X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFastaFile.java;h=c698a31b81963fe24ec8c3044ceaf6a10eb0fb15;hb=5a352aa2f3330ae269d9b70c4a7374c2518bfb2e;hp=2ee715da3028d61d614229df9cd2f583fcca8b8d;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java index 2ee715d..c698a31 100755 --- a/src/jalview/io/FastaFile.java +++ b/src/jalview/io/FastaFile.java @@ -1,26 +1,32 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; -import java.io.*; +import java.io.IOException; -import jalview.datamodel.*; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; /** * DOCUMENT ME! @@ -48,42 +54,54 @@ public class FastaFile extends AlignFile * Creates a new FastaFile object. * * @param inFile - * DOCUMENT ME! - * @param type - * DOCUMENT ME! + * DOCUMENT ME! + * @param sourceType + * DOCUMENT ME! * * @throws IOException - * DOCUMENT ME! + * DOCUMENT ME! */ - public FastaFile(String inFile, String type) throws IOException + public FastaFile(String inFile, DataSourceType sourceType) + throws IOException { - super(inFile, type); + super(inFile, sourceType); } public FastaFile(FileParse source) throws IOException { - super(source); + this(source, true); + } + + public FastaFile(FileParse source, boolean closeData) throws IOException + { + super(true, source, closeData); + } + + public FastaFile(SequenceI[] seqs) + { + super(seqs); } /** * DOCUMENT ME! * * @throws IOException - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void parse() throws IOException { StringBuffer sb = new StringBuffer(); boolean firstLine = true; - String line; + String line, uline; Sequence seq = null; boolean annotation = false; - while ((line = nextLine()) != null) + while ((uline = nextLine()) != null) { - line = line.trim(); + line = uline.trim(); if (line.length() > 0) { if (line.charAt(0) == '>') @@ -92,17 +110,7 @@ public class FastaFile extends AlignFile { if (annotation) { - Annotation[] anots = new Annotation[sb.length()]; - String anotString = sb.toString(); - for (int i = 0; i < sb.length(); i++) - { - anots[i] = new Annotation(anotString.substring(i, i + 1), - null, ' ', 0); - } - AlignmentAnnotation aa = new AlignmentAnnotation(seq - .getName().substring(2), seq.getDescription(), anots); - - annotations.addElement(aa); + annotations.addElement(makeAnnotation(seq, sb)); } } else @@ -132,24 +140,14 @@ public class FastaFile extends AlignFile } else { - sb.append(line); + sb.append(annotation ? uline : line); } } } if (annotation) { - Annotation[] anots = new Annotation[sb.length()]; - String anotString = sb.toString(); - for (int i = 0; i < sb.length(); i++) - { - anots[i] = new Annotation(anotString.substring(i, i + 1), null, - ' ', 0); - } - AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName() - .substring(2), seq.getDescription(), anots); - - annotations.addElement(aa); + annotations.addElement(makeAnnotation(seq, sb)); } else if (!firstLine) @@ -159,6 +157,23 @@ public class FastaFile extends AlignFile } } + private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb) + { + Annotation[] anots = new Annotation[sb.length()]; + char cb; + for (int i = 0; i < anots.length; i++) + { + char cn = sb.charAt(i); + if (cn != ' ') + { + anots[i] = new Annotation("" + cn, null, ' ', Float.NaN); + } + } + AlignmentAnnotation aa = new AlignmentAnnotation( + seq.getName().substring(2), seq.getDescription(), anots); + return aa; + } + /** * called by AppletFormatAdapter to generate an annotated alignment, rather * than bare sequences. @@ -170,43 +185,30 @@ public class FastaFile extends AlignFile addProperties(al); for (int i = 0; i < annotations.size(); i++) { - AlignmentAnnotation aa = (AlignmentAnnotation) annotations - .elementAt(i); + AlignmentAnnotation aa = annotations.elementAt(i); aa.setPadGaps(true, al.getGapCharacter()); al.addAnnotation(aa); } } - /** - * 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) + @Override + public String print(SequenceI[] s, boolean jvsuffix) { out = new StringBuffer(); int i = 0; while ((i < s.length) && (s[i] != null)) { - out.append(">" + printId(s[i])); + out.append(">" + printId(s[i], jvsuffix)); if (s[i].getDescription() != null) { out.append(" " + s[i].getDescription()); } - out.append("\n"); + out.append(newline); - int nochunks = (s[i].getLength() / len) + 1; + int nochunks = (s[i].getLength() / len) + + (s[i].getLength() % len > 0 ? 1 : 0); for (int j = 0; j < nochunks; j++) { @@ -215,12 +217,12 @@ public class FastaFile extends AlignFile if (end < s[i].getLength()) { - out.append(s[i].getSequenceAsString(start, end) + "\n"); + out.append(s[i].getSequenceAsString(start, end) + newline); } else if (start < s[i].getLength()) { out.append(s[i].getSequenceAsString(start, s[i].getLength()) - + "\n"); + + newline); } } @@ -229,14 +231,4 @@ public class FastaFile extends AlignFile return out.toString(); } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String print() - { - return print(getSeqsAsArray()); - } }