2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 import jalview.datamodel.*;
26 public class PIRFile extends AlignFile
28 public static boolean useModellerOutput = false;
30 Vector words = new Vector(); // Stores the words in a line after splitting
36 public PIRFile(String inFile, String type) throws IOException
41 public PIRFile(FileParse source) throws IOException
46 public void parse() throws IOException
48 StringBuffer sequence;
50 ModellerDescription md;
52 while ((line = nextLine()) != null)
54 if (line.length() == 0)
56 // System.out.println("blank line");
59 if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
63 Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
65 sequence = new StringBuffer();
67 newSeq.setDescription(nextLine()); // this is the title line
69 boolean starFound = false;
74 sequence.append(line);
81 if (line.indexOf("*") > -1)
87 if (sequence.length() > 0)
89 sequence.setLength(sequence.length() - 1);
90 newSeq.setSequence(sequence.toString());
92 seqs.addElement(newSeq);
94 md = new ModellerDescription(newSeq.getDescription());
95 md.updateSequenceI(newSeq);
100 public String print()
102 return print(getSeqsAsArray());
105 public String print(SequenceI[] s)
107 boolean is_NA = jalview.util.Comparison.isNucleotide(s);
109 StringBuffer out = new StringBuffer();
111 ModellerDescription md;
113 while ((i < s.length) && (s[i] != null))
115 String seq = s[i].getSequenceAsString();
120 // modeller doesn't really do nucleotides, so we don't do anything fancy
121 // Official tags area as follows, for now we'll use P1 and DL
122 // Protein (complete) P1
123 // Protein (fragment) F1
129 // other functional RNA N1
131 out.append(">N1;" + s[i].getName() + "\n");
132 if (s[i].getDescription() == null)
134 out.append(s[i].getName() + " "
135 + (s[i].getEnd() - s[i].getStart() + 1));
136 out.append(is_NA ? " bases\n" : " residues\n");
140 out.append(s[i].getDescription() + "\n");
146 if (useModellerOutput)
148 out.append(">P1;" + s[i].getName() + "\n");
149 md = new ModellerDescription(s[i]);
150 out.append(md.getDescriptionLine() + "\n");
154 out.append(">P1;" + printId(s[i]) + "\n");
155 if (s[i].getDescription() != null)
157 out.append(s[i].getDescription() + "\n");
162 .append(s[i].getName() + " "
163 + (s[i].getEnd() - s[i].getStart() + 1)
168 int nochunks = (seq.length() / len) + 1;
170 for (int j = 0; j < nochunks; j++)
173 int end = start + len;
175 if (end < seq.length())
177 out.append(seq.substring(start, end) + "\n");
179 else if (start < seq.length())
181 out.append(seq.substring(start) + "\n");
188 return out.toString();