT>\r
 150 <NOSCRIPT>\r
 151   <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
 152 </NOSCRIPT>\r
 153 \r
 154 \r
 155 </FONT></TD>\r
 156 </TR>\r
 157 </TABLE>\r
 158 <A NAME="skip-navbar_bottom"></A>\r
 159 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 160 \r
 161 <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
 162 \r
 163 </BODY>\r
 164 </HTML>\r