2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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21 import jalview.analysis.*;
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23 import jalview.datamodel.*;
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30 public class PIRFile extends AlignFile {
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31 Vector words = new Vector(); //Stores the words in a line after splitting
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36 public PIRFile(String inStr) {
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40 public PIRFile(String inFile, String type) throws IOException {
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41 super(inFile, type);
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44 public void parse() {
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49 StringBuffer sequence;
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52 while ((line = nextLine()) != null) {
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54 id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));
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55 line = line.substring(line.indexOf("/") + 1);
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56 start = line.substring(0, line.indexOf("-"));
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57 end = line.substring(line.indexOf("-") + 1);
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58 } catch (Exception ex) {
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64 sequence = new StringBuffer();
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66 line = nextLine(); // this is the title line
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68 boolean starFound = false;
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72 sequence.append(line);
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74 if (line.indexOf("*") > -1) {
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77 } while (!starFound);
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79 sequence.setLength(sequence.length() - 1);
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81 Sequence newSeq = new Sequence(id, sequence.toString(),
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82 Integer.parseInt(start), Integer.parseInt(end));
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83 seqs.addElement(newSeq);
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85 } catch (Exception ex) {
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86 ex.printStackTrace();
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90 public String print() {
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91 return print(getSeqsAsArray());
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94 public static String print(SequenceI[] s) {
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95 return print(s, 72, true);
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98 public static String print(SequenceI[] s, int len) {
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99 return print(s, len, true);
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102 public static String print(SequenceI[] s, int len, boolean gaps) {
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103 StringBuffer out = new StringBuffer();
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106 while ((i < s.length) && (s[i] != null)) {
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110 seq = s[i].getSequence() + "*";
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112 seq = AlignSeq.extractGaps(s[i].getSequence(), "-");
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113 seq = AlignSeq.extractGaps(seq, ".");
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114 seq = AlignSeq.extractGaps(seq, " ");
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118 out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +
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119 s[i].getEnd() + "\n");
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120 out.append(" Dummy title\n");
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122 int nochunks = (seq.length() / len) + 1;
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124 for (int j = 0; j < nochunks; j++) {
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125 int start = j * len;
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126 int end = start + len;
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128 if (end < seq.length()) {
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129 out.append(seq.substring(start, end) + "\n");
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130 } else if (start < seq.length()) {
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131 out.append(seq.substring(start) + "\n");
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138 return out.toString();
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141 public static void main(String[] args) {
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142 String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";
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143 PIRFile fa = new PIRFile(inStr);
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