X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=e8266873cae529d7f726810ce402d6ba740964c5;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=cd465419ba703a83e6f072b5fbb6cfda9c3be900;hpb=3a993bbe274824870c78bd7695c42fa93908cb30;p=jalview.git diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java index cd46541..e826687 100755 --- a/src/jalview/io/PileUpfile.java +++ b/src/jalview/io/PileUpfile.java @@ -1,41 +1,46 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors + * + * 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. - * - * 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 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; /** - *

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 + *

+ * 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 jalview.datamodel.SequenceI; +import jalview.util.Format; + +import java.io.IOException; + +public class PileUpfile extends MSFfile { /** @@ -47,24 +52,28 @@ public class PileUpfile /** * Creates a new MSFfile object. - * - * @param inFile DOCUMENT ME! - * @param type DOCUMENT ME! - * - * @throws IOException DOCUMENT ME! + * + * @param inFile + * DOCUMENT ME! + * @param type + * DOCUMENT ME! + * + * @throws IOException + * DOCUMENT ME! */ - public PileUpfile(String inFile, String type) - throws IOException + public PileUpfile(String inFile, String type) throws IOException { super(inFile, type); } + public PileUpfile(FileParse source) throws IOException { super(source); } + /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public String print() @@ -74,7 +83,9 @@ public class PileUpfile public String print(SequenceI[] s) { - StringBuffer out = new StringBuffer("PileUp\n\n"); + StringBuffer out = new StringBuffer("PileUp"); + out.append(newline); + out.append(newline); int max = 0; int maxid = 0; @@ -89,17 +100,19 @@ public class PileUpfile 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 + " .."); + out.append(newline); + out.append(newline); + out.append(newline); i = 0; - while ( (i < s.length) && (s[i] != null)) + 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"); + out.append(" Name: " + printId(s[i]) + " oo Len: " + seq.length() + + " Check: " + checksums[i] + " Weight: 1.00"); + out.append(newline); if (seq.length() > max) { @@ -120,13 +133,17 @@ public class PileUpfile } 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; - if ( (max % len) == 0) + if ((max % len) == 0) { nochunks--; } @@ -135,7 +152,7 @@ public class PileUpfile { int j = 0; - while ( (j < s.length) && (s[j] != null)) + while ((j < s.length) && (s[j] != null)) { String name = printId(s[j]); @@ -146,8 +163,8 @@ public class PileUpfile 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(start, end)); @@ -157,7 +174,7 @@ public class PileUpfile } else { - out.append("\n"); + out.append(newline); } } else @@ -165,13 +182,13 @@ public class PileUpfile 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); } } } @@ -180,7 +197,7 @@ public class PileUpfile j++; } - out.append("\n"); + out.append(newline); } return out.toString();