1 Clazz.declarePackage ("jalview.analysis");
2 Clazz.load (null, "jalview.analysis.Grouping", ["jalview.datamodel.SequenceGroup", "java.lang.StringBuilder", "java.util.ArrayList", "$.HashMap"], function () {
3 c$ = Clazz.declareType (jalview.analysis, "Grouping");
4 c$.makeGroupsFrom = Clazz.defineMethod (c$, "makeGroupsFrom",
5 function (sequences, selectedChars, list) {
6 var gps = new java.util.HashMap ();
9 var pgroup = new java.util.HashMap ();
11 for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
12 for (var sq, $sq = sg.getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {
13 pgroup.put (sq.toString (), sg);
16 }for (i = 0; i < sequences.length; i++) {
17 var schar = selectedChars[i];
18 var pgp = pgroup.get ((sequences[i]).toString ());
20 schar = pgp.getName () + ":" + schar;
21 }var svec = gps.get (schar);
23 svec = new java.util.ArrayList ();
24 gps.put (schar, svec);
25 }if (width < sequences[i].getLength ()) {
26 width = sequences[i].getLength ();
27 }svec.add (sequences[i]);
29 var groups = new Array (gps.size ());
31 for (var key, $key = gps.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) {
32 var group = new jalview.datamodel.SequenceGroup (gps.get (key), "Subseq: " + key, null, true, true, false, 0, width - 1);
38 }, "~A,~A,java.util.List");
39 c$.makeGroupsFromCols = Clazz.defineMethod (c$, "makeGroupsFromCols",
40 function (sequences, cs, list) {
41 var gps = new java.util.HashMap ();
42 var pgroup = new java.util.HashMap ();
44 for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
45 for (var sq, $sq = sg.getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {
46 pgroup.put (sq.toString (), sg);
49 }var spos = Clazz.newIntArray (cs.getSelected ().size (), 0);
52 for (var pos, $pos = cs.getSelected ().iterator (); $pos.hasNext () && ((pos = $pos.next ()) || true);) {
53 spos[i++] = pos.intValue ();
55 ;for (i = 0; i < sequences.length; i++) {
56 var slen = sequences[i].getLength ();
59 }var pgp = pgroup.get ((sequences[i]).toString ());
60 var schar = new StringBuilder ();
62 schar.append (pgp.getName () + ":");
63 }for (var p, $p = 0, $$p = spos; $p < $$p.length && ((p = $$p[$p]) || true); $p++) {
67 schar.append (sequences[i].getCharAt (p));
69 var svec = gps.get (schar.toString ());
71 svec = new java.util.ArrayList ();
72 gps.put (schar.toString (), svec);
73 }svec.add (sequences[i]);
75 var groups = new Array (gps.size ());
77 for (var key, $key = gps.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) {
78 var group = new jalview.datamodel.SequenceGroup (gps.get (key), "Subseq: " + key, null, true, true, false, 0, width - 1);
84 }, "~A,jalview.datamodel.ColumnSelection,java.util.List");
85 c$.divideByFeature = Clazz.defineMethod (c$, "divideByFeature",
86 function (featureLabels, groupLabels, start, stop, sequences, exgroups, method) {
87 }, "~A,~A,~N,~N,~A,java.util.Vector,~S");