X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fdatamodel%2FSequenceFeature.js;h=d2f14a8b46c405bf9553008a96718520f73973e8;hp=f8ce54881bca427e83003b3f12b00e8d885d9368;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/datamodel/SequenceFeature.js b/bin/jalview/datamodel/SequenceFeature.js
index f8ce548..d2f14a8 100644
--- a/bin/jalview/datamodel/SequenceFeature.js
+++ b/bin/jalview/datamodel/SequenceFeature.js
@@ -1,170 +1,170 @@
-Clazz.declarePackage ("jalview.datamodel");
-Clazz.load (null, "jalview.datamodel.SequenceFeature", ["java.util.Hashtable", "$.Vector"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.begin = 0;
-this.end = 0;
-this.score = 0;
-this.type = null;
-this.description = null;
-this.otherDetails = null;
-this.links = null;
-this.featureGroup = null;
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel, "SequenceFeature");
-Clazz.makeConstructor (c$, 
-function () {
-});
-Clazz.makeConstructor (c$, 
-function (cpy) {
-if (cpy != null) {
-this.begin = cpy.begin;
-this.end = cpy.end;
-this.score = cpy.score;
-if (cpy.type != null) {
-this.type =  String.instantialize (cpy.type);
-}if (cpy.description != null) {
-this.description =  String.instantialize (cpy.description);
-}if (cpy.featureGroup != null) {
-this.featureGroup =  String.instantialize (cpy.featureGroup);
-}if (cpy.otherDetails != null) {
-try {
-this.otherDetails = cpy.otherDetails.clone ();
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-} else {
-throw e;
-}
-}
-}if (cpy.links != null && cpy.links.size () > 0) {
-this.links =  new java.util.Vector ();
-for (var i = 0, iSize = cpy.links.size (); i < iSize; i++) {
-this.links.addElement (cpy.links.elementAt (i));
-}
-}}}, "jalview.datamodel.SequenceFeature");
-Clazz.makeConstructor (c$, 
-function (type, desc, status, begin, end, featureGroup) {
-this.type = type;
-this.description = desc;
-this.setValue ("status", status);
-this.begin = begin;
-this.end = end;
-this.featureGroup = featureGroup;
-}, "~S,~S,~S,~N,~N,~S");
-Clazz.makeConstructor (c$, 
-function (type, desc, begin, end, score, featureGroup) {
-this.type = type;
-this.description = desc;
-this.begin = begin;
-this.end = end;
-this.score = score;
-this.featureGroup = featureGroup;
-}, "~S,~S,~N,~N,~N,~S");
-Clazz.defineMethod (c$, "equals", 
-function (sf) {
-if (this.begin != sf.begin || this.end != sf.end || this.score != sf.score) {
-return false;
-}if (!(this.type + this.description + this.featureGroup).equals (sf.type + sf.description + sf.featureGroup)) {
-return false;
-}return true;
-}, "jalview.datamodel.SequenceFeature");
-Clazz.defineMethod (c$, "getBegin", 
-function () {
-return this.begin;
-});
-Clazz.defineMethod (c$, "setBegin", 
-function (start) {
-this.begin = start;
-}, "~N");
-Clazz.defineMethod (c$, "getEnd", 
-function () {
-return this.end;
-});
-Clazz.defineMethod (c$, "setEnd", 
-function (end) {
-this.end = end;
-}, "~N");
-Clazz.defineMethod (c$, "getType", 
-function () {
-return this.type;
-});
-Clazz.defineMethod (c$, "setType", 
-function (type) {
-this.type = type;
-}, "~S");
-Clazz.defineMethod (c$, "getDescription", 
-function () {
-return this.description;
-});
-Clazz.defineMethod (c$, "setDescription", 
-function (desc) {
-this.description = desc;
-}, "~S");
-Clazz.defineMethod (c$, "getFeatureGroup", 
-function () {
-return this.featureGroup;
-});
-Clazz.defineMethod (c$, "setFeatureGroup", 
-function (featureGroup) {
-this.featureGroup = featureGroup;
-}, "~S");
-Clazz.defineMethod (c$, "addLink", 
-function (labelLink) {
-if (this.links == null) {
-this.links =  new java.util.Vector ();
-}this.links.insertElementAt (labelLink, 0);
-}, "~S");
-Clazz.defineMethod (c$, "getScore", 
-function () {
-return this.score;
-});
-Clazz.defineMethod (c$, "setScore", 
-function (value) {
-this.score = value;
-}, "~N");
-Clazz.defineMethod (c$, "getValue", 
-function (key) {
-if (this.otherDetails == null) {
-return null;
-} else {
-return this.otherDetails.get (key);
-}}, "~S");
-Clazz.defineMethod (c$, "setValue", 
-function (key, value) {
-if (value != null) {
-if (this.otherDetails == null) {
-this.otherDetails =  new java.util.Hashtable ();
-}this.otherDetails.put (key, value);
-}}, "~S,~O");
-Clazz.defineMethod (c$, "setStatus", 
-function (status) {
-this.setValue ("status", status);
-}, "~S");
-Clazz.defineMethod (c$, "getStatus", 
-function () {
-if (this.otherDetails != null) {
-var stat = this.otherDetails.get ("status");
-if (stat != null) {
-return  String.instantialize (stat);
-}}return null;
-});
-Clazz.defineMethod (c$, "setPosition", 
-function (pos) {
-this.begin = pos;
-this.end = pos;
-}, "~N");
-Clazz.defineMethod (c$, "getPosition", 
-function () {
-return this.begin;
-});
-Clazz.defineMethod (c$, "getStrand", 
-function () {
