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 16:46:49 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="Program";
\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"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
\r
42 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
\r
43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Program.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
\r
44 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>
\r
59 <A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
61 <A HREF="../../../index.html?compbio/data/sequence/Program.html" target="_top"><B>FRAMES</B></A>
\r
62 <A HREF="Program.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 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
79 SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>
\r
80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
81 DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>
\r
84 <A NAME="skip-navbar_top"></A>
\r
85 <!-- ========= END OF TOP NAVBAR ========= -->
\r
88 <!-- ======== START OF CLASS DATA ======== -->
\r
91 compbio.data.sequence</FONT>
\r
96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by ">java.lang.Enum<<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>>
\r
97 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Program</B>
\r
100 <DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable, java.lang.Comparable<<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>></DD>
\r
104 <DT><PRE>public enum <B>Program</B><DT>extends java.lang.Enum<<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>></DL>
\r
108 Programmes that can produce alignments
\r
113 <DT><B>Author:</B></DT>
\r
119 <!-- =========== ENUM CONSTANT SUMMARY =========== -->
\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
127 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
128 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#CLUSTAL">CLUSTAL</A></B></CODE>
\r
131 ClustalW</TD>
\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
137 Mafft</TD>
\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
143 Muscle</TD>
\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
149 Probcons</TD>
\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
155 Tcoffee</TD>
\r
159 <!-- ========== METHOD SUMMARY =========== -->
\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
167 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
169 <CODE>static <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>(java.lang.String name)</CODE>
\r
173 Returns the enum constant of this type with the specified name.</TD>
\r
175 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
176 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
177 <CODE>static <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
181 Returns an array containing the constants of this enum type, in
182 the order they are declared.</TD>
\r
185 <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.Enum</B></TH>
\r
190 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
191 <TD><CODE>compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf</CODE></TD>
\r
194 <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.Object</B></TH>
\r
199 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
200 <TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>
\r
206 <!-- ============ ENUM CONSTANT DETAIL =========== -->
\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
216 <A NAME="CLUSTAL"><!-- --></A><H3>
\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
228 <A NAME="MAFFT"><!-- --></A><H3>
\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
240 <A NAME="MUSCLE"><!-- --></A><H3>
\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
252 <A NAME="Tcoffee"><!-- --></A><H3>
\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
264 <A NAME="Probcons"><!-- --></A><H3>
\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
275 <!-- ============ METHOD DETAIL ========== -->
\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
285 <A NAME="values()"><!-- --></A><H3>
\r
288 public static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[] <B>values</B>()</PRE>
\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:
294 for (Program c : Program.values())
295 System.out.println(c);
300 <DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
301 the order they are declared</DL>
\r
306 <A NAME="valueOf(java.lang.String)"><!-- --></A><H3>
\r
309 public static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>valueOf</B>(java.lang.String name)</PRE>
\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
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
320 <DD><CODE>java.lang.IllegalArgumentException</CODE> - if this enum type has no constant
321 with the specified name
\r
322 <DD><CODE>java.lang.NullPointerException</CODE> - if the argument is null</DL>
\r
325 <!-- ========= END OF CLASS DATA ========= -->
\r
329 <!-- ======= START OF BOTTOM NAVBAR ====== -->
\r
330 <A NAME="navbar_bottom"><!-- --></A>
\r
331 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
\r
332 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
\r
334 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
\r
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> </TD>
\r
339 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
\r
340 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
\r
341 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Program.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
\r
342 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
\r
343 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
\r
344 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
\r
345 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
\r
349 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
\r
355 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
356 <A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>
\r
357 <A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
\r
358 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
359 <A HREF="../../../index.html?compbio/data/sequence/Program.html" target="_top"><B>FRAMES</B></A>
\r
360 <A HREF="Program.html" target="_top"><B>NO FRAMES</B></A>
\r
361 <SCRIPT type="text/javascript">
\r
364 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
\r
369 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
\r
376 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
377 SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>
\r
378 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
379 DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>
\r
382 <A NAME="skip-navbar_bottom"></A>
\r
383 <!-- ======== END OF BOTTOM NAVBAR ======= -->
\r