X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=ceeac648b12964b1f95944155d17f63cfe101e18;hb=e6879a932d0144d64a5ab703ae311aed0eeb83e5;hp=e0750d528147006a8c981ce5fa768d1d581e27c1;hpb=1d6ae39a6442c455d362b933f1da89b0a481e5f5;p=jalview.git diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java index e0750d5..ceeac64 100755 --- a/src/jalview/io/BLCFile.java +++ b/src/jalview/io/BLCFile.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* 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 @@ -25,26 +25,51 @@ import java.io.*; import java.util.*; -public class BLCFile extends AlignFile { +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class BLCFile extends AlignFile +{ Vector titles; - public BLCFile() { + /** + * Creates a new BLCFile object. + */ + public BLCFile() + { } - public BLCFile(String inStr) { - super(inStr); - } - public BLCFile(String inFile, String type) throws IOException { + /** + * 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 void initData() { + /** + * DOCUMENT ME! + */ + public void initData() + { super.initData(); titles = new Vector(); } - public void parse() { + /** + * DOCUMENT ME! + */ + public void parse() throws IOException + { boolean idsFound = false; Vector ids = new Vector(); StringBuffer[] seqstrings; @@ -53,12 +78,13 @@ public class BLCFile extends AlignFile { String line = null; - try { - do { + do + { line = nextLine(); // seek end of ids - if (line.indexOf("*") > -1) { + if (line.indexOf("*") > -1) + { idsFound = true; break; @@ -66,101 +92,104 @@ public class BLCFile extends AlignFile { 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"); - } - - } + if (abracket > -1) + { + if (line.indexOf(" ") > -1) // + { + line = line.substring(abracket + 1, + line.indexOf(" ", abracket + 1)); + } + else + line = line.substring(abracket+1); + + + Sequence seq = parseId(line); + ids.addElement(seq.getName()); + starts.addElement(seq.getStart() + ""); + ends.addElement(seq.getEnd() + ""); } - } while (!idsFound); + } + while (!idsFound); int starCol = line.indexOf("*"); seqstrings = new StringBuffer[ids.size()]; - for (int i = 0; i < ids.size(); i++) { - if (seqstrings[i] == null) { + 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)) { + 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())); + 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())); + + if (!isValidProteinSequence(newSeq.getSequence())) + { + throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS + +" : "+ newSeq.getName() + +" : "+invalidCharacter); + + } + seqs.addElement(newSeq); } - } catch (Exception ex) { - ex.printStackTrace(); - } + } - public String print() { + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String print() + { return print(getSeqsAsArray()); } - public static String print(SequenceI[] s) { + /** + * 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(">" + s[i].getName() + "/" + s[i].getStart() + "-" + - s[i].getEnd() + "\n"); + while ((i < s.length) && (s[i] != null)) + { + out.append(">" + printId(s[i]) +"\n"); - if (s[i].getSequence().length() > max) { + if (s[i].getSequence().length() > max) + { max = s[i].getSequence().length(); } @@ -169,13 +198,18 @@ public class BLCFile extends AlignFile { out.append("* iteration 1\n"); - for (int j = 0; j < max; j++) { + for (int j = 0; j < max; j++) + { i = 0; - while ((i < s.length) && (s[i] != null)) { - if (s[i].getSequence().length() > j) { + while ((i < s.length) && (s[i] != null)) + { + if (s[i].getSequence().length() > j) + { out.append(s[i].getSequence().substring(j, j + 1)); - } else { + } + else + { out.append("-"); }