Refactored client class to accomodate new WS interface and reduce the complexity
[jabaws.git] / website / dm_javadoc / compbio / data / sequence / class-use / Program.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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
6 <TITLE>\r
7 Uses of Class compbio.data.sequence.Program\r
8 </TITLE>\r
9 \r
10 <META NAME="date" CONTENT="2010-11-24">\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="Uses of Class compbio.data.sequence.Program";\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">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
43   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></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="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&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;PREV&nbsp;\r
59 &nbsp;NEXT</FONT></TD>\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
61   <A HREF="../../../../index.html?compbio/data/sequence/\class-useProgram.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
62 &nbsp;<A HREF="Program.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 <HR>\r
82 <CENTER>\r
83 <H2>\r
84 <B>Uses of Class<br>compbio.data.sequence.Program</B></H2>\r
85 </CENTER>\r
86 \r
87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
90 Packages that use <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></TH>\r
91 </TR>\r
92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
93 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
94 <TD>A data model for multiple sequence alignment web services and utility methods
95  that work on the objects of this model.&nbsp;</TD>\r
96 </TR>\r
97 </TABLE>\r
98 &nbsp;\r
99 <P>\r
100 <A NAME="compbio.data.sequence"><!-- --></A>\r
101 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
102 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
103 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
104 Uses of <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
105 </TR>\r
106 </TABLE>\r
107 &nbsp;\r
108 <P>\r
109 \r
110 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
111 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
112 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></TH>\r
113 </TR>\r
114 <TR BGCOLOR="white" CLASS="TableRowColor">\r
115 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
116 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
117 <TD><CODE><B>AlignmentMetadata.</B><B><A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html#getProgram()">getProgram</A></B>()</CODE>\r
118 \r
119 <BR>\r
120 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
121 </TR>\r
122 <TR BGCOLOR="white" CLASS="TableRowColor">\r
123 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
124 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
125 <TD><CODE><B>Program.</B><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
126 \r
127 <BR>\r
128 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</TD>\r
129 </TR>\r
130 <TR BGCOLOR="white" CLASS="TableRowColor">\r
131 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
132 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[]</CODE></FONT></TD>\r
133 <TD><CODE><B>Program.</B><B><A HREF="../../../../compbio/data/sequence/Program.html#values()">values</A></B>()</CODE>\r
134 \r
135 <BR>\r
136 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
137 the order they are declared.</TD>\r
138 </TR>\r
139 </TABLE>\r
140 &nbsp;\r
141 <P>\r
142 \r
143 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
144 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
145 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></TH>\r
146 </TR>\r
147 <TR BGCOLOR="white" CLASS="TableRowColor">\r
148 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
149           <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
150           char&nbsp;gapchar)</CODE>\r
151 \r
152 <BR>\r
153 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
154 </TR>\r
155 <TR BGCOLOR="white" CLASS="TableRowColor">\r
156 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)">AlignmentMetadata</A></B>(<A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,\r
157                   char&nbsp;gapchar)</CODE>\r
158 \r
159 <BR>\r
160 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
161 </TR>\r
162 </TABLE>\r
163 &nbsp;\r
164 <P>\r
165 <HR>\r
166 \r
167 \r
168 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
169 <A NAME="navbar_bottom"><!-- --></A>\r
170 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
171 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
172 <TR>\r
173 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
174 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
175 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
176   <TR ALIGN="center" VALIGN="top">\r
177   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
178   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
179   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
180   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
181   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
182   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
183   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
184   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
185   </TR>\r
186 </TABLE>\r
187 </TD>\r
188 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
189 </EM>\r
190 </TD>\r
191 </TR>\r
192 \r
193 <TR>\r
194 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
195 &nbsp;PREV&nbsp;\r
196 &nbsp;NEXT</FONT></TD>\r
197 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
198   <A HREF="../../../../index.html?compbio/data/sequence/\class-useProgram.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
199 &nbsp;<A HREF="Program.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
200 &nbsp;<SCRIPT type="text/javascript">\r
201   <!--\r
202   if(window==top) {\r
203     document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
204   }\r
205   //-->\r
206 </SCRIPT>\r
207 <NOSCRIPT>\r
208   <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
209 </NOSCRIPT>\r
210 \r
211 \r
212 </FONT></TD>\r
213 </TR>\r
214 </TABLE>\r
215 <A NAME="skip-navbar_bottom"></A>\r
216 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
217 \r
218 <HR>\r
219 \r
220 </BODY>\r
221 </HTML>\r