1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
\r
5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->
\r
10 <META NAME="date" CONTENT="2010-02-17">
\r
12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">
\r
14 <SCRIPT type="text/javascript">
\r
15 function windowTitle()
\r
17 if (location.href.indexOf('is-external=true') == -1) {
\r
18 parent.document.title="BlastParser";
\r
27 <BODY BGCOLOR="white" onload="windowTitle();">
\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
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> </TD>
\r
41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
\r
42 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
\r
43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/BlastParser.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
\r
44 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
\r
45 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
\r
46 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
\r
47 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
\r
51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
\r
57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
58 PREV CLASS
\r
59 <A HREF="../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred"><B>NEXT CLASS</B></A></FONT></TD>
\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
61 <A HREF="../../../index.html?compbio/pipeline/_jpred/BlastParser.html" target="_top"><B>FRAMES</B></A>
\r
62 <A HREF="BlastParser.html" target="_top"><B>NO FRAMES</B></A>
\r
63 <SCRIPT type="text/javascript">
\r
66 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
\r
71 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
\r
78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
79 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
\r
80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
81 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
\r
84 <A NAME="skip-navbar_top"></A>
\r
85 <!-- ========= END OF TOP NAVBAR ========= -->
\r
88 <!-- ======== START OF CLASS DATA ======== -->
\r
91 compbio.pipeline._jpred</FONT>
\r
93 Class BlastParser</H2>
\r
96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.pipeline._jpred.BlastParser</B>
\r
100 <DT><PRE>public class <B>BlastParser</B><DT>extends java.lang.Object</DL>
\r
108 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
\r
110 <A NAME="constructor_summary"><!-- --></A>
\r
111 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
112 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
113 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
114 <B>Constructor Summary</B></FONT></TH>
\r
116 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
117 <TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/BlastParser.html#BlastParser()">BlastParser</A></B>()</CODE>
\r
120 </TD>
\r
124 <!-- ========== METHOD SUMMARY =========== -->
\r
126 <A NAME="method_summary"><!-- --></A>
\r
127 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
128 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
129 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
130 <B>Method Summary</B></FONT></TH>
\r
132 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
133 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
134 <CODE>static void</CODE></FONT></TD>
\r
135 <TD><CODE><B><A HREF="../../../compbio/pipeline/_jpred/BlastParser.html#main(java.lang.String[])">main</A></B>(java.lang.String[] args)</CODE>
\r
138 args[0] is assumed to be the name of a Blast output file</TD>
\r
141 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
\r
142 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
143 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
144 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
\r
146 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
147 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
\r
153 <!-- ========= CONSTRUCTOR DETAIL ======== -->
\r
155 <A NAME="constructor_detail"><!-- --></A>
\r
156 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
157 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
158 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
\r
159 <B>Constructor Detail</B></FONT></TH>
\r
163 <A NAME="BlastParser()"><!-- --></A><H3>
\r
166 public <B>BlastParser</B>()</PRE>
\r
170 <!-- ============ METHOD DETAIL ========== -->
\r
172 <A NAME="method_detail"><!-- --></A>
\r
173 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
174 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
175 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
\r
176 <B>Method Detail</B></FONT></TH>
\r
180 <A NAME="main(java.lang.String[])"><!-- --></A><H3>
\r
183 public static void <B>main</B>(java.lang.String[] args)
\r
184 throws java.io.FileNotFoundException,
\r
185 javax.xml.stream.XMLStreamException</PRE>
\r
187 <DD>args[0] is assumed to be the name of a Blast output file
\r
192 <DD><CODE>javax.xml.stream.XMLStreamException</CODE>
\r
193 <DD><CODE>java.io.FileNotFoundException</CODE></DL>
\r
196 <!-- ========= END OF CLASS DATA ========= -->
\r
200 <!-- ======= START OF BOTTOM NAVBAR ====== -->
\r
201 <A NAME="navbar_bottom"><!-- --></A>
\r
202 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
\r
203 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
\r
205 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
\r
206 <A NAME="navbar_bottom_firstrow"><!-- --></A>
\r
207 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
\r
208 <TR ALIGN="center" VALIGN="top">
\r
209 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
\r
210 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
\r
211 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
\r
212 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/BlastParser.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
\r
213 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
\r
214 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
\r
215 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
\r
216 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
\r
220 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
\r
226 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
227 PREV CLASS
\r
228 <A HREF="../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred"><B>NEXT CLASS</B></A></FONT></TD>
\r
229 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
230 <A HREF="../../../index.html?compbio/pipeline/_jpred/BlastParser.html" target="_top"><B>FRAMES</B></A>
\r
231 <A HREF="BlastParser.html" target="_top"><B>NO FRAMES</B></A>
\r
232 <SCRIPT type="text/javascript">
\r
235 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
\r
240 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
\r
247 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
248 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
\r
249 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
250 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
\r
253 <A NAME="skip-navbar_bottom"></A>
\r
254 <!-- ======== END OF BOTTOM NAVBAR ======= -->
\r