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