X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fstructure%2FStructureMapping.js;h=40c774f8db731143d0a2b80ea1f5c4fdd7e2fa1b;hp=8cf2f338d20400c9fa6fc48aca229515c84c2aa3;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6

diff --git a/site/j2s/jalview/structure/StructureMapping.js b/site/j2s/jalview/structure/StructureMapping.js
index 8cf2f33..40c774f 100644
--- a/site/j2s/jalview/structure/StructureMapping.js
+++ b/site/j2s/jalview/structure/StructureMapping.js
@@ -1,69 +1,69 @@
-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");
-});
+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");
+});