updated javadoc
[jabaws.git] / website / dm_javadoc / index-files / index-5.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 14:32:04 BST 2011 -->\r
6 <TITLE>\r
7 F-Index\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="F-Index";\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">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
44   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-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="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&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="index-4.html"><B>PREV LETTER</B></A>&nbsp;\r
59 &nbsp;<A HREF="index-6.html"><B>NEXT LETTER</B></A></FONT></TD>\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
61   <A HREF="../index.html?index-filesindex-5.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
62 &nbsp;<A HREF="index-5.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 <A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
82 <A NAME="_F_"><!-- --></A><H2>\r
83 <B>F</B></H2>\r
84 <DL>\r
85 <DT><A HREF="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence"><B>FastaReader</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Reads files with FASTA formatted sequences.<DT><A HREF="../compbio/data/sequence/FastaReader.html#FastaReader(java.lang.String)"><B>FastaReader(String)</B></A> - \r
86 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A>\r
87 <DD>Header data can contain non-ASCII symbols and read in UTF8\r
88 <DT><A HREF="../compbio/data/sequence/FastaReader.html#FastaReader(java.io.InputStream)"><B>FastaReader(InputStream)</B></A> - \r
89 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A>\r
90 <DD>This class will not close the incoming stream! So the client should do
91  so.\r
92 <DT><A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>FastaSequence</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>A FASTA formatted sequence.<DT><A HREF="../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)"><B>FastaSequence(String, String)</B></A> - \r
93 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
94 <DD>Upon construction the any whitespace characters are removed from the
95  sequence\r
96 <DT><A HREF="../compbio/data/sequence/Range.html#from"><B>from</B></A> - \r
97 Variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
98 <DD>&nbsp;\r
99 </DL>\r
100 <HR>\r
101 \r
102 \r
103 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
104 <A NAME="navbar_bottom"><!-- --></A>\r
105 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
106 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
107 <TR>\r
108 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
109 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
110 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
111   <TR ALIGN="center" VALIGN="top">\r
112   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
113   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
114   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
115   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
116   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
117   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
118   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
119   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
120   </TR>\r
121 </TABLE>\r
122 </TD>\r
123 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
124 </EM>\r
125 </TD>\r
126 </TR>\r
127 \r
128 <TR>\r
129 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
130 &nbsp;<A HREF="index-4.html"><B>PREV LETTER</B></A>&nbsp;\r
131 &nbsp;<A HREF="index-6.html"><B>NEXT LETTER</B></A></FONT></TD>\r
132 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
133   <A HREF="../index.html?index-filesindex-5.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
134 &nbsp;<A HREF="index-5.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
135 &nbsp;<SCRIPT type="text/javascript">\r
136   <!--\r
137   if(window==top) {\r
138     document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
139   }\r
140   //-->\r
141 </SCRIPT>\r
142 <NOSCRIPT>\r
143   <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
144 </NOSCRIPT>\r
145 \r
146 \r
147 </FONT></TD>\r
148 </TR>\r
149 </TABLE>\r
150 <A NAME="skip-navbar_bottom"></A>\r
151 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
152 \r
153 <A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
154 \r
155 </BODY>\r
156 </HTML>\r