X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fio%2FModellerDescription.js;h=c08736d44036c99deffc21a678d43c4337f4ad71;hp=1232c0523e5d39a28fe345e76ea3bcb62c8e7655;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/io/ModellerDescription.js b/bin/jalview/io/ModellerDescription.js
index 1232c05..c08736d 100644
--- a/bin/jalview/io/ModellerDescription.js
+++ b/bin/jalview/io/ModellerDescription.js
@@ -1,236 +1,236 @@
-Clazz.declarePackage ("jalview.io");
-Clazz.load (["java.util.Hashtable"], "jalview.io.ModellerDescription", ["jalview.datamodel.DBRefSource", "jalview.jsdev.RegExp", "java.util.StringTokenizer"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.seqTypes = null;
-this.Fields = null;
-this.TYPE = 0;
-this.LOCALID = 1;
-this.START = 2;
-this.START_CHAIN = 3;
-this.END = 4;
-this.END_CHAIN = 5;
-this.DESCRIPTION1 = 6;
-this.DESCRIPTION2 = 7;
-this.RESOLUTION = 8;
-this.TAIL = 9;
-this.Types = null;
-this.Padding = null;
-this.fields = null;
-if (!Clazz.isClassDefined ("jalview.io.ModellerDescription.resCode")) {
-jalview.io.ModellerDescription.$ModellerDescription$resCode$ ();
-}
-Clazz.instantialize (this, arguments);
-}, jalview.io, "ModellerDescription");
-Clazz.prepareFields (c$, function () {
-this.seqTypes =  Clazz.newArray (-1, ["sequence", "structure", "structureX", "structureN"]);
-this.Fields =  Clazz.newArray (-1, ["objectType", "objectId", "startField", "startCode", "endField", "endCode", "description1", "description2", "resolutionField", "tailField"]);
-this.Types =  Clazz.newIntArray (-1, [0, 0, 1, 0, 1, 0, 0, 0, 0, 0]);
-this.Padding =  Clazz.newCharArray (-1, [' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.']);
-this.fields =  new java.util.Hashtable ();
-});
-Clazz.makeConstructor (c$, 
-function () {
-this.fields.put (this.Fields[9], "");
-});
-Clazz.defineMethod (c$, "validResidueCode", 
-($fz = function (field) {
-var val = null;
-var r = jalview.jsdev.RegExp.newRegex (["\\s*((([-0-9]+).?)|FIRST|LAST|@)"]);
-if (!r.search (field)) {
-return null;
-}var value = r.stringMatchedI (3);
-if (value == null) {
-value = r.stringMatchedI (1);
-}try {
-val = Integer.$valueOf (value);
-return Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, field, val);
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-} else {
-throw e;
-}
-}
-return Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, field, null);
-}, $fz.isPrivate = true, $fz), "~S");
-Clazz.defineMethod (c$, "parseDescription", 
-($fz = function (desc) {
-var fields =  new java.util.Hashtable ();
-var st =  new java.util.StringTokenizer (desc, ":", true);
-var field;
-var type = -1;
-if (st.countTokens () > 0) {
-var i = 0;
-field = st.nextToken (":");
-do {
-if (this.seqTypes[i].equalsIgnoreCase (field)) {
-break;
-}} while (++i < this.seqTypes.length);
-if (i < this.seqTypes.length) {
-st.nextToken ();
-type = i;
-i = 1;
-while (i < 9 && st.hasMoreTokens ()) {
-if ((field = st.nextToken (":")) != null) {
-if (!field.equals (":")) {
-if (this.Types[i] == 1) {
-var val = this.validResidueCode (field);
-if (val != null) {
-fields.put ( String.instantialize (this.Fields[i] + "num"), val);
-} else {
-type = -1;
-};}fields.put (this.Fields[i++], field);
-if (st.hasMoreTokens ()) {
-st.nextToken ();
-}} else {
-i++;
-}}}
-if (i == 9) {
-while (st.hasMoreTokens ()) {
-var tl = st.nextToken (":");
-field += tl.equals (":") ? tl : (":" + tl);
