updated javadoc
[jabaws.git] / website / full_javadoc / compbio / runner / msa / package-summary.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 compbio.runner.msa\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="compbio.runner.msa";\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="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>\r
42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
44   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-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;<A HREF="../../../compbio/runner/disorder/package-summary.html"><B>PREV PACKAGE</B></A>&nbsp;\r
59 &nbsp;<A HREF="../../../compbio/stat/collector/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
61   <A HREF="../../../index.html?compbio/runner/msa/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
62 &nbsp;<A HREF="package-summary.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 <H2>\r
83 Package compbio.runner.msa\r
84 </H2>\r
85 Wrappers for native executables for multiple sequence alignment (msa)\r
86 <P>\r
87 <B>See:</B>\r
88 <BR>\r
89 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<A HREF="#package_description"><B>Description</B></A>\r
90 <P>\r
91 \r
92 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
93 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
94 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
95 <B>Class Summary</B></FONT></TH>\r
96 </TR>\r
97 <TR BGCOLOR="white" CLASS="TableRowColor">\r
98 <TD WIDTH="15%"><B><A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A></B></TD>\r
99 <TD>&nbsp;</TD>\r
100 </TR>\r
101 <TR BGCOLOR="white" CLASS="TableRowColor">\r
102 <TD WIDTH="15%"><B><A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></B></TD>\r
103 <TD>&nbsp;</TD>\r
104 </TR>\r
105 <TR BGCOLOR="white" CLASS="TableRowColor">\r
106 <TD WIDTH="15%"><B><A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></TD>\r
107 <TD>&nbsp;</TD>\r
108 </TR>\r
109 <TR BGCOLOR="white" CLASS="TableRowColor">\r
110 <TD WIDTH="15%"><B><A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></B></TD>\r
111 <TD>&nbsp;</TD>\r
112 </TR>\r
113 <TR BGCOLOR="white" CLASS="TableRowColor">\r
114 <TD WIDTH="15%"><B><A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></TD>\r
115 <TD>&nbsp;</TD>\r
116 </TR>\r
117 <TR BGCOLOR="white" CLASS="TableRowColor">\r
118 <TD WIDTH="15%"><B><A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></TD>\r
119 <TD>&nbsp;</TD>\r
120 </TR>\r
121 </TABLE>\r
122 &nbsp;\r
123 \r
124 <P>\r
125 <A NAME="package_description"><!-- --></A><H2>\r
126 Package compbio.runner.msa Description\r
127 </H2>\r
128 \r
129 <P>\r
130 Wrappers for native executables for multiple sequence alignment (msa)\r
131 <P>\r
132 \r
133 <P>\r
134 <DL>\r
135 <DT><B>Author:</B></DT>\r
136   <DD>Petr Troshin 
137  
138         Date January 2010</DD>\r
139 </DL>\r
140 <HR>\r
141 \r
142 \r
143 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
144 <A NAME="navbar_bottom"><!-- --></A>\r
145 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
146 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
147 <TR>\r
148 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
149 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
150 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
151   <TR ALIGN="center" VALIGN="top">\r
152   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
153   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>\r
154   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
155   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
156   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
157   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
158   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
159   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
160   </TR>\r
161 </TABLE>\r
162 </TD>\r
163 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
164 </EM>\r
165 </TD>\r
166 </TR>\r
167 \r
168 <TR>\r
169 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
170 &nbsp;<A HREF="../../../compbio/runner/disorder/package-summary.html"><B>PREV PACKAGE</B></A>&nbsp;\r
171 &nbsp;<A HREF="../../../compbio/stat/collector/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
172 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
173   <A HREF="../../../index.html?compbio/runner/msa/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
174 &nbsp;<A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
175 &nbsp;<SCRIPT type="text/javascript">\r
176   <!--\r
177   if(window==top) {\r
178     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
179   }\r
180   //-->\r
181 </SCRIPT>\r
182 <NOSCRIPT>\r
183   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
184 </NOSCRIPT>\r
185 \r
186 \r
187 </FONT></TD>\r
188 </TR>\r
189 </TABLE>\r
190 <A NAME="skip-navbar_bottom"></A>\r
191 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
192 \r
193 <HR>\r
194 \r
195 </BODY>\r
196 </HTML>\r