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 16:46:49 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="FastaSequence";
\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/FastaSequence.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 <A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>
\r
59 <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
61 <A HREF="../../../index.html?compbio/data/sequence/FastaSequence.html" target="_top"><B>FRAMES</B></A>
\r
62 <A HREF="FastaSequence.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.data.sequence</FONT>
\r
93 Class FastaSequence</H2>
\r
96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.FastaSequence</B>
\r
100 <DT><PRE><FONT SIZE="-1">@Immutable
\r
101 </FONT>public class <B>FastaSequence</B><DT>extends java.lang.Object</DL>
\r
105 A FASTA formatted sequence. Please note that this class does not make any
106 assumptions as to what sequence it store e.g. it could be nucleotide, protein
107 or even gapped alignment sequence! The only guarantee it makes is that the
108 sequence does not contain white space characters e.g. spaces, new lines etc
\r
113 <DT><B>Author:</B></DT>
\r
116 Date September 2009</DD>
\r
122 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
\r
124 <A NAME="constructor_summary"><!-- --></A>
\r
125 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
126 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
127 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
128 <B>Constructor Summary</B></FONT></TH>
\r
130 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
131 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)">FastaSequence</A></B>(java.lang.String id,
\r
132 java.lang.String sequence)</CODE>
\r
135 Upon construction the any whitespace characters are removed from the
140 <!-- ========== METHOD SUMMARY =========== -->
\r
142 <A NAME="method_summary"><!-- --></A>
\r
143 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
144 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
145 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
146 <B>Method Summary</B></FONT></TH>
\r
148 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
149 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
150 <CODE>static int</CODE></FONT></TD>
\r
151 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)">countMatchesInSequence</A></B>(java.lang.String theString,
\r
152 java.lang.String theRegExp)</CODE>
\r
155 </TD>
\r
157 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
159 <CODE> boolean</CODE></FONT></TD>
\r
160 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object obj)</CODE>
\r
163 </TD>
\r
165 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
167 <CODE> java.lang.String</CODE></FONT></TD>
\r
168 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)">getFormatedSequence</A></B>(int width)</CODE>
\r
171 Format sequence per width letter in one string.</TD>
\r
173 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
174 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
175 <CODE> java.lang.String</CODE></FONT></TD>
\r
176 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormattedFasta()">getFormattedFasta</A></B>()</CODE>
\r
179 </TD>
\r
181 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
182 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
183 <CODE> java.lang.String</CODE></FONT></TD>
\r
184 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getId()">getId</A></B>()</CODE>
\r
187 Gets the value of id</TD>
\r
189 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
190 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
191 <CODE> int</CODE></FONT></TD>
\r
192 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getLength()">getLength</A></B>()</CODE>
\r
195 </TD>
\r
197 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
199 <CODE> java.lang.String</CODE></FONT></TD>
\r
200 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getOnelineFasta()">getOnelineFasta</A></B>()</CODE>
\r
203 </TD>
\r
205 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
206 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
207 <CODE> java.lang.String</CODE></FONT></TD>
\r
208 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getSequence()">getSequence</A></B>()</CODE>
\r
211 Gets the value of sequence</TD>
\r
213 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
214 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
215 <CODE> java.lang.String</CODE></FONT></TD>
\r
216 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#toString()">toString</A></B>()</CODE>
\r
219 Same as oneLineFasta</TD>
\r
222 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
\r
223 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
224 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
225 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
\r
227 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
228 <TD><CODE>getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
\r
234 <!-- ========= CONSTRUCTOR DETAIL ======== -->
\r
236 <A NAME="constructor_detail"><!-- --></A>
\r
237 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
238 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
239 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
\r
240 <B>Constructor Detail</B></FONT></TH>
\r
244 <A NAME="FastaSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>
\r
247 public <B>FastaSequence</B>(java.lang.String id,
\r
248 java.lang.String sequence)</PRE>
\r
250 <DD>Upon construction the any whitespace characters are removed from the
254 <DT><B>Parameters:</B><DD><CODE>id</CODE> - <DD><CODE>sequence</CODE> - </DL>
\r
257 <!-- ============ METHOD DETAIL ========== -->
\r
259 <A NAME="method_detail"><!-- --></A>
\r
260 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
261 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
262 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
\r
263 <B>Method Detail</B></FONT></TH>
\r
267 <A NAME="getId()"><!-- --></A><H3>
\r
270 public java.lang.String <B>getId</B>()</PRE>
\r
272 <DD>Gets the value of id
\r
276 <DT><B>Returns:</B><DD>the value of id</DL>
\r
281 <A NAME="getSequence()"><!-- --></A><H3>
\r
284 public java.lang.String <B>getSequence</B>()</PRE>
\r
286 <DD>Gets the value of sequence
\r
290 <DT><B>Returns:</B><DD>the value of sequence</DL>
\r
295 <A NAME="countMatchesInSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>
\r
296 countMatchesInSequence</H3>
\r
298 public static int <B>countMatchesInSequence</B>(java.lang.String theString,
\r
299 java.lang.String theRegExp)</PRE>
\r
307 <A NAME="getFormattedFasta()"><!-- --></A><H3>
\r
308 getFormattedFasta</H3>
\r
310 public java.lang.String <B>getFormattedFasta</B>()</PRE>
\r
318 <A NAME="getOnelineFasta()"><!-- --></A><H3>
\r
319 getOnelineFasta</H3>
\r
321 public java.lang.String <B>getOnelineFasta</B>()</PRE>
\r
325 <DT><B>Returns:</B><DD>one line name, next line sequence, no matter what the sequence
331 <A NAME="getFormatedSequence(int)"><!-- --></A><H3>
\r
332 getFormatedSequence</H3>
\r
334 public java.lang.String <B>getFormatedSequence</B>(int width)</PRE>
\r
336 <DD>Format sequence per width letter in one string. Without spaces.
\r
340 <DT><B>Returns:</B><DD>multiple line formated sequence, one line width letters length</DL>
\r
345 <A NAME="getLength()"><!-- --></A><H3>
\r
348 public int <B>getLength</B>()</PRE>
\r
352 <DT><B>Returns:</B><DD>sequence length</DL>
\r
357 <A NAME="toString()"><!-- --></A><H3>
\r
360 public java.lang.String <B>toString</B>()</PRE>
\r
362 <DD>Same as oneLineFasta
\r
365 <DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>
\r
373 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>
\r
376 public boolean <B>equals</B>(java.lang.Object obj)</PRE>
\r
379 <DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>
\r
385 <!-- ========= END OF CLASS DATA ========= -->
\r
389 <!-- ======= START OF BOTTOM NAVBAR ====== -->
\r
390 <A NAME="navbar_bottom"><!-- --></A>
\r
391 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
\r
392 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
\r
394 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
\r
395 <A NAME="navbar_bottom_firstrow"><!-- --></A>
\r
396 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
\r
397 <TR ALIGN="center" VALIGN="top">
\r
398 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
\r
399 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
\r
400 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
\r
401 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FastaSequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
\r
402 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
\r
403 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
\r
404 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
\r
405 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
\r
409 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
\r
415 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
416 <A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>
\r
417 <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
\r
418 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
419 <A HREF="../../../index.html?compbio/data/sequence/FastaSequence.html" target="_top"><B>FRAMES</B></A>
\r
420 <A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A>
\r
421 <SCRIPT type="text/javascript">
\r
424 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
\r
429 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
\r
436 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
437 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
\r
438 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
439 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
\r
442 <A NAME="skip-navbar_bottom"></A>
\r
443 <!-- ======== END OF BOTTOM NAVBAR ======= -->
\r