updated javadoc
[jabaws.git] / website / full_javadoc / compbio / runner / _impl / 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_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
6 <TITLE>\r
7 Uses of Package compbio.runner._impl\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="Uses of Package compbio.runner._impl";\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/runner/_impl/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.runner._impl</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/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
91 </TR>\r
92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
93 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
94 <TD>&nbsp;&nbsp;</TD>\r
95 </TR>\r
96 </TABLE>\r
97 &nbsp;\r
98 <P>\r
99 <A NAME="compbio.runner._impl"><!-- --></A>\r
100 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
101 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
102 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
103 Classes in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> used by <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
104 </TR>\r
105 <TR BGCOLOR="white" CLASS="TableRowColor">\r
106 <TD><B><A HREF="../../../compbio/runner/_impl/class-use/BlastAll.html#compbio.runner._impl"><B>BlastAll</B></A></B>\r
107 \r
108 <BR>\r
109 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
110 </TR>\r
111 <TR BGCOLOR="white" CLASS="TableRowColor">\r
112 <TD><B><A HREF="../../../compbio/runner/_impl/class-use/Mcl.html#compbio.runner._impl"><B>Mcl</B></A></B>\r
113 \r
114 <BR>\r
115 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
116 </TR>\r
117 <TR BGCOLOR="white" CLASS="TableRowColor">\r
118 <TD><B><A HREF="../../../compbio/runner/_impl/class-use/NetNglyc.html#compbio.runner._impl"><B>NetNglyc</B></A></B>\r
119 \r
120 <BR>\r
121 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
122 </TR>\r
123 <TR BGCOLOR="white" CLASS="TableRowColor">\r
124 <TD><B><A HREF="../../../compbio/runner/_impl/class-use/OB.html#compbio.runner._impl"><B>OB</B></A></B>\r
125 \r
126 <BR>\r
127 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;TODO this needs fixing! Executable does not work</TD>\r
128 </TR>\r
129 <TR BGCOLOR="white" CLASS="TableRowColor">\r
130 <TD><B><A HREF="../../../compbio/runner/_impl/class-use/PSIBlast.html#compbio.runner._impl"><B>PSIBlast</B></A></B>\r
131 \r
132 <BR>\r
133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
134 </TR>\r
135 <TR BGCOLOR="white" CLASS="TableRowColor">\r
136 <TD><B><A HREF="../../../compbio/runner/_impl/class-use/Ronn.html#compbio.runner._impl"><B>Ronn</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 <TR BGCOLOR="white" CLASS="TableRowColor">\r
142 <TD><B><A HREF="../../../compbio/runner/_impl/class-use/RPSBlast.html#compbio.runner._impl"><B>RPSBlast</B></A></B>\r
143 \r
144 <BR>\r
145 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
146 </TR>\r
147 </TABLE>\r
148 &nbsp;\r
149 <P>\r
150 <HR>\r
151 \r
152 \r
153 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
154 <A NAME="navbar_bottom"><!-- --></A>\r
155 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
156 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
157 <TR>\r
158 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
159 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
160 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
161   <TR ALIGN="center" VALIGN="top">\r
162   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
163   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
164   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
165   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
166   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
167   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
168   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
169   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
170   </TR>\r
171 </TABLE>\r
172 </TD>\r
173 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
174 </EM>\r
175 </TD>\r
176 </TR>\r
177 \r
178 <TR>\r
179 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
180 &nbsp;PREV&nbsp;\r
181 &nbsp;NEXT</FONT></TD>\r
182 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
183   <A HREF="../../../index.html?compbio/runner/_impl/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
184 &nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
185 &nbsp;<SCRIPT type="text/javascript">\r
186   <!--\r
187   if(window==top) {\r
188     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
189   }\r
190   //-->\r
191 </SCRIPT>\r
192 <NOSCRIPT>\r
193   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
194 </NOSCRIPT>\r
195 \r
196 \r
197 </FONT></TD>\r
198 </TR>\r
199 </TABLE>\r
200 <A NAME="skip-navbar_bottom"></A>\r
201 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
202 \r
203 <HR>\r
204 \r
205 </BODY>\r
206 </HTML>\r