1 Clazz.declarePackage ("jalview.io");
2 Clazz.load (["jalview.io.MSFfile"], "jalview.io.PileUpfile", ["jalview.util.Format", "java.lang.StringBuffer"], function () {
3 c$ = Clazz.declareType (jalview.io, "PileUpfile", jalview.io.MSFfile);
4 Clazz.makeConstructor (c$,
6 Clazz.superConstructor (this, jalview.io.PileUpfile, []);
8 Clazz.defineMethod (c$, "print",
10 return this.print (this.getSeqsAsArray ());
12 Clazz.defineMethod (c$, "print",
14 var out = new StringBuffer ("PileUp");
15 out.append (this.newline);
16 out.append (this.newline);
21 var checksums = Clazz.newIntArray (s.length, 0);
22 while (i < s.length) {
23 checksums[i] = this.checkSum (s[i].getSequenceAsString ());
24 bigChecksum += checksums[i];
27 out.append (" MSF: " + s[0].getSequence ().length + " Type: P Check: " + bigChecksum % 10000 + " ..");
28 out.append (this.newline);
29 out.append (this.newline);
30 out.append (this.newline);
32 while ((i < s.length) && (s[i] != null)) {
33 var seq = s[i].getSequenceAsString ();
34 out.append (" Name: " + this.printId (s[i]) + " oo Len: " + seq.length + " Check: " + checksums[i] + " Weight: 1.00");
35 out.append (this.newline);
36 if (seq.length > max) {
38 }if (s[i].getName ().length > maxid) {
39 maxid = s[i].getName ().length;
45 out.append (this.newline);
46 out.append (this.newline);
48 out.append (this.newline);
49 out.append (this.newline);
51 var nochunks = (Clazz.doubleToInt (max / len)) + 1;
52 if ((max % len) == 0) {
54 }for (i = 0; i < nochunks; i++) {
56 while ((j < s.length) && (s[j] != null)) {
57 var name = this.printId (s[j]);
58 out.append ( new jalview.util.Format ("%-" + maxid + "s").form (name + " "));
59 for (var k = 0; k < 5; k++) {
60 var start = (i * 50) + (k * 10);
62 if ((end < s[j].getSequence ().length) && (start < s[j].getSequence ().length)) {
63 out.append (s[j].getSequence (start, end));
67 out.append (this.newline);
69 if (start < s[j].getSequence ().length) {
70 out.append (s[j].getSequenceAsString ().substring (start));
71 out.append (this.newline);
74 out.append (this.newline);
78 out.append (this.newline);
80 return out.toString ();