2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.bin.Cache;
24 import jalview.datamodel.Sequence;
25 import jalview.datamodel.SequenceI;
26 import jalview.util.Comparison;
28 import java.io.IOException;
30 public class PIRFile extends AlignFile
32 // Vector words = new Vector(); // Stores the words in a line after splitting
38 public PIRFile(String inFile, DataSourceType sourceType)
41 super(inFile, sourceType);
44 public PIRFile(FileParse source) throws IOException
50 public void parse() throws IOException
52 StringBuffer sequence;
54 ModellerDescription md;
56 while ((line = nextLine()) != null)
58 if (line.length() == 0)
60 // System.out.println("blank line");
63 if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
67 Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
69 sequence = new StringBuffer();
71 newSeq.setDescription(nextLine()); // this is the title line
73 boolean starFound = false;
78 sequence.append(line);
85 if (line.indexOf("*") > -1)
91 if (sequence.length() > 0)
93 sequence.setLength(sequence.length() - 1);
94 newSeq.setSequence(sequence.toString());
96 seqs.addElement(newSeq);
98 md = new ModellerDescription(newSeq.getDescription());
99 md.updateSequenceI(newSeq);
105 public String print(SequenceI[] s, boolean jvsuffix)
107 boolean is_NA = Comparison.isNucleotide(s);
109 StringBuffer out = new StringBuffer();
111 ModellerDescription md;
112 boolean useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
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());
133 if (s[i].getDescription() == null)
135 out.append(s[i].getName() + " "
136 + (s[i].getEnd() - s[i].getStart() + 1));
137 out.append(is_NA ? " bases" : " residues");
142 out.append(s[i].getDescription());
148 if (useModellerOutput)
150 out.append(">P1;" + s[i].getName());
152 md = new ModellerDescription(s[i]);
153 out.append(md.getDescriptionLine());
158 out.append(">P1;" + printId(s[i], jvsuffix));
160 if (s[i].getDescription() != null)
162 out.append(s[i].getDescription());
167 out.append(s[i].getName() + " "
168 + (s[i].getEnd() - s[i].getStart() + 1) + " residues");
173 int nochunks = (seq.length() / len)
174 + (seq.length() % len > 0 ? 1 : 0);
176 for (int j = 0; j < nochunks; j++)
179 int end = start + len;
181 if (end < seq.length())
183 out.append(seq.substring(start, end));
186 else if (start < seq.length())
188 out.append(seq.substring(start));
196 return out.toString();