website/dm_javadoc/compbio/data/sequence/Program.html

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   7 Program\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  81 DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  89 <H2>\r
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  91 compbio.data.sequence</FONT>\r
  92 <BR>\r
  93 Enum Program</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 "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A>&lt;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Program</B>\r
  98 </PRE>\r
  99 <DL>\r
 100 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public enum <B>Program</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&gt;</DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 The list of programmes that can produce alignments\r
 109 <P>\r
 110 \r
 111 <P>\r
 112 <DL>\r
 113 <DT><B>Author:</B></DT>\r
 114   <DD>pvtroshin</DD>\r
 115 </DL>\r
 116 <HR>\r
 117 \r
 118 <P>\r
 119 <!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
 120 \r
 121 <A NAME="enum_constant_summary"><!-- --></A>\r
 122 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 123 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 124 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 125 <B>Enum Constant Summary</B></FONT></TH>\r
 126 </TR>\r
 127 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 128 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#CLUSTAL">CLUSTAL</A></B></CODE>\r
 129 \r
 130 <BR>\r
 131 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ClustalW</TD>\r
 132 </TR>\r
 133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 134 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#MAFFT">MAFFT</A></B></CODE>\r
 135 \r
 136 <BR>\r
 137 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Mafft</TD>\r
 138 </TR>\r
 139 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 140 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#MUSCLE">MUSCLE</A></B></CODE>\r
 141 \r
 142 <BR>\r
 143 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Muscle</TD>\r
 144 </TR>\r
 145 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 146 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#Probcons">Probcons</A></B></CODE>\r
 147 \r
 148 <BR>\r
 149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Probcons</TD>\r
 150 </TR>\r
 151 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 152 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#Tcoffee">Tcoffee</A></B></CODE>\r
 153 \r
 154 <BR>\r
 155 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Tcoffee</TD>\r
 156 </TR>\r
 157 </TABLE>\r
 158 &nbsp;\r
 159 <!-- ========== METHOD SUMMARY =========== -->\r
 160 \r
 161 <A NAME="method_summary"><!-- --></A>\r
 162 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 163 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 164 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 165 <B>Method Summary</B></FONT></TH>\r
 166 </TR>\r
 167 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 169 <CODE>static&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
 170 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#valueOf(java.lang.String)">valueOf</A></B>(<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>&nbsp;name)</CODE>\r
 171 \r
 172 <BR>\r
 173 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
 174 </TR>\r
 175 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 176 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 177 <CODE>static&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[]</CODE></FONT></TD>\r
 178 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#values()">values</A></B>()</CODE>\r
 179 \r
 180 <BR>\r
 181 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
 182 the order they are declared.</TD>\r
 183 </TR>\r
 184 </TABLE>\r
 185 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
 186 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 187 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 188 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A></B></TH>\r
 189 </TR>\r
 190 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 191 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.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/Enum.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.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/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.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/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></TD>\r
 192 </TR>\r
 193 </TABLE>\r
 194 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 195 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 196 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 197 <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
 198 </TR>\r
 199 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 200 <TD><CODE><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#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#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
 201 </TR>\r
 202 </TABLE>\r
 203 &nbsp;\r
 204 <P>\r
 205 \r
 206 <!-- ============ ENUM CONSTANT DETAIL =========== -->\r
 207 \r
 208 <A NAME="enum_constant_detail"><!-- --></A>\r
 209 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 210 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 211 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 212 <B>Enum Constant Detail</B></FONT></TH>\r
 213 </TR>\r
 214 </TABLE>\r
 215 \r
 216 <A NAME="CLUSTAL"><!-- --></A><H3>\r
 217 CLUSTAL</H3>\r
 218 <PRE>\r
 219 public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>CLUSTAL</B></PRE>\r
 220 <DL>\r
 221 <DD>ClustalW\r
 222 <P>\r
 223 <DL>\r
 224 </DL>\r
 225 </DL>\r
 226 <HR>\r
 227 \r
 228 <A NAME="MAFFT"><!-- --></A><H3>\r
 229 MAFFT</H3>\r
 230 <PRE>\r
 231 public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>MAFFT</B></PRE>\r
 232 <DL>\r
 233 <DD>Mafft\r
 234 <P>\r
 235 <DL>\r
 236 </DL>\r
 237 </DL>\r
 238 <HR>\r
 239 \r
 240 <A NAME="MUSCLE"><!-- --></A><H3>\r
 241 MUSCLE</H3>\r
 242 <PRE>\r
 243 public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>MUSCLE</B></PRE>\r
 244 <DL>\r
 245 <DD>Muscle\r
 246 <P>\r
 247 <DL>\r
 248 </DL>\r
 249 </DL>\r
 250 <HR>\r
 251 \r
 252 <A NAME="Tcoffee"><!-- --></A><H3>\r
 253 Tcoffee</H3>\r
 254 <PRE>\r
 255 public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>Tcoffee</B></PRE>\r
 256 <DL>\r
 257 <DD>Tcoffee\r
 258 <P>\r
 259 <DL>\r
 260 </DL>\r
 261 </DL>\r
 262 <HR>\r
 263 \r
 264 <A NAME="Probcons"><!-- --></A><H3>\r
 265 Probcons</H3>\r
 266 <PRE>\r
 267 public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>Probcons</B></PRE>\r
 268 <DL>\r
 269 <DD>Probcons\r
 270 <P>\r
 271 <DL>\r
 272 </DL>\r
 273 </DL>\r
 274 \r
 275 <!-- ============ METHOD DETAIL ========== -->\r
 276 \r
 277 <A NAME="method_detail"><!-- --></A>\r
 278 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 279 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 280 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 281 <B>Method Detail</B></FONT></TH>\r
 282 </TR>\r
 283 </TABLE>\r
 284 \r
 285 <A NAME="values()"><!-- --></A><H3>\r
 286 values</H3>\r
 287 <PRE>\r
 288 public static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[] <B>values</B>()</PRE>\r
 289 <DL>\r
 290 <DD>Returns an array containing the constants of this enum type, in
 291 the order they are declared.  This method may be used to iterate
 292 over the constants as follows:
 293 <pre>
 294 for (Program c : Program.values())
 295 &nbsp;   System.out.println(c);
 296 </pre>\r
 297 <P>\r
 298 <DD><DL>\r
 299 \r
 300 <DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
 301 the order they are declared</DL>\r
 302 </DD>\r
 303 </DL>\r
 304 <HR>\r
 305 \r
 306 <A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
 307 valueOf</H3>\r
 308 <PRE>\r
 309 public static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>valueOf</B>(<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>&nbsp;name)</PRE>\r
 310 <DL>\r
 311 <DD>Returns the enum constant of this type with the specified name.
 312 The string must match <I>exactly</I> an identifier used to declare an
 313 enum constant in this type.  (Extraneous whitespace characters are
 314 not permitted.)\r
 315 <P>\r
 316 <DD><DL>\r
 317 <DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
 318 <DT><B>Returns:</B><DD>the enum constant with the specified name\r
 319 <DT><B>Throws:</B>\r
 320 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
 321 with the specified name\r
 322 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the argument is null</DL>\r
 323 </DD>\r
 324 </DL>\r
 325 <!-- ========= END OF CLASS DATA ========= -->\r
 326 <HR>\r
 327 \r
 328 \r
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 335 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 336 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 337   <TR ALIGN="center" VALIGN="top">\r
 338   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 339   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 340   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 341   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Program.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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