Next version of JABA
[jabaws.git] / website / dm_javadoc / compbio / data / sequence / package-use.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_14) on Wed Feb 17 16:46:28 GMT 2010 -->\r
6 <TITLE>\r
7 Uses of Package compbio.data.sequence\r
8 </TITLE>\r
9 \r
10 <META NAME="date" CONTENT="2010-02-17">\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 Package compbio.data.sequence";\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">    <FONT CLASS="NavBarFont1">Class</FONT>&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="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;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/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
62 &nbsp;<A HREF="package-use.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 Package<br>compbio.data.sequence</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/package-summary.html">compbio.data.sequence</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 
95  Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
96 </TR>\r
97 <TR BGCOLOR="white" CLASS="TableRowColor">\r
98 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
99 <TD>A meta-data model for multiple sequence alignment web services 
100  Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
101 </TR>\r
102 </TABLE>\r
103 &nbsp;\r
104 <P>\r
105 <A NAME="compbio.data.sequence"><!-- --></A>\r
106 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
107 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
108 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
109 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
110 </TR>\r
111 <TR BGCOLOR="white" CLASS="TableRowColor">\r
112 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.sequence"><B>Alignment</B></A></B>\r
113 \r
114 <BR>\r
115 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Multiple sequence alignment.</TD>\r
116 </TR>\r
117 <TR BGCOLOR="white" CLASS="TableRowColor">\r
118 <TD><B><A HREF="../../../compbio/data/sequence/class-use/AlignmentMetadata.html#compbio.data.sequence"><B>AlignmentMetadata</B></A></B>\r
119 \r
120 <BR>\r
121 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Alignment metadata e.g.</TD>\r
122 </TR>\r
123 <TR BGCOLOR="white" CLASS="TableRowColor">\r
124 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence"><B>FastaSequence</B></A></B>\r
125 \r
126 <BR>\r
127 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
128 </TR>\r
129 <TR BGCOLOR="white" CLASS="TableRowColor">\r
130 <TD><B><A HREF="../../../compbio/data/sequence/class-use/Program.html#compbio.data.sequence"><B>Program</B></A></B>\r
131 \r
132 <BR>\r
133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Programmes that can produce alignments</TD>\r
134 </TR>\r
135 <TR BGCOLOR="white" CLASS="TableRowColor">\r
136 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence"><B>UnknownFileFormatException</B></A></B>\r
137 \r
138 <BR>\r
139 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
140 </TR>\r
141 </TABLE>\r
142 &nbsp;\r
143 <P>\r
144 <A NAME="compbio.metadata"><!-- --></A>\r
145 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
146 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
147 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
148 Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
149 </TR>\r
150 <TR BGCOLOR="white" CLASS="TableRowColor">\r
151 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.metadata"><B>FastaSequence</B></A></B>\r
152 \r
153 <BR>\r
154 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
155 </TR>\r
156 </TABLE>\r
157 &nbsp;\r
158 <P>\r
159 <HR>\r
160 \r
161 \r
162 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
163 <A NAME="navbar_bottom"><!-- --></A>\r
164 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
165 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
166 <TR>\r
167 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
168 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
169 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
170   <TR ALIGN="center" VALIGN="top">\r
171   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
172   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
173   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
174   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
175   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
176   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
177   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
178   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
179   </TR>\r
180 </TABLE>\r
181 </TD>\r
182 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
183 </EM>\r
184 </TD>\r
185 </TR>\r
186 \r
187 <TR>\r
188 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
189 &nbsp;PREV&nbsp;\r
190 &nbsp;NEXT</FONT></TD>\r
191 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
192   <A HREF="../../../index.html?compbio/data/sequence/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
193 &nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
194 &nbsp;<SCRIPT type="text/javascript">\r
195   <!--\r
196   if(window==top) {\r
197     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
198   }\r
199   //-->\r
200 </SCRIPT>\r
201 <NOSCRIPT>\r
202   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
203 </NOSCRIPT>\r
204 \r
205 \r
206 </FONT></TD>\r
207 </TR>\r
208 </TABLE>\r
209 <A NAME="skip-navbar_bottom"></A>\r
210 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
211 \r
212 <HR>\r
213 \r
214 </BODY>\r
215 </HTML>\r