2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
29 * Read and write PileUp style MSF Files. This used to be the MSFFile class, and
30 * was written according to the EBI's idea of a subset of the MSF alignment
31 * format. But, that was updated to reflect current GCG style IO fashion, as
32 * found in Emboss (thanks David Martin!)
37 import jalview.datamodel.*;
38 import jalview.util.*;
40 public class PileUpfile extends MSFfile
44 * Creates a new MSFfile object.
51 * Creates a new MSFfile object.
61 public PileUpfile(String inFile, String type) throws IOException
66 public PileUpfile(FileParse source) throws IOException
74 * @return DOCUMENT ME!
78 return print(getSeqsAsArray());
81 public String print(SequenceI[] s)
83 StringBuffer out = new StringBuffer("PileUp");
92 int[] checksums = new int[s.length];
95 checksums[i] = checkSum(s[i].getSequenceAsString());
96 bigChecksum += checksums[i];
100 out.append(" MSF: " + s[0].getSequence().length
101 + " Type: P Check: " + bigChecksum % 10000
108 while ((i < s.length) && (s[i] != null))
110 String seq = s[i].getSequenceAsString();
111 out.append(" Name: " + printId(s[i]) + " oo Len: " + seq.length()
112 + " Check: " + checksums[i] + " Weight: 1.00");
115 if (seq.length() > max)
120 if (s[i].getName().length() > maxid)
122 maxid = s[i].getName().length();
134 out.append(newline);out.append(newline);out.append("//");
135 out.append(newline);out.append(newline);
139 int nochunks = (max / len) + 1;
141 if ((max % len) == 0)
146 for (i = 0; i < nochunks; i++)
150 while ((j < s.length) && (s[j] != null))
152 String name = printId(s[j]);
154 out.append(new Format("%-" + maxid + "s").form(name + " "));
156 for (int k = 0; k < 5; k++)
158 int start = (i * 50) + (k * 10);
159 int end = start + 10;
161 if ((end < s[j].getSequence().length)
162 && (start < s[j].getSequence().length))
164 out.append(s[j].getSequence(start, end));
177 if (start < s[j].getSequence().length)
179 out.append(s[j].getSequenceAsString().substring(start));
198 return out.toString();