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.datamodel.*;
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28 public abstract class AlignFile extends FileParse {
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36 public AlignFile() {
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39 public AlignFile(String inStr) {
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41 System.out.println("is this ever called??");
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45 } catch (Exception ex) {
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50 * Constructor which parses the data from a file of some specified type.
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51 * @param inFile Filename to read from.
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52 * @param type What type of file to read from (File, URL)
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54 public AlignFile(String inFile, String type) throws IOException {
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55 super(inFile, type);
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63 * Return the seqs Vector
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65 public Vector getSeqs() {
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70 * Return the Sequences in the seqs Vector as an array of Sequences
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72 public SequenceI[] getSeqsAsArray() {
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73 SequenceI[] s = new SequenceI[seqs.size()];
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75 for (int i = 0; i < seqs.size(); i++) {
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76 s[i] = (SequenceI) seqs.elementAt(i);
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83 * Initialise objects to store sequence data in.
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85 protected void initData() {
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86 seqs = new Vector();
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87 headers = new Vector();
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90 protected void setSeqs(SequenceI[] s) {
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91 seqs = new Vector();
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93 for (int i = 0; i < s.length; i++) {
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94 seqs.addElement(s[i]);
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98 // Checks whether sequence is valid aa characters
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99 protected boolean isValidProteinSequence(String sequence) {
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100 for (int i = 0; i < sequence.length(); i++)
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101 if (!jalview.schemes.ResidueProperties.aaHash.containsKey(
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102 String.valueOf(sequence.charAt(i)))) {
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110 * This method must be implemented to parse the contents of the file.
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112 public abstract void parse() throws IOException;
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115 * Print out in alignment file format the Sequences in the seqs Vector.
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117 public abstract String print();
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