-var str;
-if (this.otherDetails == null || (str = this.otherDetails.get ("STRAND").toString ()) == null) {
-return 0;
-}if (str.equals ("-")) {
-return -1;
-}if (str.equals ("+")) {
-return 1;
-}return 0;
-});
-});
+Clazz.declarePackage ("jalview.datamodel");
+Clazz.load (null, "jalview.datamodel.SequenceFeature", ["java.util.Hashtable", "$.Vector"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.begin = 0;
+this.end = 0;
+this.score = 0;
+this.type = null;
+this.description = null;
+this.otherDetails = null;
+this.links = null;
+this.featureGroup = null;
+Clazz.instantialize (this, arguments);
+}, jalview.datamodel, "SequenceFeature");
+Clazz.makeConstructor (c$, 
+function () {
+});
+Clazz.makeConstructor (c$, 
+function (cpy) {
+if (cpy != null) {
+this.begin = cpy.begin;
+this.end = cpy.end;
+this.score = cpy.score;
+if (cpy.type != null) {
+this.type =  String.instantialize (cpy.type);
+}if (cpy.description != null) {
+this.description =  String.instantialize (cpy.description);
+}if (cpy.featureGroup != null) {
+this.featureGroup =  String.instantialize (cpy.featureGroup);
+}if (cpy.otherDetails != null) {
+try {
+this.otherDetails = cpy.otherDetails.clone ();
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+} else {
+throw e;
+}
+}
+}if (cpy.links != null && cpy.links.size () > 0) {
+this.links =  new java.util.Vector ();
+for (var i = 0, iSize = cpy.links.size (); i < iSize; i++) {
+this.links.addElement (cpy.links.elementAt (i));
+}
+}}}, "jalview.datamodel.SequenceFeature");
+Clazz.makeConstructor (c$, 
+function (type, desc, status, begin, end, featureGroup) {
+this.type = type;
+this.description = desc;
+this.setValue ("status", status);
+this.begin = begin;
+this.end = end;
+this.featureGroup = featureGroup;
+}, "~S,~S,~S,~N,~N,~S");
+Clazz.makeConstructor (c$, 
+function (type, desc, begin, end, score, featureGroup) {
+this.type = type;
+this.description = desc;
+this.begin = begin;
+this.end = end;
+this.score = score;
+this.featureGroup = featureGroup;
+}, "~S,~S,~N,~N,~N,~S");
+Clazz.defineMethod (c$, "equals", 
+function (sf) {
+if (this.begin != sf.begin || this.end != sf.end || this.score != sf.score) {
+return false;
+}if (!(this.type + this.description + this.featureGroup).equals (sf.type + sf.description + sf.featureGroup)) {
+return false;
+}return true;
+}, "jalview.datamodel.SequenceFeature");
+Clazz.defineMethod (c$, "getBegin", 
+function () {
+return this.begin;
+});
+Clazz.defineMethod (c$, "setBegin", 
+function (start) {
+this.begin = start;
+}, "~N");
+Clazz.defineMethod (c$, "getEnd", 
+function () {
+return this.end;
+});
+Clazz.defineMethod (c$, "setEnd", 
+function (end) {
+this.end = end;
+}, "~N");
+Clazz.defineMethod (c$, "getType", 
+function () {
+return this.type;
+});
+Clazz.defineMethod (c$, "setType", 
+function (type) {
+this.type = type;
+}, "~S");
+Clazz.defineMethod (c$, "getDescription", 
+function () {
+return this.description;
+});
+Clazz.defineMethod (c$, "setDescription", 
+function (desc) {
+this.description = desc;
+}, "~S");
+Clazz.defineMethod (c$, "getFeatureGroup", 
+function () {
+return this.featureGroup;
+});
+Clazz.defineMethod (c$, "setFeatureGroup", 
+function (featureGroup) {
+this.featureGroup = featureGroup;
+}, "~S");
+Clazz.defineMethod (c$, "addLink", 
+function (labelLink) {
+if (this.links == null) {
+this.links =  new java.util.Vector ();
+}this.links.insertElementAt (labelLink, 0);
+}, "~S");
+Clazz.defineMethod (c$, "getScore", 
+function () {
+return this.score;
+});
+Clazz.defineMethod (c$, "setScore", 
+function (value) {
+this.score = value;
+}, "~N");
+Clazz.defineMethod (c$, "getValue", 
+function (key) {
+if (this.otherDetails == null) {
+return null;
+} else {
+return this.otherDetails.get (key);
+}}, "~S");
+Clazz.defineMethod (c$, "setValue", 
+function (key, value) {
+if (value != null) {
+if (this.otherDetails == null) {
+this.otherDetails =  new java.util.Hashtable ();
+}this.otherDetails.put (key, value);
+}}, "~S,~O");
+Clazz.defineMethod (c$, "setStatus", 
+function (status) {
+this.setValue ("status", status);
+}, "~S");
+Clazz.defineMethod (c$, "getStatus", 
+function () {
+if (this.otherDetails != null) {
+var stat = this.otherDetails.get ("status");
+if (stat != null) {
+return  String.instantialize (stat);
+}}return null;
+});
+Clazz.defineMethod (c$, "setPosition", 
+function (pos) {
+this.begin = pos;
+this.end = pos;
+}, "~N");
+Clazz.defineMethod (c$, "getPosition", 
+function () {
+return this.begin;
+});
+Clazz.defineMethod (c$, "getStrand", 
+function () {
+var str;
+if (this.otherDetails == null || (str = this.otherDetails.get ("STRAND").toString ()) == null) {
+return 0;
+}if (str.equals ("-")) {
+return -1;
+}if (str.equals ("+")) {
+return 1;
+}return 0;
+});
+});