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