X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=5dd0e40f82092213f9b9ab2db4cb95308073a7bf;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=b43e3ead651d9237ab44f18627f9647db41ae572;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java index b43e3ea..5dd0e40 100755 --- a/src/jalview/io/ClustalFile.java +++ b/src/jalview/io/ClustalFile.java @@ -1,223 +1,271 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 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 - */ -package jalview.io; - -import java.io.*; -import java.util.*; - -import jalview.datamodel.*; -import jalview.util.*; - -public class ClustalFile - extends AlignFile -{ - - public ClustalFile() - { - } - - public ClustalFile(String inFile, String type) - throws IOException - { - super(inFile, type); - } - - public void initData() - { - super.initData(); - } - - public void parse() throws IOException - { - int i = 0; - boolean flag = false; - - Vector headers = new Vector(); - Hashtable seqhash = new Hashtable(); - StringBuffer tempseq; - String line, id; - StringTokenizer str; - - try - { - while ( (line = nextLine()) != null) - { - if (line.indexOf(" ") != 0) - { - str = new StringTokenizer(line, " "); - - if (str.hasMoreTokens()) - { - id = str.nextToken(); - - if (id.equalsIgnoreCase("CLUSTAL")) - { - flag = true; - } - else - { - if (flag) - { - if (seqhash.containsKey(id)) - { - tempseq = (StringBuffer) seqhash.get(id); - } - else - { - tempseq = new StringBuffer(); - seqhash.put(id, tempseq); - } - - if (! (headers.contains(id))) - { - headers.addElement(id); - } - - if (str.hasMoreTokens()) - { - tempseq.append(str.nextToken()); - } - } - } - } - else - flag = true; - } - } - } - catch (IOException e) - { - System.err.println("Exception parsing clustal file " + e); - e.printStackTrace(); - } - - if (flag) - { - this.noSeqs = headers.size(); - - //Add sequences to the hash - for (i = 0; i < headers.size(); i++) - { - if (seqhash.get(headers.elementAt(i)) != null) - { - if (maxLength < seqhash.get(headers.elementAt(i)).toString() - .length()) - { - maxLength = seqhash.get(headers.elementAt(i)).toString() - .length(); - } - - Sequence newSeq = parseId(headers.elementAt(i).toString()); - newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() ); - - if (!isValidProteinSequence(newSeq.getSequence())) - { - throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS - + " : " + newSeq.getName() - + " : " + invalidCharacter); - } - - - seqs.addElement(newSeq); - } - else - { - System.err.println( - "Clustal File Reader: Can't find sequence for " + - headers.elementAt(i)); - } - } - } - } - - public String print() - { - return print(getSeqsAsArray()); - } - - public String print(SequenceI[] s) - { - StringBuffer out = new StringBuffer("CLUSTAL\n\n"); - - int max = 0; - int maxid = 0; - - int i = 0; - - while ( (i < s.length) && (s[i] != null)) - { - String tmp = printId(s[i]); - - if (s[i].getSequence().length > max) - { - max = s[i].getSequence().length; - } - - if (tmp.length() > maxid) - { - maxid = tmp.length(); - } - - i++; - } - - if (maxid < 15) - { - maxid = 15; - } - - maxid++; - - int len = 60; - int nochunks = (max / len) + 1; - - for (i = 0; i < nochunks; i++) - { - int j = 0; - - while ( (j < s.length) && (s[j] != null)) - { - out.append(new Format("%-" + maxid + "s").form( printId(s[j]) + " ")); - - int start = i * len; - int end = start + len; - - if ( (end < s[j].getSequence().length) && - (start < s[j].getSequence().length)) - { - out.append(s[j].getSequenceAsString(start, end)); - } - else - { - if (start < s[j].getSequence().length) - { - out.append(s[j].getSequenceAsString().substring(start)); - } - } - - out.append("\n"); - j++; - } - - out.append("\n"); - } - - return out.toString(); - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.io; + +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.util.Format; + +import java.io.IOException; +import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; + +public class ClustalFile extends AlignFile +{ + + public ClustalFile() + { + } + + public