-}
-fields.put (this.Fields[9], field);
-}}}if (type == -1) {
-fields =  new java.util.Hashtable ();
-fields.put (this.Fields[9],  String.instantialize (desc));
-} else {
-fields.put (this.Fields[0], this.seqTypes[type]);
-}return fields;
-}, $fz.isPrivate = true, $fz), "~S");
-Clazz.makeConstructor (c$, 
-function (desc) {
-if (desc == null) {
-desc = "";
-}this.fields = this.parseDescription (desc);
-}, "~S");
-Clazz.defineMethod (c$, "setStartCode", 
-function (v) {
-var r;
-this.fields.put (this.Fields[2] + "num", r = Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, v));
-this.fields.put (this.Fields[2], r.field);
-}, "~N");
-Clazz.defineMethod (c$, "setEndCode", 
-function (v) {
-var r;
-this.fields.put (this.Fields[4] + "num", r = Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, v));
-this.fields.put (this.Fields[4], r.field);
-}, "~N");
-Clazz.makeConstructor (c$, 
-function (seq) {
-if (seq.getDescription () != null) {
-this.fields = this.parseDescription (seq.getDescription ());
-}if (this.isModellerFieldset ()) {
-if (this.getStartCode () == null || (this.getStartNum () != seq.getStart () && this.getStartCode ().val != null)) {
-this.setStartCode (seq.getStart ());
-}if (this.getEndCode () == null || (this.getEndNum () != seq.getEnd () && this.getStartCode () != null && this.getStartCode ().val != null)) {
-this.setEndCode (seq.getEnd ());
-}} else {
-this.setStartCode (seq.getStart ());
-this.setEndCode (seq.getEnd ());
-this.fields.put (this.Fields[1], seq.getName ());
-var t = 0;
-if (seq.getDatasetSequence () != null && seq.getDatasetSequence ().getDBRef () != null) {
-var dbr = seq.getDatasetSequence ().getDBRef ();
-var i;
-var j;
-for (i = 0, j = dbr.length; i < j; i++) {
-if (dbr[i] != null) {
-if (dbr[i].getSource ().equals (jalview.datamodel.DBRefSource.PDB)) {
-this.fields.put (this.Fields[1], dbr[i].getAccessionId ());
-t = 2;
-break;
-}}}
-}this.fields.put (this.Fields[0], this.seqTypes[t]);
-}}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "isModellerFieldset", 
-function () {
-return (this.fields.containsKey (this.Fields[0]));
-});
-Clazz.defineMethod (c$, "getDescriptionLine", 
-function () {
-var desc = "";
-var lastfield = this.Fields.length - 1;
-if (this.isModellerFieldset ()) {
-var value;
-for (; lastfield > 6; lastfield--) {
-if (this.fields.containsKey (this.Fields[lastfield])) {
-break;
-}}
-for (var i = 0; i < lastfield; i++) {
-value = this.fields.get (this.Fields[i]);
-if (value != null && value.length > 0) {
-desc += (this.fields.get (this.Fields[i])) + ":";
-} else {
-desc += this.Padding[i] + ":";
-}}
-}if (this.fields.containsKey (this.Fields[lastfield])) {
-desc += this.fields.get (this.Fields[lastfield]);
-} else {
-desc += ".";
-}return desc;
-});
-Clazz.defineMethod (c$, "getStartNum", 
-function () {
-var start = 0;
-var val = this.getStartCode ();
-if (val != null && val.val != null) {
-return val.val.intValue ();
-}return start;
-});
-Clazz.defineMethod (c$, "getStartCode", 
-function () {
-if (this.isModellerFieldset () && this.fields.containsKey (this.Fields[2] + "num")) {
-return this.fields.get (this.Fields[2] + "num");
-}return null;
-});
-Clazz.defineMethod (c$, "getEndCode", 
-function () {
-if (this.isModellerFieldset () && this.fields.containsKey (this.Fields[4] + "num")) {
-return this.fields.get (this.Fields[4] + "num");
-}return null;
-});
-Clazz.defineMethod (c$, "getEndNum", 
