-Clazz.declarePackage ("jalview.datamodel");\r
-Clazz.load (null, "jalview.datamodel.AlignmentOrder", ["java.lang.Error", "java.util.ArrayList", "$.Arrays"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.Type = 0;\r
-this.Name = null;\r
-this.Order = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.datamodel, "AlignmentOrder");\r
-Clazz.makeConstructor (c$, \r
-function () {\r
-});\r
-Clazz.makeConstructor (c$, \r
-function (anOrder) {\r
-this.Order = anOrder;\r
-}, "java.util.List");\r
-Clazz.makeConstructor (c$, \r
-function (orderFrom) {\r
-this.Order = new java.util.ArrayList ();\r
-for (var seq, $seq = orderFrom.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {\r
-this.Order.add (seq);\r
-}\r
-}, "jalview.datamodel.AlignmentI");\r
-Clazz.makeConstructor (c$, \r
-function (orderFrom) {\r
-this.Order = new java.util.ArrayList (java.util.Arrays.asList (orderFrom));\r
-}, "~A");\r
-Clazz.defineMethod (c$, "setType", \r
-function (Type) {\r
-this.Type = Type;\r
-}, "~N");\r
-Clazz.defineMethod (c$, "getType", \r
-function () {\r
-return this.Type;\r
-});\r
-Clazz.defineMethod (c$, "setName", \r
-function (Name) {\r
-this.Name = Name;\r
-}, "~S");\r
-Clazz.defineMethod (c$, "getName", \r
-function () {\r
-return this.Name;\r
-});\r
-Clazz.defineMethod (c$, "setOrder", \r
-function (Order) {\r
-this.Order = Order;\r
-}, "java.util.List");\r
-Clazz.defineMethod (c$, "getOrder", \r
-function () {\r
-return this.Order;\r
-});\r
-Clazz.defineMethod (c$, "updateSequence", \r
-function (oldref, newref) {\r
-var found = this.Order.indexOf (oldref);\r
-if (found > -1) {\r
-this.Order.set (found, newref);\r
-}return found > -1;\r
-}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");\r
-Clazz.defineMethod (c$, "equals", \r
-function (o) {\r
-if (o == null || !(Clazz.instanceOf (o, jalview.datamodel.AlignmentOrder))) {\r
-return false;\r
-}return this.equals (o, true);\r
-}, "~O");\r
-Clazz.defineMethod (c$, "equals", \r
-function (o, identity) {\r
-if (o !== this) {\r
-if (o == null) {\r
-return false;\r
-}if (this.Order != null && o.Order != null && this.Order.size () == o.Order.size ()) {\r
-if (!identity) {\r
-throw new Error ("Weak sequenceI equivalence not yet implemented.");\r
-} else {\r
-for (var i = 0, j = o.Order.size (); i < j; i++) {\r
-if (this.Order.get (i) !== o.Order.get (i)) {\r
-return false;\r
-}}\r
-}} else {\r
-return false;\r
-}}return true;\r
-}, "jalview.datamodel.AlignmentOrder,~B");\r
-Clazz.defineMethod (c$, "isConsistent", \r
-function (o) {\r
-return this.isConsistent (o, true);\r
-}, "jalview.datamodel.AlignmentOrder");\r
-Clazz.defineMethod (c$, "isConsistent", \r
-function (o, identity) {\r
-if (o !== this) {\r
-if (o == null) {\r
-return false;\r
-}if (this.Order != null && o.Order != null) {\r
-var c;\r
-var s;\r
-if (o.Order.size () > this.Order.size ()) {\r
-c = o.Order;\r
-s = this.Order;\r
-} else {\r
-c = this.Order;\r
-s = o.Order;\r
-}if (!identity) {\r
-throw new Error ("Weak sequenceI equivalence not yet implemented.");\r
-} else {\r
-var last = -1;\r
-for (var i = 0, j = s.size (); i < j; i++) {\r
-var pos = c.indexOf (s.get (i));\r
-if (pos > last) {\r
-last = pos;\r
-} else {\r
-return false;\r
-}}\r
-}} else {\r
-return false;\r
-}}return true;\r