ClustalFile(String inFile, String type) throws IOException + { + super(inFile, type); + } + + public ClustalFile(FileParse source) throws IOException + { + super(source); + } + + public void initData() + { + super.initData(); + } + + public void parse() throws IOException + { + int i = 0; + boolean flag = false; + boolean rna = false; + boolean top = false; + StringBuffer pssecstr = new StringBuffer(), consstr = new StringBuffer(); + Vector headers = new Vector(); + Hashtable seqhash = new Hashtable(); + StringBuffer tempseq; + String line, id; + StringTokenizer str; + + try + { + while ((line = nextLine()) != null) + { + if (line.length() == 0) + { + top = true; + } + if (line.indexOf(" ") != 0) + { + str = new StringTokenizer(line, " "); + + if (str.hasMoreTokens()) + { + id = str.nextToken(); + + if (id.equalsIgnoreCase("CLUSTAL")) + { + flag = true; + } + else + { + if (flag) + { + if (seqhash.containsKey(id)) + { + tempseq = (StringBuffer) seqhash.get(id); + } + else + { + tempseq = new StringBuffer(); + seqhash.put(id, tempseq); + } + + if (!(headers.contains(id))) + { + headers.addElement(id); + } + + if (str.hasMoreTokens()) + { + tempseq.append(str.nextToken()); + } + top = false; + } + } + } + else + { + flag = true; + } + } + else + { + if (line.matches("\\s+(-|\\.|\\(|\\[|\\]|\\))+")) + { + if (top) + { + pssecstr.append(line.trim()); + } + else + { + consstr.append(line.trim()); + } + } + } + } + } catch (IOException e) + { + System.err.println("Exception parsing clustal file " + e); + e.printStackTrace(); + } + + if (flag) + { + this.noSeqs = headers.size(); + + // Add sequences to the hash + for (i = 0; i < headers.size(); i++) + { + if (seqhash.get(headers.elementAt(i)) != null) + { + if (maxLength < seqhash.get(headers.elementAt(i)).toString() + .length()) + { + maxLength = seqhash.get(headers.elementAt(i)).toString() + .length(); + } + + Sequence newSeq = parseId(headers.elementAt(i).toString()); + newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()) + .toString()); + + seqs.addElement(newSeq); + } + else + { + System.err + .println("Clustal File Reader: Can't find sequence for " + + headers.elementAt(i)); + } + } + AlignmentAnnotation lastssa = null; + if (pssecstr.length() == maxLength) + { + Vector ss = new Vector(); + AlignmentAnnotation ssa = lastssa = StockholmFile + .parseAnnotationRow(ss, "secondary structure", + pssecstr.toString()); + ssa.label = "Secondary Structure"; + annotations.addElement(ssa); + } + if (consstr.length() == maxLength) + { + Vector ss = new Vector(); + AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss, + "secondary structure", consstr.toString()); + ssa.label = "Consensus Secondary Structure"; + if (lastssa == null + || !lastssa.getRNAStruc().equals( + ssa.getRNAStruc().replace('-', '.'))) + { + annotations.addElement(ssa); + } + } + } + } + + public String print() + { + return print(getSeqsAsArray()); + // TODO: locaRNA style aln output + } + + public String print(SequenceI[] s) + { + StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline); + + int max = 0; + int maxid = 0; + + int i = 0; + + while ((i < s.length) && (s[i] != null)) + { + String tmp = printId(s[i]); + + if (s[i].getSequence().length > max) + { + max = s[i].getSequence().length; + } + + if (tmp.length() > maxid) + { + maxid = tmp.length(); + } + + i++; + } + + if (maxid < 15) + { + maxid = 15; + } + + maxid++; + + int len = 60; + int nochunks = (max / len) + 1; + + for (i = 0; i < nochunks; i++) + { + int j = 0; + + while ((j < s.length) && (s[j] != null)) + { + out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " ")); + + int start = i * len; + int end = start + len; + + if ((end < s[j].getSequence().length) + && (start < s[j].getSequence().length)) + { + out.append(s[j].getSequenceAsString(start, end)); + } + else + { + if (start < s[j].getSequence().length) + { + out.append(s[j].getSequenceAsString().substring(start)); + } + } + + out.append(newline); + j++; + } + + out.append(newline); + } + + return out.toString(); + } +}