website/full_javadoc/compbio/runner/_impl/Environment.html

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   7 Environment\r
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  10 <META NAME="date" CONTENT="2011-08-12">\r
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  16 {\r
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  18         parent.document.title="Environment";\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  89 <H2>\r
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  91 compbio.runner._impl</FONT>\r
  92 <BR>\r
  93 Class Environment</H2>\r
  94 <PRE>\r
  95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
  96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.Environment</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public final class <B>Environment</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
 101 </PRE>\r
 102 \r
 103 <P>\r
 104 This is utility class to encapsulate environmental variables like directory paths\r
 105 <P>\r
 106 \r
 107 <P>\r
 108 <DL>\r
 109 <DT><B>Author:</B></DT>\r
 110   <DD>pvtroshin</DD>\r
 111 </DL>\r
 112 <HR>\r
 113 \r
 114 <P>\r
 115 \r
 116 <!-- ========== METHOD SUMMARY =========== -->\r
 117 \r
 118 <A NAME="method_summary"><!-- --></A>\r
 119 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 120 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 121 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 122 <B>Method Summary</B></FONT></TH>\r
 123 </TR>\r
 124 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 125 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 126 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 127 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Environment.html#getBlastBinDir()">getBlastBinDir</A></B>()</CODE>\r
 128 \r
 129 <BR>\r
 130 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 131 </TR>\r
 132 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 133 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 134 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 135 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Environment.html#getBlastDatabasesDir()">getBlastDatabasesDir</A></B>()</CODE>\r
 136 \r
 137 <BR>\r
 138 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 139 </TR>\r
 140 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 141 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 142 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 143 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Environment.html#getRPSBlastDatabasesDir()">getRPSBlastDatabasesDir</A></B>()</CODE>\r
 144 \r
 145 <BR>\r
 146 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 147 </TR>\r
 148 </TABLE>\r
 149 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 150 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 151 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 152 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
 153 </TR>\r
 154 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 155 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
 156 </TR>\r
 157 </TABLE>\r
 158 &nbsp;\r
 159 <P>\r
 160 \r
 161 <!-- ============ METHOD DETAIL ========== -->\r
 162 \r
 163 <A NAME="method_detail"><!-- --></A>\r
 164 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 165 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 166 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 167 <B>Method Detail</B></FONT></TH>\r
 168 </TR>\r
 169 </TABLE>\r
 170 \r
 171 <A NAME="getBlastBinDir()"><!-- --></A><H3>\r
 172 getBlastBinDir</H3>\r
 173 <PRE>\r
 174 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getBlastBinDir</B>()</PRE>\r
 175 <DL>\r
 176 <DD><DL>\r
 177 </DL>\r
 178 </DD>\r
 179 </DL>\r
 180 <HR>\r
 181 \r
 182 <A NAME="getBlastDatabasesDir()"><!-- --></A><H3>\r
 183 getBlastDatabasesDir</H3>\r
 184 <PRE>\r
 185 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getBlastDatabasesDir</B>()</PRE>\r
 186 <DL>\r
 187 <DD><DL>\r
 188 </DL>\r
 189 </DD>\r
 190 </DL>\r
 191 <HR>\r
 192 \r
 193 <A NAME="getRPSBlastDatabasesDir()"><!-- --></A><H3>\r
 194 getRPSBlastDatabasesDir</H3>\r
 195 <PRE>\r
 196 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getRPSBlastDatabasesDir</B>()</PRE>\r
 197 <DL>\r
 198 <DD><DL>\r
 199 </DL>\r
 200 </DD>\r
 201 </DL>\r
 202 <!-- ========= END OF CLASS DATA ========= -->\r
 203 <HR>\r
 204 \r
 205 \r
 206 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 207 <A NAME="navbar_bottom"><!-- --></A>\r
 208 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 209 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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 211 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 212 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 213 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 214   <TR ALIGN="center" VALIGN="top">\r
 215   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 216   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 217   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 218   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Environment.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 219   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 220   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 221   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 222   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 223   </TR>\r
 224 </TABLE>\r
 225 </TD>\r
 226 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 227 </EM>\r
 228 </TD>\r
 229 </TR>\r
 230 \r
 231 <TR>\r
 232 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 233 &nbsp;<A HREF="../../../compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
 234 &nbsp;<A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
 235 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 236   <A HREF="../../../index.html?compbio/runner/_impl/Environment.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 237 &nbsp;<A HREF="Environment.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 238 &nbsp;<SCRIPT type="text/javascript">\r
 239   <!--\r
 240   if(window==top) {\r
 241     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 242   }\r
 243   //-->\r
 244 </SCRIPT>\r
 245 <NOSCRIPT>\r
 246   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 247 </NOSCRIPT>\r
 248 \r
 249 \r
 250 </FONT></TD>\r
 251 </TR>\r
 252 <TR>\r
 253 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 254   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
 255 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 256 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 257 </TR>\r
 258 </TABLE>\r
 259 <A NAME="skip-navbar_bottom"></A>\r
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