X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fdatamodel%2FAlignmentOrder.js;h=0fb0cbb378ee1be79afc5491d0048d3b6a7d4c64;hp=281aa172bf0b5b23a5d1e127f867343abec5fdc1;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6

diff --git a/site/j2s/jalview/datamodel/AlignmentOrder.js b/site/j2s/jalview/datamodel/AlignmentOrder.js
index 281aa17..0fb0cbb 100644
--- a/site/j2s/jalview/datamodel/AlignmentOrder.js
+++ b/site/j2s/jalview/datamodel/AlignmentOrder.js
@@ -1,118 +1,118 @@
-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);
-});
+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);
+});