1 Clazz.declarePackage ("jalview.io");
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2 Clazz.load (["jalview.io.AlignFile"], "jalview.io.MSFfile", ["jalview.datamodel.Sequence", "jalview.util.Comparison", "$.Format", "java.lang.StringBuffer", "java.util.Hashtable", "$.StringTokenizer", "$.Vector"], function () {
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3 c$ = Clazz.declareType (jalview.io, "MSFfile", jalview.io.AlignFile);
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4 Clazz.makeConstructor (c$,
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6 Clazz.superConstructor (this, jalview.io.MSFfile, []);
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8 Clazz.overrideMethod (c$, "parse",
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11 var seqFlag = false;
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12 var key = String.instantialize ();
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13 var headers = new java.util.Vector ();
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14 var seqhash = new java.util.Hashtable ();
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17 while ((line = this.nextLine ()) != null) {
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18 var str = new java.util.StringTokenizer (line);
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19 while (str.hasMoreTokens ()) {
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20 var inStr = str.nextToken ();
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21 if (inStr.indexOf ("Name:") != -1) {
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22 key = str.nextToken ();
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23 headers.addElement (key);
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24 }if (inStr.indexOf ("//") != -1) {
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26 }if ((inStr.indexOf ("//") == -1) && (seqFlag == true)) {
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29 if (seqhash.containsKey (key)) {
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30 tempseq = seqhash.get (key);
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32 tempseq = new StringBuffer ();
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33 seqhash.put (key, tempseq);
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34 }while (str.hasMoreTokens ()) {
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35 tempseq.append (str.nextToken ());
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40 if (Clazz.exceptionOf (e, java.io.IOException)) {
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41 System.err.println ("Exception parsing MSFFile " + e);
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42 e.printStackTrace ();
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47 this.noSeqs = headers.size ();
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48 for (i = 0; i < headers.size (); i++) {
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49 if (seqhash.get (headers.elementAt (i)) != null) {
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50 var head = headers.elementAt (i).toString ();
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51 var seq = seqhash.get (head).toString ();
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52 if (this.maxLength < head.length) {
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53 this.maxLength = head.length;
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54 }seq = seq.$replace ('~', '-');
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55 var newSeq = this.parseId (head);
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56 newSeq.setSequence (seq);
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57 this.seqs.addElement (newSeq);
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59 System.err.println ("MSFFile Parser: Can't find sequence for " + headers.elementAt (i));
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62 Clazz.defineMethod (c$, "checkSum",
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65 var sequence = seq.toUpperCase ();
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66 for (var i = 0; i < sequence.length; i++) {
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68 var value = sequence.charCodeAt (i);
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70 check += (i % 57 + 1) * value;
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72 if (Clazz.exceptionOf (e, Exception)) {
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73 System.err.println ("Exception during MSF Checksum calculation");
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74 e.printStackTrace ();
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80 return check % 10000;
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82 Clazz.defineMethod (c$, "print",
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84 var is_NA = jalview.util.Comparison.isNucleotide (seqs);
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85 var s = new Array (seqs.length);
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86 var out = new StringBuffer ("!!" + (is_NA ? "NA" : "AA") + "_MULTIPLE_ALIGNMENT 1.0");
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87 out.append (this.newline);
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88 out.append (this.newline);
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92 while ((i < seqs.length) && (seqs[i] != null)) {
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93 s[i] = new jalview.datamodel.Sequence (seqs[i].getName (), seqs[i].getSequenceAsString ().$replace ('-', '.'), seqs[i].getStart (), seqs[i].getEnd ());
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94 var sb = new StringBuffer ();
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95 sb.append (s[i].getSequence ());
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96 for (var ii = 0; ii < sb.length (); ii++) {
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97 if (sb.charAt (ii) == '.') {
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98 sb.setCharAt (ii, '~');
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102 for (var ii = sb.length () - 1; ii > 0; ii--) {
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103 if (sb.charAt (ii) == '.') {
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104 sb.setCharAt (ii, '~');
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108 s[i].setSequence (sb.toString ());
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109 if (s[i].getSequence ().length > max) {
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110 max = s[i].getSequence ().length;
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113 var maxLenpad = new jalview.util.Format ("%" + ( String.instantialize ("" + max)).length + "d");
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114 var maxChkpad = new jalview.util.Format ("%" + ( String.instantialize ("1" + max)).length + "d");
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116 var bigChecksum = 0;
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117 var checksums = Clazz.newIntArray (s.length, 0);
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118 while (i < s.length) {
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119 checksums[i] = this.checkSum (s[i].getSequenceAsString ());
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120 bigChecksum += checksums[i];
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124 out.append (" MSF: " + s[0].getSequence ().length + " Type: " + (is_NA ? "N" : "P") + " Check: " + (bigChecksum % 10000) + " ..");
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125 out.append (this.newline);
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126 out.append (this.newline);
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127 out.append (this.newline);
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128 var nameBlock = new Array (s.length);
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129 var idBlock = new Array (s.length);
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131 while ((i < s.length) && (s[i] != null)) {
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132 nameBlock[i] = String.instantialize (" Name: " + this.printId (s[i]) + " ");
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133 idBlock[i] = String.instantialize ("Len: " + maxLenpad.formLong (s[i].getSequence ().length) + " Check: " + maxChkpad.formLong (checksums[i]) + " Weight: 1.00" + this.newline);
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134 if (s[i].getName ().length > maxid) {
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135 maxid = s[i].getName ().length;
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136 }if (nameBlock[i].length > maxNB) {
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137 maxNB = nameBlock[i].length;
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144 }var nbFormat = new jalview.util.Format ("%-" + maxNB + "s");
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145 for (i = 0; (i < s.length) && (s[i] != null); i++) {
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146 out.append (nbFormat.form (nameBlock[i]) + idBlock[i]);
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149 out.append (this.newline);
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150 out.append (this.newline);
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152 out.append (this.newline);
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153 out.append (this.newline);
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155 var nochunks = (Clazz.doubleToInt (max / len)) + 1;
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156 if ((max % len) == 0) {
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158 }for (i = 0; i < nochunks; i++) {
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160 while ((j < s.length) && (s[j] != null)) {
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161 var name = this.printId (s[j]);
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162 out.append ( new jalview.util.Format ("%-" + maxid + "s").form (name + " "));
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163 for (var k = 0; k < 5; k++) {
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164 var start = (i * 50) + (k * 10);
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165 var end = start + 10;
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166 if ((end < s[j].getSequence ().length) && (start < s[j].getSequence ().length)) {
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167 out.append (s[j].getSequence (start, end));
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171 out.append (this.newline);
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173 if (start < s[j].getSequence ().length) {
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174 out.append (s[j].getSequenceAsString ().substring (start));
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175 out.append (this.newline);
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178 out.append (this.newline);
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182 out.append (this.newline);
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184 return out.toString ();
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186 Clazz.defineMethod (c$, "print",
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188 return this.print (this.getSeqsAsArray ());
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