1 Clazz.declarePackage ("jalview.datamodel");
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2 Clazz.load (null, "jalview.datamodel.AlignmentOrder", ["java.lang.Error", "java.util.ArrayList", "$.Arrays"], function () {
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3 c$ = Clazz.decorateAsClass (function () {
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7 Clazz.instantialize (this, arguments);
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8 }, jalview.datamodel, "AlignmentOrder");
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9 Clazz.makeConstructor (c$,
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12 Clazz.makeConstructor (c$,
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13 function (anOrder) {
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14 this.Order = anOrder;
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15 }, "java.util.List");
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16 Clazz.makeConstructor (c$,
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17 function (orderFrom) {
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18 this.Order = new java.util.ArrayList ();
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19 for (var seq, $seq = orderFrom.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
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20 this.Order.add (seq);
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22 }, "jalview.datamodel.AlignmentI");
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23 Clazz.makeConstructor (c$,
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24 function (orderFrom) {
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25 this.Order = new java.util.ArrayList (java.util.Arrays.asList (orderFrom));
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27 Clazz.defineMethod (c$, "setType",
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31 Clazz.defineMethod (c$, "getType",
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35 Clazz.defineMethod (c$, "setName",
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39 Clazz.defineMethod (c$, "getName",
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43 Clazz.defineMethod (c$, "setOrder",
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46 }, "java.util.List");
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47 Clazz.defineMethod (c$, "getOrder",
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51 Clazz.defineMethod (c$, "updateSequence",
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52 function (oldref, newref) {
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53 var found = this.Order.indexOf (oldref);
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55 this.Order.set (found, newref);
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57 }, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");
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58 Clazz.defineMethod (c$, "equals",
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60 if (o == null || !(Clazz.instanceOf (o, jalview.datamodel.AlignmentOrder))) {
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62 }return this.equals (o, true);
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64 Clazz.defineMethod (c$, "equals",
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65 function (o, identity) {
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69 }if (this.Order != null && o.Order != null && this.Order.size () == o.Order.size ()) {
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71 throw new Error ("Weak sequenceI equivalence not yet implemented.");
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73 for (var i = 0, j = o.Order.size (); i < j; i++) {
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74 if (this.Order.get (i) !== o.Order.get (i)) {
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80 }, "jalview.datamodel.AlignmentOrder,~B");
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81 Clazz.defineMethod (c$, "isConsistent",
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83 return this.isConsistent (o, true);
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84 }, "jalview.datamodel.AlignmentOrder");
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85 Clazz.defineMethod (c$, "isConsistent",
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86 function (o, identity) {
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90 }if (this.Order != null && o.Order != null) {
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93 if (o.Order.size () > this.Order.size ()) {
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100 throw new Error ("Weak sequenceI equivalence not yet implemented.");
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103 for (var i = 0, j = s.size (); i < j; i++) {
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104 var pos = c.indexOf (s.get (i));
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113 }, "jalview.datamodel.AlignmentOrder,~B");
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114 Clazz.defineStatics (c$,
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