X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=de0d8a34d122164dede50dc4d6a16e17a4213c9c;hb=6b1d4e765d7a6beafcc1eb1fec38e041f3fb780f;hp=f5f709e8147b3880fa457181a7627d5a680d7c47;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index f5f709e..de0d8a3 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,267 +1,202 @@
/*
-* 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
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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
Title:
- * PileUpfile - *Description:
- * - * Read and write PileUp style MSF Files. - * This used to be the MSFFile class, and was written according to the EBI's idea - * of a subset of the MSF alignment format. But, that was updated to reflect current - * GCG style IO fashion, as found in Emboss (thanks David Martin!) - * - **/ - + *+ * Title: + *
+ * PileUpfile + *+ * Description: + *
+ * + * Read and write PileUp style MSF Files. This used to be the MSFFile class, and + * was written according to the EBI's idea of a subset of the MSF alignment + * format. But, that was updated to reflect current GCG style IO fashion, as + * found in Emboss (thanks David Martin!) + * + */ +import java.io.*; import jalview.datamodel.*; import jalview.util.*; -import java.io.*; -import java.util.*; - - -public class PileUpfile - extends AlignFile +public class PileUpfile extends MSFfile { -public PileUpfile() -{} - -public PileUpfile(String inStr) { - super(inStr); -} - -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(); + /** + * Creates a new MSFfile object. + */ + public PileUpfile() + { } - this.noSeqs = headers.size(); + /** + * 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); + } - //Add sequences to the hash - for (i = 0; i < headers.size(); i++ ) { + public PileUpfile(FileParse source) throws IOException + { + super(source); + } - if ( seqhash.get(headers.elementAt(i)) != null) { - String head = headers.elementAt(i).toString(); - String seq = seqhash.get(head).toString(); + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String print() + { + return print(getSeqsAsArray()); + } - int start = 1; - int end = seq.length(); + public String print(SequenceI[] s) + { + StringBuffer out = new StringBuffer("PileUp"); + out.append(newline); + out.append(newline); + + int max = 0; + int maxid = 0; + + int i = 0; + int bigChecksum = 0; + int[] checksums = new int[s.length]; + while (i < s.length) + { + checksums[i] = checkSum(s[i].getSequenceAsString()); + bigChecksum += checksums[i]; + i++; + } - if (maxLength < head.length() ) { - maxLength = head.length(); + out.append(" MSF: " + s[0].getSequence().length + + " Type: P Check: " + bigChecksum % 10000 + " .."); + out.append(newline); + out.append(newline); + out.append(newline); + + i = 0; + while ((i < s.length) && (s[i] != null)) + { + String seq = s[i].getSequenceAsString(); + out.append(" Name: " + printId(s[i]) + " oo Len: " + seq.length() + + " Check: " + checksums[i] + " Weight: 1.00"); + out.append(newline); + + if (seq.length() > max) + { + max = seq.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(); - } - } + if (s[i].getName().length() > maxid) + { + maxid = s[i].getName().length(); } - 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)); + i++; } - } - -} - -public static int checkSum(String seq) { - //String chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@"; - int check = 0; - - String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@"; - index += "--------------------------------------------------------------------------------------------------------------------------------"; - for(int i = 0; i < seq.length(); i++) { - try { - if (i