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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23 import jalview.util.*;
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30 public class ClustalFile extends AlignFile {
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33 public ClustalFile() {
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36 public ClustalFile(String inStr) {
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40 public ClustalFile(String inFile, String type) throws IOException {
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41 super(inFile, type);
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44 public void initData() {
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49 public void parse() {
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51 boolean flag = false;
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53 Vector headers = new Vector();
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54 Hashtable seqhash = new Hashtable();
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59 while ((line = nextLine()) != null) {
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60 if (line.indexOf(" ") != 0) {
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61 StringTokenizer str = new StringTokenizer(line, " ");
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64 if (str.hasMoreTokens()) {
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65 id = str.nextToken();
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67 if (id.equals("CLUSTAL")) {
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71 StringBuffer tempseq;
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73 if (seqhash.containsKey(id)) {
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74 tempseq = (StringBuffer) seqhash.get(id);
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76 tempseq = new StringBuffer();
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77 seqhash.put(id, tempseq);
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80 if (!(headers.contains(id))) {
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81 headers.addElement(id);
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84 if (str.hasMoreTokens()) {
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85 tempseq.append(str.nextToken());
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92 } catch (IOException e) {
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93 System.err.println("Exception parsing clustal file " + e);
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94 e.printStackTrace();
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98 this.noSeqs = headers.size();
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100 //Add sequences to the hash
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101 for (i = 0; i < headers.size(); i++) {
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105 if (seqhash.get(headers.elementAt(i)) != null) {
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106 if (maxLength < seqhash.get(headers.elementAt(i)).toString()
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108 maxLength = seqhash.get(headers.elementAt(i)).toString()
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112 String head = headers.elementAt(i).toString();
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114 end = seqhash.get(headers.elementAt(i)).toString().length();
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116 if (head.indexOf("/") > 0) {
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117 StringTokenizer st = new StringTokenizer(head, "/");
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119 if (st.countTokens() == 2) {
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120 ids.addElement(st.nextToken());
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122 String tmp = st.nextToken();
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123 st = new StringTokenizer(tmp, "-");
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125 if (st.countTokens() == 2) {
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126 start = Integer.valueOf(st.nextToken())
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128 end = Integer.valueOf(st.nextToken()).intValue();
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131 ids.addElement(headers.elementAt(i));
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134 ids.addElement(headers.elementAt(i));
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137 Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
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138 seqhash.get(headers.elementAt(i).toString())
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139 .toString(), start, end);
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141 seqs.addElement(newSeq);
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143 System.err.println(
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144 "Clustal File Reader: Can't find sequence for " +
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145 headers.elementAt(i));
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151 public String print() {
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152 return print(getSeqsAsArray());
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155 public static String print(SequenceI[] s) {
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156 StringBuffer out = new StringBuffer("CLUSTAL\n\n");
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163 while ((i < s.length) && (s[i] != null)) {
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164 String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +
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167 if (s[i].getSequence().length() > max) {
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168 max = s[i].getSequence().length();
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171 if (tmp.length() > maxid) {
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172 maxid = tmp.length();
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185 int nochunks = (max / len) + 1;
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187 for (i = 0; i < nochunks; i++) {
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190 while ((j < s.length) && (s[j] != null)) {
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191 out.append(new Format("%-" + maxid + "s").form(s[j].getName() +
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192 "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
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194 int start = i * len;
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195 int end = start + len;
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197 if ((end < s[j].getSequence().length()) &&
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198 (start < s[j].getSequence().length())) {
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199 out.append(s[j].getSequence().substring(start, end));
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201 if (start < s[j].getSequence().length()) {
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202 out.append(s[j].getSequence().substring(start));
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213 return out.toString();
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