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.datamodel.Sequence;
24 import jalview.datamodel.SequenceI;
26 import java.io.IOException;
27 import java.util.Vector;
29 public class PIRFile extends AlignFile
31 public static boolean useModellerOutput = false;
33 Vector words = new Vector(); // Stores the words in a line after splitting
39 public PIRFile(String inFile, String type) throws IOException
44 public PIRFile(FileParse source) throws IOException
49 public void parse() throws IOException
51 StringBuffer sequence;
53 ModellerDescription md;
55 while ((line = nextLine()) != null)
57 if (line.length() == 0)
59 // System.out.println("blank line");
62 if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
66 Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
68 sequence = new StringBuffer();
70 newSeq.setDescription(nextLine()); // this is the title line
72 boolean starFound = false;
77 sequence.append(line);
84 if (line.indexOf("*") > -1)
90 if (sequence.length() > 0)
92 sequence.setLength(sequence.length() - 1);
93 newSeq.setSequence(sequence.toString());
95 seqs.addElement(newSeq);
97 md = new ModellerDescription(newSeq.getDescription());
98 md.updateSequenceI(newSeq);
103 public String print()
105 return print(getSeqsAsArray());
108 public String print(SequenceI[] s)
110 boolean is_NA = jalview.util.Comparison.isNucleotide(s);
112 StringBuffer out = new StringBuffer();
114 ModellerDescription md;
116 while ((i < s.length) && (s[i] != null))
118 String seq = s[i].getSequenceAsString();
123 // modeller doesn't really do nucleotides, so we don't do anything fancy
124 // Official tags area as follows, for now we'll use P1 and DL
125 // Protein (complete) P1
126 // Protein (fragment) F1
132 // other functional RNA N1
134 out.append(">N1;" + s[i].getName());
136 if (s[i].getDescription() == null)
138 out.append(s[i].getName() + " "
139 + (s[i].getEnd() - s[i].getStart() + 1));
140 out.append(is_NA ? " bases" : " residues");
145 out.append(s[i].getDescription());
152 if (useModellerOutput)
154 out.append(">P1;" + s[i].getName());
156 md = new ModellerDescription(s[i]);
157 out.append(md.getDescriptionLine());
162 out.append(">P1;" + printId(s[i]));
164 if (s[i].getDescription() != null)
166 out.append(s[i].getDescription());
171 out.append(s[i].getName() + " "
172 + (s[i].getEnd() - s[i].getStart() + 1) + " residues");
177 int nochunks = (seq.length() / len) + 1;
179 for (int j = 0; j < nochunks; j++)
182 int end = start + len;
184 if (end < seq.length())
186 out.append(seq.substring(start, end));
189 else if (start < seq.length())
191 out.append(seq.substring(start));
199 return out.toString();