-}, "jalview.datamodel.AlignmentOrder,~B");\r
-Clazz.defineStatics (c$,\r
-"FILE", 0,\r
-"MSA", 1,\r
-"USER", 2);\r
-});\r
+Clazz.declarePackage ("jalview.datamodel");
+Clazz.load (null, "jalview.datamodel.AlignmentOrder", ["java.lang.Error", "java.util.ArrayList", "$.Arrays"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.Type = 0;
+this.Name = null;
+this.Order = null;
+Clazz.instantialize (this, arguments);
+}, jalview.datamodel, "AlignmentOrder");
+Clazz.makeConstructor (c$,
+function () {
+});
+Clazz.makeConstructor (c$,
+function (anOrder) {
+this.Order = anOrder;
+}, "java.util.List");
+Clazz.makeConstructor (c$,
+function (orderFrom) {
+this.Order = new java.util.ArrayList ();
+for (var seq, $seq = orderFrom.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
+this.Order.add (seq);
+}
+}, "jalview.datamodel.AlignmentI");
+Clazz.makeConstructor (c$,
+function (orderFrom) {
+this.Order = new java.util.ArrayList (java.util.Arrays.asList (orderFrom));
+}, "~A");
+Clazz.defineMethod (c$, "setType",
+function (Type) {
+this.Type = Type;
+}, "~N");
+Clazz.defineMethod (c$, "getType",
+function () {
+return this.Type;
+});
+Clazz.defineMethod (c$, "setName",
+function (Name) {
+this.Name = Name;
+}, "~S");
+Clazz.defineMethod (c$, "getName",
+function () {
+return this.Name;
+});
+Clazz.defineMethod (c$, "setOrder",
+function (Order) {
+this.Order = Order;
+}, "java.util.List");
+Clazz.defineMethod (c$, "getOrder",
+function () {
+return this.Order;
+});
+Clazz.defineMethod (c$, "updateSequence",
+function (oldref, newref) {
+var found = this.Order.indexOf (oldref);
+if (found > -1) {
+this.Order.set (found, newref);
+}return found > -1;
+}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "equals",
+function (o) {
+if (o == null || !(Clazz.instanceOf (o, jalview.datamodel.AlignmentOrder))) {
+return false;
+}return this.equals (o, true);
+}, "~O");
+Clazz.defineMethod (c$, "equals",
+function (o, identity) {
+if (o !== this) {
+if (o == null) {
+return false;
+}if (this.Order != null && o.Order != null && this.Order.size () == o.Order.size ()) {
+if (!identity) {
+throw new Error ("Weak sequenceI equivalence not yet implemented.");
+} else {
+for (var i = 0, j = o.Order.size (); i < j; i++) {
+if (this.Order.get (i) !== o.Order.get (i)) {
+return false;
+}}
+}} else {
+return false;
+}}return true;
+}, "jalview.datamodel.AlignmentOrder,~B");
+Clazz.defineMethod (c$, "isConsistent",
+function (o) {
+return this.isConsistent (o, true);
+}, "jalview.datamodel.AlignmentOrder");
+Clazz.defineMethod (c$, "isConsistent",
+function (o, identity) {
+if (o !== this) {
+if (o == null) {
+return false;
+}if (this.Order != null && o.Order != null) {
+var c;
+var s;
+if (o.Order.size () > this.Order.size ()) {
+c = o.Order;
+s = this.Order;
+} else {
+c = this.Order;
+s = o.Order;
+}if (!identity) {
+throw new Error ("Weak sequenceI equivalence not yet implemented.");
+} else {
+var last = -1;
+for (var i = 0, j = s.size (); i < j; i++) {
+var pos = c.indexOf (s.get (i));
+if (pos > last) {
+last = pos;
+} else {
+return false;
+}}
+}} else {
+return false;
+}}return true;
+}, "jalview.datamodel.AlignmentOrder,~B");
+Clazz.defineStatics (c$,
+"FILE", 0,
+"MSA", 1,
+"USER", 2);
+});
git://source.jalview.org / jalviewjs.git / blobdiff