3 import jalview.datamodel.*;
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4 import jalview.util.*;
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9 public class ClustalFile extends AlignFile {
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13 public ClustalFile()
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16 public ClustalFile(String inStr) {
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21 public void initData() {
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26 public ClustalFile(String inFile, String type) throws IOException {
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30 public void parse() {
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32 boolean flag = false;
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34 Vector headers = new Vector();
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35 Hashtable seqhash = new Hashtable();
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40 while ((line = nextLine()) != null) {
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41 if (line.indexOf(" ") != 0) {
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42 StringTokenizer str = new StringTokenizer(line," ");
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45 if (str.hasMoreTokens()) {
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46 id = str.nextToken();
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47 if (id.equals("CLUSTAL")) {
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51 StringBuffer tempseq;
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52 if (seqhash.containsKey(id)) {
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53 tempseq = (StringBuffer)seqhash.get(id);
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55 tempseq = new StringBuffer();
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56 seqhash.put(id,tempseq);
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59 if (!(headers.contains(id))) {
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60 headers.addElement(id);
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63 tempseq.append(str.nextToken());
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69 } catch (IOException e) {
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70 System.out.println("Exception parsing clustal file " + e);
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74 this.noSeqs = headers.size();
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76 //Add sequences to the hash
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77 for (i = 0; i < headers.size(); i++ ) {
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81 if ( seqhash.get(headers.elementAt(i)) != null) {
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82 if (maxLength < seqhash.get(headers.elementAt(i)).toString().length() ) {
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83 maxLength = seqhash.get(headers.elementAt(i)).toString().length();
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85 String head = headers.elementAt(i).toString();
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87 end = seqhash.get(headers.elementAt(i)).toString().length();
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89 if (head.indexOf("/") > 0 ) {
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90 StringTokenizer st = new StringTokenizer(head,"/");
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91 if (st.countTokens() == 2) {
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93 ids.addElement(st.nextToken());
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95 String tmp = st.nextToken();
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96 st = new StringTokenizer(tmp,"-");
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97 if (st.countTokens() == 2) {
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98 start = Integer.valueOf(st.nextToken()).intValue();
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99 end = Integer.valueOf(st.nextToken()).intValue();
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102 ids.addElement(headers.elementAt(i));
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105 ids.addElement(headers.elementAt(i));
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108 Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
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109 seqhash.get(headers.elementAt(i).toString()).toString(),start,end);
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111 seqs.addElement(newSeq);
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114 System.out.println("Can't find sequence for " + headers.elementAt(i));
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121 public String print() {
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122 return print(getSeqsAsArray());
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124 public static String print(SequenceI[] s) {
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125 StringBuffer out = new StringBuffer("CLUSTAL\n\n");
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132 while (i < s.length && s[i] != null) {
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133 String tmp = s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd();
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135 if (s[i].getSequence().length() > max) {
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136 max = s[i].getSequence().length();
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138 if (tmp.length() > maxid) {
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139 maxid = tmp.length();
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149 int nochunks = max / len + 1;
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151 for (i = 0; i < nochunks; i++) {
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153 while ( j < s.length && s[j] != null) {
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154 out.append( new Format("%-" + maxid + "s").form(s[j].getName() + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
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156 int end = start + len;
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158 if (end < s[j].getSequence().length() && start < s[j].getSequence().length() ) {
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159 out.append(s[j].getSequence().substring(start,end) + "\n");
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161 if (start < s[j].getSequence().length()) {
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162 out.append(s[j].getSequence().substring(start) + "\n");
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170 return out.toString();
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