/* * 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; /** *

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.*; public class PileUpfile extends MSFfile { /** * Creates a new MSFfile object. */ public PileUpfile() { } /** * 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); } /** * DOCUMENT ME! * * @return DOCUMENT ME! */ public String print() { return print(getSeqsAsArray()); } public String print(SequenceI[] s) { StringBuffer out = new StringBuffer("PileUp\n\n"); 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++; } out.append(" MSF: " + s[0].getSequence().length + " Type: P Check: " + bigChecksum % 10000 + " ..\n\n\n"); 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\n"); if (seq.length() > max) { max = seq.length(); } if (s[i].getName().length() > maxid) { maxid = s[i].getName().length(); } i++; } if (maxid < 10) { maxid = 10; } maxid++; out.append("\n\n//\n\n"); int len = 50; int nochunks = (max / len) + 1; if ( (max % len) == 0) { nochunks--; } for (i = 0; i < nochunks; i++) { int j = 0; while ( (j < s.length) && (s[j] != null)) { 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)) { out.append(s[j].getSequence(start, end)); if (k < 4) { out.append(" "); } else { out.append("\n"); } } else { if (start < s[j].getSequence().length) { out.append(s[j].getSequenceAsString().substring(start)); out.append("\n"); } else { if (k == 0) { out.append("\n"); } } } } j++; } out.append("\n"); } return out.toString(); } }