X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=e0750d528147006a8c981ce5fa768d1d581e27c1;hb=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;hp=8db0a9ad177152cb4d5fc1e903b8c4259d2e49e4;hpb=2bb0a2c4156ec75795c595df0c6300411557b066;p=jalview.git diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java index 8db0a9a..e0750d5 100755 --- a/src/jalview/io/BLCFile.java +++ b/src/jalview/io/BLCFile.java @@ -1,148 +1,192 @@ -/* Jalview - a java multiple alignment editor - * Copyright (C) 1998 Michele Clamp - * - * 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. - */ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 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.*; -import java.net.*; -import java.awt.Font; -public class BLCFile extends AlignFile { - Vector titles; +public class BLCFile extends AlignFile { + Vector titles; - public BLCFile() - {} + public BLCFile() { + } - public BLCFile(String inStr) { - super(inStr); - } + public BLCFile(String inStr) { + super(inStr); + } - public void initData() { - super.initData(); - titles = new Vector(); - } + public BLCFile(String inFile, String type) throws IOException { + super(inFile, type); + } - public BLCFile(String inFile, String type) throws IOException { - super(inFile,type); - } + public void initData() { + super.initData(); + titles = new Vector(); + } + public void parse() { + boolean idsFound = false; + Vector ids = new Vector(); + StringBuffer[] seqstrings; + Vector starts = new Vector(); + Vector ends = new Vector(); + + String line = null; + + try { + do { + line = nextLine(); + + // seek end of ids + if (line.indexOf("*") > -1) { + idsFound = true; + + break; + } + + int abracket = line.indexOf(">"); + + if (abracket > -1) { + if (line.indexOf(" ") > -1) // + { + ///Colur it be this format? + //>54402046 0 1 137 137: + // or this?? + // 1 >L1H14 30539 343 + try { + ids.addElement(line.substring(abracket + 1, + line.indexOf(" ", abracket + 1))); + + // remove p Value + line = line.substring(abracket + 1); + line = line.substring(line.indexOf(" ") + 1); + line = line.trim(); + line = line.substring(line.indexOf(" ") + 1); + line = line.trim(); + + int value = Integer.parseInt(line.substring(0, + line.indexOf(" "))); + starts.addElement(value + ""); + line = line.substring(line.indexOf(" ") + 1); + line = line.trim(); + value = Integer.parseInt(line.substring(0, + line.indexOf(" "))); + ends.addElement(value + ""); + } catch (Exception ex) { + System.err.println("Error during blockfile read."); + ex.printStackTrace(); + starts.addElement("0"); + ends.addElement("0"); + } + } else { + if(line.indexOf("/")>-1) + { + ids.addElement(line.substring(abracket + 1, + line.indexOf("/"))); + line = line.substring(line.indexOf("/") + 1); + starts.addElement(line.substring(0, line.indexOf("-"))); + ends.addElement(line.substring(line.indexOf("-") + 1)); + } + else{ + ids.addElement(line.substring(abracket+1)); + starts.addElement("0"); + ends.addElement("0"); + } + + } + } + } while (!idsFound); + + int starCol = line.indexOf("*"); + seqstrings = new StringBuffer[ids.size()]; + + for (int i = 0; i < ids.size(); i++) { + if (seqstrings[i] == null) { + seqstrings[i] = new StringBuffer(); + } + } + + while ((line = nextLine()).indexOf("*") == -1) { + for (int i = 0; i < ids.size(); i++) { + if (line.length() > (i + starCol)) { + seqstrings[i].append(line.charAt(i + starCol)); + } + } + } + + for (int i = 0; i < ids.size(); i++) { + Sequence newSeq = new Sequence(ids.elementAt(i).toString(), + seqstrings[i].toString(), + Integer.parseInt(starts.elementAt(i).toString()), + Integer.parseInt(ends.elementAt(i).toString())); + seqs.addElement(newSeq); + } + } catch (Exception ex) { + ex.printStackTrace(); + } + } - public void parse() - { - boolean idsFound=false; - Vector ids = new Vector(); - StringBuffer seqstrings []; - Vector starts = new Vector(); - Vector ends = new Vector(); + public String print() { + return print(getSeqsAsArray()); + } - String line=null; - try{ - do{ - line = nextLine(); + public static String print(SequenceI[] s) { + StringBuffer out = new StringBuffer(); - // seek end of ids - if (line.indexOf("*") > -1) - { - idsFound=true; - break; - } + int i = 0; + int max = -1; - int abracket = line.indexOf(">"); + while ((i < s.length) && (s[i] != null)) { + out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" + + s[i].getEnd() + "\n"); - if (abracket > -1) - { + if (s[i].getSequence().length() > max) { + max = s[i].getSequence().length(); + } - if(line.indexOf(" ")>-1) - { - ids.addElement(line.substring(abracket+1, line.indexOf(" ", abracket+1))); - starts.addElement("0"); - ends.addElement("0"); - } - else - { - ids.addElement( line.substring(abracket + 1, line.indexOf("/"))); - line = line.substring(line.indexOf("/") + 1); - starts.addElement(line.substring(0, line.indexOf("-"))); - ends.addElement(line.substring(line.indexOf("-") + 1)); + i++; } - } - }while(!idsFound); - - int starCol = line.indexOf("*"); - seqstrings = new StringBuffer[ids.size()]; - for(int i=0; ii+starCol) - seqstrings[i].append(line.charAt(i + starCol)); - } - } + out.append("* iteration 1\n"); - for(int i=0; i" + s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd() + "\n"); - if (s[i].getSequence().length() > max) { max = s[i].getSequence().length();} - i++; - } + while ((i < s.length) && (s[i] != null)) { + if (s[i].getSequence().length() > j) { + out.append(s[i].getSequence().substring(j, j + 1)); + } else { + out.append("-"); + } + + 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].getSequence().substring(j,j+1)); - else - out.append("-"); - i++; + out.append("\n"); } - out.append("\n"); - } - out.append("*\n"); - return out.toString(); - } + out.append("*\n"); + + return out.toString(); + } }