JAL-1807 includes ?j2sdebug flag and DebugJS._(msg)

[jalviewjs.git] / bin / jalview / structure / StructureMapping.js

diff --git a/bin/jalview/structure/StructureMapping.js b/bin/jalview/structure/StructureMapping.js
index 8cf2f33..40c774f 100644 (file)
--- a/bin/jalview/structure/StructureMapping.js
+++ b/bin/jalview/structure/StructureMapping.js
@@ -1,69 +1,69 @@
-Clazz.declarePackage ("jalview.structure");\r
-Clazz.load (null, "jalview.structure.StructureMapping", ["jalview.datamodel.AlignmentAnnotation"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.mappingDetails = null;\r
-this.sequence = null;\r
-this.pdbfile = null;\r
-this.pdbid = null;\r
-this.pdbchain = null;\r
-this.mapping = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.structure, "StructureMapping");\r
-Clazz.makeConstructor (c$, \r
-function (seq, pdbfile, pdbid, chain, mapping, mappingDetails) {\r
-this.sequence = seq;\r
-this.pdbfile = pdbfile;\r
-this.pdbid = pdbid;\r
-this.pdbchain = chain;\r
-this.mapping = mapping;\r
-this.mappingDetails = mappingDetails;\r
-}, "jalview.datamodel.SequenceI,~S,~S,~S,~A,~S");\r
-Clazz.defineMethod (c$, "getSequence", \r
-function () {\r
-return this.sequence;\r
-});\r
-Clazz.defineMethod (c$, "getChain", \r
-function () {\r
-return this.pdbchain;\r
-});\r
-Clazz.defineMethod (c$, "getPdbId", \r
-function () {\r
-return this.pdbid;\r
-});\r
-Clazz.defineMethod (c$, "getAtomNum", \r
-function (seqpos) {\r
-if (this.mapping.length > seqpos) {\r
-return this.mapping[seqpos][1];\r
-} else {\r
-return 0;\r
-}}, "~N");\r
-Clazz.defineMethod (c$, "getPDBResNum", \r
-function (seqpos) {\r
-if (this.mapping.length > seqpos) {\r
-return this.mapping[seqpos][0];\r
-} else {\r
-return 0;\r
-}}, "~N");\r
-Clazz.defineMethod (c$, "getSeqPos", \r
-function (pdbResNum) {\r
-for (var i = 0; i < this.mapping.length; i++) {\r
-if (this.mapping[i][0] == pdbResNum) {\r
-return i;\r
-}}\r
-return -1;\r
-}, "~N");\r
-Clazz.defineMethod (c$, "transfer", \r
-function (ana) {\r
-var ala_copy =  new jalview.datamodel.AlignmentAnnotation (ana);\r
-var ds = this.sequence;\r
-while (ds.getDatasetSequence () != null) {\r
-ds = ds.getDatasetSequence ();\r
-}\r
-ala_copy.remap (ds, this.mapping, -1, -1, 0);\r
-ds.addAlignmentAnnotation (ala_copy);\r
-if (ds !== this.sequence) {\r
-ala_copy =  new jalview.datamodel.AlignmentAnnotation (ala_copy);\r
-this.sequence.addAlignmentAnnotation (ala_copy);\r
-}return ala_copy;\r
-}, "jalview.datamodel.AlignmentAnnotation");\r
-});\r
+Clazz.declarePackage ("jalview.structure");
+Clazz.load (null, "jalview.structure.StructureMapping", ["jalview.datamodel.AlignmentAnnotation"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.mappingDetails = null;
+this.sequence = null;
+this.pdbfile = null;
+this.pdbid = null;
+this.pdbchain = null;
+this.mapping = null;
+Clazz.instantialize (this, arguments);
+}, jalview.structure, "StructureMapping");
+Clazz.makeConstructor (c$, 
+function (seq, pdbfile, pdbid, chain, mapping, mappingDetails) {
+this.sequence = seq;
+this.pdbfile = pdbfile;
+this.pdbid = pdbid;
+this.pdbchain = chain;
+this.mapping = mapping;
+this.mappingDetails = mappingDetails;
+}, "jalview.datamodel.SequenceI,~S,~S,~S,~A,~S");
+Clazz.defineMethod (c$, "getSequence", 
+function () {
+return this.sequence;
+});
+Clazz.defineMethod (c$, "getChain", 
+function () {
+return this.pdbchain;
+});
+Clazz.defineMethod (c$, "getPdbId", 
+function () {
+return this.pdbid;
+});
+Clazz.defineMethod (c$, "getAtomNum", 
+function (seqpos) {
+if (this.mapping.length > seqpos) {
+return this.mapping[seqpos][1];
+} else {
+return 0;
+}}, "~N");
+Clazz.defineMethod (c$, "getPDBResNum", 
+function (seqpos) {
+if (this.mapping.length > seqpos) {
+return this.mapping[seqpos][0];
+} else {
+return 0;
+}}, "~N");
+Clazz.defineMethod (c$, "getSeqPos", 
+function (pdbResNum) {
+for (var i = 0; i < this.mapping.length; i++) {
+if (this.mapping[i][0] == pdbResNum) {
+return i;
+}}
+return -1;
+}, "~N");
+Clazz.defineMethod (c$, "transfer", 
+function (ana) {
+var ala_copy =  new jalview.datamodel.AlignmentAnnotation (ana);
+var ds = this.sequence;
+while (ds.getDatasetSequence () != null) {
+ds = ds.getDatasetSequence ();
+}
+ala_copy.remap (ds, this.mapping, -1, -1, 0);
+ds.addAlignmentAnnotation (ala_copy);
+if (ds !== this.sequence) {
+ala_copy =  new jalview.datamodel.AlignmentAnnotation (ala_copy);
+this.sequence.addAlignmentAnnotation (ala_copy);
+}return ala_copy;
+}, "jalview.datamodel.AlignmentAnnotation");
+});