build client source when build all
[jabaws.git] / website / full_javadoc / compbio / runner / _impl / BlastParameters.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 16:46:49 GMT 2010 -->\r
6 <TITLE>\r
7 BlastParameters\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="BlastParameters";\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="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/BlastParameters.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/_impl/BlastAll.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
59 &nbsp;<A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
61   <A HREF="../../../index.html?compbio/runner/_impl/BlastParameters.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
62 &nbsp;<A HREF="BlastParameters.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 <TR>\r
78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
81 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;METHOD</FONT></TD>\r
82 </TR>\r
83 </TABLE>\r
84 <A NAME="skip-navbar_top"></A>\r
85 <!-- ========= END OF TOP NAVBAR ========= -->\r
86 \r
87 <HR>\r
88 <!-- ======== START OF CLASS DATA ======== -->\r
89 <H2>\r
90 <FONT SIZE="-1">\r
91 compbio.runner._impl</FONT>\r
92 <BR>\r
93 Class BlastParameters</H2>\r
94 <PRE>\r
95 java.lang.Object\r
96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.BlastParameters</B>\r
97 </PRE>\r
98 <HR>\r
99 <DL>\r
100 <DT><PRE>public class <B>BlastParameters</B><DT>extends java.lang.Object</DL>\r
101 </PRE>\r
102 \r
103 <P>\r
104 Utility class for common Blast parameters\r
105 <P>\r
106 \r
107 <P>\r
108 <DL>\r
109 <DT><B>Author:</B></DT>\r
110   <DD>pvtroshin
111  TODO</DD>\r
112 </DL>\r
113 <HR>\r
114 \r
115 <P>\r
116 \r
117 <!-- ========== METHOD SUMMARY =========== -->\r
118 \r
119 <A NAME="method_summary"><!-- --></A>\r
120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
121 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
122 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
123 <B>Method Summary</B></FONT></TH>\r
124 </TR>\r
125 </TABLE>\r
126 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
127 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
128 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
129 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
130 </TR>\r
131 <TR BGCOLOR="white" CLASS="TableRowColor">\r
132 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
133 </TR>\r
134 </TABLE>\r
135 &nbsp;\r
136 <P>\r
137 <!-- ========= END OF CLASS DATA ========= -->\r
138 <HR>\r
139 \r
140 \r
141 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
142 <A NAME="navbar_bottom"><!-- --></A>\r
143 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
144 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
145 <TR>\r
146 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
147 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
148 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
149   <TR ALIGN="center" VALIGN="top">\r
150   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
151   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
152   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
153   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/BlastParameters.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
154   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
155   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
156   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
157   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
158   </TR>\r
159 </TABLE>\r
160 </TD>\r
161 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
162 </EM>\r
163 </TD>\r
164 </TR>\r
165 \r
166 <TR>\r
167 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
168 &nbsp;<A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
169 &nbsp;<A HREF="../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
170 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
171   <A HREF="../../../index.html?compbio/runner/_impl/BlastParameters.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
172 &nbsp;<A HREF="BlastParameters.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
173 &nbsp;<SCRIPT type="text/javascript">\r
174   <!--\r
175   if(window==top) {\r
176     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
177   }\r
178   //-->\r
179 </SCRIPT>\r
180 <NOSCRIPT>\r
181   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
182 </NOSCRIPT>\r
183 \r
184 \r
185 </FONT></TD>\r
186 </TR>\r
187 <TR>\r
188 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
189   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
190 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
191 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;METHOD</FONT></TD>\r
192 </TR>\r
193 </TABLE>\r
194 <A NAME="skip-navbar_bottom"></A>\r
195 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
196 \r
197 <HR>\r
198 \r
199 </BODY>\r
200 </HTML>\r