X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=b3cdfe810e24260d4987f298be64946c8201bf9b;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=73d0f0f6fa5dca4d1cad9dab68e4b5301d8dfea0;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java index 73d0f0f..b3cdfe8 100755 --- a/src/jalview/io/MSFfile.java +++ b/src/jalview/io/MSFfile.java @@ -1,28 +1,33 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; -import java.io.*; -import java.util.*; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.util.Format; -import jalview.datamodel.*; -import jalview.util.*; +import java.io.IOException; +import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; /** * DOCUMENT ME! @@ -44,12 +49,12 @@ public class MSFfile extends AlignFile * Creates a new MSFfile object. * * @param inFile - * DOCUMENT ME! + * DOCUMENT ME! * @param type - * DOCUMENT ME! + * DOCUMENT ME! * * @throws IOException - * DOCUMENT ME! + * DOCUMENT ME! */ public MSFfile(String inFile, String type) throws IOException { @@ -61,10 +66,6 @@ public class MSFfile extends AlignFile super(source); } - { - // TODO Auto-generated constructor stub - } - /** * DOCUMENT ME! */ @@ -170,7 +171,7 @@ public class MSFfile extends AlignFile * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -203,9 +204,9 @@ public class MSFfile extends AlignFile * DOCUMENT ME! * * @param s - * DOCUMENT ME! + * DOCUMENT ME! * @param is_NA - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -217,9 +218,10 @@ public class MSFfile extends AlignFile SequenceI[] s = new SequenceI[seqs.length]; StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") - + "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't - // remember NA or AA yet. - + + "_MULTIPLE_ALIGNMENT 1.0"); + // TODO: JBPNote : Jalview doesn't remember NA or AA yet. + out.append(newline); + out.append(newline); int max = 0; int maxid = 0; int i = 0; @@ -228,7 +230,7 @@ public class MSFfile extends AlignFile { // Replace all internal gaps with . and external spaces with ~ s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString() - .replace('-', '.')); + .replace('-', '.'), seqs[i].getStart(), seqs[i].getEnd()); StringBuffer sb = new StringBuffer(); sb.append(s[i].getSequence()); @@ -285,7 +287,10 @@ public class MSFfile extends AlignFile long maxNB = 0; out.append(" MSF: " + s[0].getSequence().length + " Type: " + (is_NA ? "N" : "P") + " Check: " + (bigChecksum % 10000) - + " ..\n\n\n"); + + " .."); + out.append(newline); + out.append(newline); + out.append(newline); String[] nameBlock = new String[s.length]; String[] idBlock = new String[s.length]; @@ -298,7 +303,7 @@ public class MSFfile extends AlignFile idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getSequence().length) + " Check: " - + maxChkpad.form(checksums[i]) + " Weight: 1.00\n"); + + maxChkpad.form(checksums[i]) + " Weight: 1.00" + newline); if (s[i].getName().length() > maxid) { @@ -331,8 +336,11 @@ public class MSFfile extends AlignFile } maxid++; - out.append("\n\n//\n\n"); - + out.append(newline); + out.append(newline); + out.append("//"); + out.append(newline); + out.append(newline); int len = 50; int nochunks = (max / len) + 1; @@ -368,7 +376,7 @@ public class MSFfile extends AlignFile } else { - out.append("\n"); + out.append(newline); } } else @@ -376,13 +384,13 @@ public class MSFfile extends AlignFile if (start < s[j].getSequence().length) { out.append(s[j].getSequenceAsString().substring(start)); - out.append("\n"); + out.append(newline); } else { if (k == 0) { - out.append("\n"); + out.append(newline); } } } @@ -391,7 +399,7 @@ public class MSFfile extends AlignFile j++; } - out.append("\n"); + out.append(newline); } return out.toString();