X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=fa6f8e24708c12b3d16a3fa382042b87e8f92092;hb=3a993bbe274824870c78bd7695c42fa93908cb30;hp=04867a2a8b2ab786889c0a21c13c93b30441f433;hpb=5d6dd4ea636ea302d2eec392b5e8858e8c7a6cbe;p=jalview.git diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java index 04867a2..fa6f8e2 100755 --- a/src/jalview/io/BLCFile.java +++ b/src/jalview/io/BLCFile.java @@ -1,213 +1,266 @@ -/* -* 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 jalview.datamodel.*; - -import java.io.*; - -import java.util.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class BLCFile extends AlignFile -{ - Vector titles; - - /** - * Creates a new BLCFile object. - */ - public BLCFile() - { - } - - - /** - * Creates a new BLCFile object. - * - * @param inFile DOCUMENT ME! - * @param type DOCUMENT ME! - * - * @throws IOException DOCUMENT ME! - */ - public BLCFile(String inFile, String type) throws IOException - { - super(inFile, type); - } - - /** - * DOCUMENT ME! - */ - public void initData() - { - super.initData(); - titles = new Vector(); - } - - /** - * DOCUMENT ME! - */ - public void parse() throws IOException - { - boolean idsFound = false; - StringBuffer[] seqstrings; - - String line = null; - - do - { - line = nextLine(); - - // seek end of ids - if (line.indexOf("*") > -1) - { - idsFound = true; - - break; - } - - int abracket = line.indexOf(">"); - - if (abracket > -1) - { - line = line.substring(abracket+1); - - Sequence seq = parseId(line); - seqs.addElement(seq); - } - } - while (!idsFound); - - int starCol = line.indexOf("*"); - seqstrings = new StringBuffer[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) - { - if (seqstrings[i] == null) - { - seqstrings[i] = new StringBuffer(); - } - } - - while ((line = nextLine()).indexOf("*") == -1) - { - for (int i = 0; i < seqs.size(); i++) - { - if (line.length() > (i + starCol)) - { - seqstrings[i].append(line.charAt(i + starCol)); - } - } - } - - for (int i = 0; i < seqs.size(); i++) - { - Sequence newSeq = (Sequence) seqs.elementAt(i); - - if (!isValidProteinSequence(newSeq.getSequence())) - { - throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS - +" : "+ newSeq.getName() - +" : "+invalidCharacter); - } - - newSeq.setSequence(seqstrings[i].toString()); - } - - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String print() - { - return print(getSeqsAsArray()); - } - - /** - * DOCUMENT ME! - * - * @param s DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String print(SequenceI[] s) - { - StringBuffer out = new StringBuffer(); - /** - * A general parser for ids. Will look for dbrefs in - * Uniprot format source|id - * And also Jalview /start-end - * - * @String id Id to be parsed - */ - int i = 0; - int max = -1; - - while ((i < s.length) && (s[i] != null)) - { - out.append(">" + printId(s[i])); - if(s[i].getDescription()!=null) - out.append(" "+s[i].getDescription()); - - out.append("\n"); - - if (s[i].getSequence().length > max) - { - max = s[i].getSequence().length; - } - - i++; - } - - out.append("* iteration 1\n"); - - for (int j = 0; j < max; j++) - { - i = 0; - - while ((i < s.length) && (s[i] != null)) - { - if (s[i].getSequence().length > j) - { - out.append(s[i].getSequenceAsString(j, j + 1)); - } - else - { - out.append("-"); - } - - i++; - } - - out.append("\n"); - } - - out.append("*\n"); - - return out.toString(); - } -} +/* + * 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 + */ +package jalview.io; + +import java.io.*; +import java.util.*; + +import jalview.datamodel.