X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFastaFile.java;h=5a15862f2ec0943dcf626ad12774eb424b30a6cb;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=1cb016c93179ac277f45ca502fb5743a25bbbe1b;hpb=3a993bbe274824870c78bd7695c42fa93908cb30;p=jalview.git diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java index 1cb016c..5a15862 100755 --- a/src/jalview/io/FastaFile.java +++ b/src/jalview/io/FastaFile.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.io; @@ -24,12 +23,11 @@ import jalview.datamodel.*; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class FastaFile - extends AlignFile +public class FastaFile extends AlignFile { /** * Length of a sequence line @@ -47,14 +45,16 @@ public class FastaFile /** * Creates a new FastaFile object. - * - * @param inFile DOCUMENT ME! - * @param type DOCUMENT ME! - * - * @throws IOException DOCUMENT ME! + * + * @param inFile + * DOCUMENT ME! + * @param type + * DOCUMENT ME! + * + * @throws IOException + * DOCUMENT ME! */ - public FastaFile(String inFile, String type) - throws IOException + public FastaFile(String inFile, String type) throws IOException { super(inFile, type); } @@ -66,11 +66,11 @@ public class FastaFile /** * DOCUMENT ME! - * - * @throws IOException DOCUMENT ME! + * + * @throws IOException + * DOCUMENT ME! */ - public void parse() - throws IOException + public void parse() throws IOException { StringBuffer sb = new StringBuffer(); boolean firstLine = true; @@ -80,7 +80,7 @@ public class FastaFile boolean annotation = false; - while ( (line = nextLine()) != null) + while ((line = nextLine()) != null) { line = line.trim(); if (line.length() > 0) @@ -96,12 +96,10 @@ public class FastaFile for (int i = 0; i < sb.length(); i++) { anots[i] = new Annotation(anotString.substring(i, i + 1), - null, - ' ', 0); + null, ' ', 0); } - AlignmentAnnotation aa = new AlignmentAnnotation( - seq.getName().substring(2), seq.getDescription(), - anots); + AlignmentAnnotation aa = new AlignmentAnnotation(seq + .getName().substring(2), seq.getDescription(), anots); annotations.addElement(aa); } @@ -144,13 +142,11 @@ public class FastaFile String anotString = sb.toString(); for (int i = 0; i < sb.length(); i++) { - anots[i] = new Annotation(anotString.substring(i, i + 1), - null, - ' ', 0); + anots[i] = new Annotation(anotString.substring(i, i + 1), null, + ' ', 0); } - AlignmentAnnotation aa = new AlignmentAnnotation( - seq.getName().substring(2), seq.getDescription(), - anots); + AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName() + .substring(2), seq.getDescription(), anots); annotations.addElement(aa); } @@ -163,9 +159,9 @@ public class FastaFile } /** - * called by AppletFormatAdapter to generate - * an annotated alignment, rather than bare - * sequences. + * called by AppletFormatAdapter to generate an annotated alignment, rather + * than bare sequences. + * * @param al */ public void addAnnotations(Alignment al) @@ -173,21 +169,25 @@ public class FastaFile addProperties(al); for (int i = 0; i < annotations.size(); i++) { - AlignmentAnnotation aa = (AlignmentAnnotation) annotations.elementAt(i); + AlignmentAnnotation aa = (AlignmentAnnotation) annotations + .elementAt(i); aa.setPadGaps(true, al.getGapCharacter()); - al.addAnnotation( aa ); + al.addAnnotation(aa); } } - /** * DOCUMENT ME! - * - * @param s DOCUMENT ME! - * @param len DOCUMENT ME! - * @param gaps DOCUMENT ME! - * @param displayId DOCUMENT ME! - * + * + * @param s + * DOCUMENT ME! + * @param len + * DOCUMENT ME! + * @param gaps + * DOCUMENT ME! + * @param displayId + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public String print(SequenceI[] s) @@ -195,7 +195,7 @@ public class FastaFile out = new StringBuffer(); int i = 0; - while ( (i < s.length) && (s[i] != null)) + while ((i < s.length) && (s[i] != null)) { out.append(">" + printId(s[i])); if (s[i].getDescription() != null) @@ -218,7 +218,8 @@ public class FastaFile } else if (start < s[i].getLength()) { - out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n"); + out.append(s[i].getSequenceAsString(start, s[i].getLength()) + + "\n"); } } @@ -230,7 +231,7 @@ public class FastaFile /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public String print()