X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=4715d9cd0f49df7bcbb97d6c296b4397c4602c1d;hb=7e1a8203d671e11bdc3eedf19c808f30f7a7c348;hp=87a1652e39ceac45d00b049b0cb627af3a24e2cd;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java index 87a1652..4715d9c 100755 --- a/src/jalview/io/PileUpfile.java +++ b/src/jalview/io/PileUpfile.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) 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 @@ -30,170 +30,46 @@ package jalview.io; * **/ import java.io.*; -import java.util.*; import jalview.datamodel.*; import jalview.util.*; public class PileUpfile - extends AlignFile + extends MSFfile { - public PileUpfile() - { - } - public PileUpfile(String inStr) + /** + * Creates a new MSFfile object. + */ + public PileUpfile() { - super(inStr); } + /** + * Creates a new MSFfile object. + * + * @param inFile DOCUMENT ME! + * @param type DOCUMENT ME! + * + * @throws IOException DOCUMENT ME! + */ public PileUpfile(String inFile, String type) throws IOException { super(inFile, type); } - public void parse() - { - int i = 0; - boolean seqFlag = false; - String key = new String(); - Vector headers = new Vector(); - Hashtable seqhash = new Hashtable(); - String line; - - try - { - while ( (line = nextLine()) != null) - { - StringTokenizer str = new StringTokenizer(line); - - while (str.hasMoreTokens()) - { - String inStr = str.nextToken(); - - //If line has header information add to the headers vector - if (inStr.indexOf("Name:") != -1) - { - key = str.nextToken(); - headers.addElement(key); - } - - //if line has // set SeqFlag to 1 so we know sequences are coming - if (inStr.indexOf("//") != -1) - { - seqFlag = true; - } - - //Process lines as sequence lines if seqFlag is set - if ( (inStr.indexOf("//") == -1) && (seqFlag == true)) - { - //seqeunce id is the first field - key = inStr; - - StringBuffer tempseq; - - //Get sequence from hash if it exists - if (seqhash.containsKey(key)) - { - tempseq = (StringBuffer) seqhash.get(key); - } - else - { - tempseq = new StringBuffer(); - seqhash.put(key, tempseq); - } - - //loop through the rest of the words - while (str.hasMoreTokens()) - { - //append the word to the sequence - tempseq.append(str.nextToken()); - } - } - } - } - } - catch (IOException e) - { - System.err.println("Exception parsing PileUpfile " + e); - e.printStackTrace(); - } - - this.noSeqs = headers.size(); - - //Add sequences to the hash - for (i = 0; i < headers.size(); i++) - { - if (seqhash.get(headers.elementAt(i)) != null) - { - String head = headers.elementAt(i).toString(); - String seq = seqhash.get(head).toString(); - - int start = 1; - int end = -1; - - if (maxLength < head.length()) - { - maxLength = head.length(); - } - - if (head.indexOf("/") > 0) - { - StringTokenizer st = new StringTokenizer(head, "/"); - - if (st.countTokens() == 2) - { - head = st.nextToken(); - - String tmp = st.nextToken(); - st = new StringTokenizer(tmp, "-"); - - if (st.countTokens() == 2) - { - start = Integer.valueOf(st.nextToken()).intValue(); - end = Integer.valueOf(st.nextToken()).intValue(); - } - } - } - - Sequence newSeq = new Sequence(head, seq, start, end); - - seqs.addElement(newSeq); - } - else - { - System.err.println( - "PileUpfile Parser: Can't find sequence for " + - headers.elementAt(i)); - } - } - } - - public static int checkSum(String seq) + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String print() { - - int check = 0; - - String sequence = seq.toUpperCase(); - - for (int i = 0; i < sequence.length(); i++) - { - if (i < sequence.length()) - { - int value = sequence.charAt(i); - if (value != -1) - { - check += (i % 57 + 1) * value; - } - } - - } - - return check % 10000; + return print(getSeqsAsArray()); } - public static String print(SequenceI[] s) + public String print(SequenceI[] s) { StringBuffer out = new StringBuffer("PileUp\n\n"); @@ -205,20 +81,21 @@ public class PileUpfile int[] checksums = new int[s.length]; while (i < s.length) { - checksums[i] = checkSum(s[i].getSequence()); + checksums[i] = checkSum(s[i].getSequenceAsString()); bigChecksum += checksums[i]; i++; } - out.append(" MSF: " + s[0].getSequence().length() + - " Type: P Check: " + bigChecksum%10000 + " ..\n\n\n"); + out.append(" MSF: " + s[0].getSequence().length + + " Type: P Check: " + bigChecksum % 10000 + " ..\n\n\n"); - i=0; + i = 0; while ( (i < s.length) && (s[i] != null)) { - String seq = s[i].getSequence(); - out.append(" Name: " + s[i].getName() + " oo Len: " + - s[i].getSequence().length() + " Check: " + checksums[i] + + String seq = s[i].getSequenceAsString(); + out.append(" Name: " + printId(s[i]) + + " oo Len: " + + seq.length() + " Check: " + checksums[i] + " Weight: 1.00\n"); if (seq.length() > max) @@ -257,18 +134,19 @@ public class PileUpfile while ( (j < s.length) && (s[j] != null)) { - String name = s[j].getName(); - out.append(new Format("%-" + maxid + "s").form(name) + " "); + String name = printId(s[j]); + + out.append(new Format("%-" + maxid + "s").form(name + " ")); for (int k = 0; k < 5; k++) { int start = (i * 50) + (k * 10); int end = start + 10; - if ( (end < s[j].getSequence().length()) && - (start < s[j].getSequence().length())) + if ( (end < s[j].getSequence().length) && + (start < s[j].getSequence().length)) { - out.append(s[j].getSequence().substring(start, end)); + out.append(s[j].getSequence(start, end)); if (k < 4) { @@ -281,9 +159,9 @@ public class PileUpfile } else { - if (start < s[j].getSequence().length()) + if (start < s[j].getSequence().length) { - out.append(s[j].getSequence().substring(start)); + out.append(s[j].getSequenceAsString().substring(start)); out.append("\n"); } else @@ -304,9 +182,4 @@ public class PileUpfile return out.toString(); } - - public String print() - { - return print(getSeqsAsArray()); - } }