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class BLCFile +extends AlignFile +{ + Vector titles; + + /** + * Creates a new BLCFile object. + */ + public BLCFile() + { + } + + /** + * Creates a new BLCFile object. + * + * @param inFile DOCUMENT ME! + * @param type DOCUMENT ME! + * + * @throws IOException DOCUMENT ME! + */ + public BLCFile(String inFile, String type) + throws IOException + { + super(inFile, type); + } + public BLCFile(FileParse source) throws IOException + { + super(source); + } + + /** + * DOCUMENT ME! + */ + public void initData() + { + super.initData(); + titles = new Vector(); + } + /** + * Control the number of block iterations to skip before returning. + * set to 0 to read first block file entry only + * set to -1 to read last block file entry only + * set to greater than zero to skip at most that many entries before parsing + */ + int iterationSkips=0; + /** + * The iteration number for the alignment actually parsed from the blc file + */ + int iterationCount=0; + + /** + * DOCUMENT ME! + */ + public void parse() + throws IOException + { + StringBuffer headerLines=new StringBuffer(); + int numHeaderLines = 0; // number of lines appended. + StringBuffer[] seqstrings=null; + if (suffix!=null) { + try { + iterationSkips = Integer.parseInt(suffix); + } catch (NumberFormatException e) { + iterationSkips = 0; // first + } + } + + String line = null; + + do { + boolean idsFound = false; + boolean newids = false; + // search for ID header. + do + { + line = nextLine(); + if (line==null) + break; + // seek end of ids + if (line.indexOf("*") > -1) + { + idsFound = true; + + break; + } + + int abracket = line.indexOf(">"); + + if (abracket > -1) + { + + if (iterationCount>0 && !newids) { + // we have a new set of IDs to record. + newids = true; + seqs.removeAllElements(); + } + + line = line.substring(abracket + 1); + + Sequence seq = parseId(line); + seqs.addElement(seq); + } else { + // header lines - keep them for the alignment comments. + headerLines.append(line); + headerLines.append("\n"); + numHeaderLines++; + } + } + while (!idsFound); + if (line==null) + break; // end of file. + int starCol = line.indexOf("*"); + seqstrings = new StringBuffer[seqs.size()]; + + for (int i = 0; i < seqs.size(); i++) + { + if (seqstrings[i] == null) + { + seqstrings[i] = new StringBuffer(); + } + } + + try { + line = nextLine(); + while (line!=null && line.indexOf("*") == -1) + { + for (int i = 0; i < seqs.size(); i++) + { + if (line.length() > (i + starCol)) + { + seqstrings[i].append(line.charAt(i + starCol)); + } + } + line = nextLine(); + } + } catch (IOException e) { + if (iterationCount==0) { + throw(e); // otherwise we've just run out of iterations. + } else { + iterationSkips=0; + } + } + iterationCount++; + } while (--iterationSkips!=-1); + + for (int i = 0; i < seqs.size(); i++) + { + Sequence newSeq = (Sequence) seqs.elementAt(i); + + newSeq.setSequence(seqstrings[i].toString()); + } + if (seqs.size()>0) + { + if (headerLines.length()>1+numHeaderLines) // could see if buffer is just whitespace or not. + setAlignmentProperty("Comments", headerLines.toString()); + setAlignmentProperty("iteration", ""+iterationCount); + } + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String print() + { + return print(getSeqsAsArray()); + } + + /** + * DOCUMENT ME! + * + * @param s DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String print(SequenceI[] s) + { + StringBuffer out = new StringBuffer(); + /** + * A general parser for ids. Will look for dbrefs in + * Uniprot format source|id + * And also Jalview /start-end + * + * @String id Id to be parsed + */ + int i = 0; + int max = -1; + + while ( (i < s.length) && (s[i] != null)) + { + out.append(">" + printId(s[i])); + if (s[i].getDescription() != null) + { + out.append(" " + s[i].getDescription()); + } + + out.append("\n"); + + if (s[i].getSequence().length > max) + { + max = s[i].getSequence().length; + } + + i++; + } + + out.append("* iteration 1\n"); + + for (int j = 0; j < max; j++) + { + i = 0; + + while ( (i < s.length) && (s[i] != null)) + { + if (s[i].getSequence().length > j) + { + out.append(s[i].getSequenceAsString(j, j + 1)); + } + else + { + out.append("-"); + } + + i++; + } + + out.append("\n"); + } + + out.append("*\n"); + + return out.toString(); + } +}