-function () {
-var end = 0;
-var val = this.getEndCode ();
-if (val != null && val.val != null) {
-return val.val.intValue ();
-}return end;
-});
-Clazz.defineMethod (c$, "updateSequenceI", 
-function (newSeq) {
-if (this.isModellerFieldset ()) {
-var rc = this.getStartCode ();
-if (rc != null && rc.val != null) {
-newSeq.setStart (this.getStartNum ());
-} else {
-newSeq.setStart (1);
-}rc = this.getEndCode ();
-if (rc != null && rc.val != null) {
-newSeq.setEnd (this.getEndNum ());
-} else {
-newSeq.setEnd (newSeq.getStart () + newSeq.getLength ());
-}return true;
-}return false;
-}, "jalview.datamodel.SequenceI");
-c$.$ModellerDescription$resCode$ = function () {
-Clazz.pu$h ();
-c$ = Clazz.decorateAsClass (function () {
-Clazz.prepareCallback (this, arguments);
-this.val = null;
-this.field = null;
-Clazz.instantialize (this, arguments);
-}, jalview.io.ModellerDescription, "resCode");
-Clazz.makeConstructor (c$, 
-function (a, b) {
-this.val = b;
-this.field = a;
-}, "~S,Integer");
-Clazz.makeConstructor (c$, 
-function (a) {
-this.val =  new Integer (a);
-this.field = this.val.toString ();
-}, "~N");
-c$ = Clazz.p0p ();
-};
-});
+Clazz.declarePackage ("jalview.io");
+Clazz.load (["java.util.Hashtable"], "jalview.io.ModellerDescription", ["jalview.datamodel.DBRefSource", "jalview.jsdev.RegExp", "java.util.StringTokenizer"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.seqTypes = null;
+this.Fields = null;
+this.TYPE = 0;
+this.LOCALID = 1;
+this.START = 2;
+this.START_CHAIN = 3;
+this.END = 4;
+this.END_CHAIN = 5;
+this.DESCRIPTION1 = 6;
+this.DESCRIPTION2 = 7;
+this.RESOLUTION = 8;
+this.TAIL = 9;
+this.Types = null;
+this.Padding = null;
+this.fields = null;
+if (!Clazz.isClassDefined ("jalview.io.ModellerDescription.resCode")) {
+jalview.io.ModellerDescription.$ModellerDescription$resCode$ ();
+}
+Clazz.instantialize (this, arguments);
+}, jalview.io, "ModellerDescription");
+Clazz.prepareFields (c$, function () {
+this.seqTypes =  Clazz.newArray (-1, ["sequence", "structure", "structureX", "structureN"]);
+this.Fields =  Clazz.newArray (-1, ["objectType", "objectId", "startField", "startCode", "endField", "endCode", "description1", "description2", "resolutionField", "tailField"]);
+this.Types =  Clazz.newIntArray (-1, [0, 0, 1, 0, 1, 0, 0, 0, 0, 0]);
+this.Padding =  Clazz.newCharArray (-1, [' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.']);
+this.fields =  new java.util.Hashtable ();
+});
+Clazz.makeConstructor (c$, 
+function () {
+this.fields.put (this.Fields[9], "");
+});
+Clazz.defineMethod (c$, "validResidueCode", 
+($fz = function (field) {
+var val = null;
+var r = jalview.jsdev.RegExp.newRegex (["\\s*((([-0-9]+).?)|FIRST|LAST|@)"]);
+if (!r.search (field)) {
+return null;
+}var value = r.stringMatchedI (3);
+if (value == null) {
+value = r.stringMatchedI (1);
+}try {
+val = Integer.$valueOf (value);
+return Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, field, val);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+} else {
+throw e;
+}
+}
+return Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, field, null);
+}, $fz.isPrivate = true, $fz), "~S");
+Clazz.defineMethod (c$, "parseDescription", 
+($fz = function (desc) {
+var fields =  new java.util.Hashtable ();
+var st =  new java.util.StringTokenizer (desc, ":", true);
+var field;
+var type = -1;
+if (st.countTokens () > 0) {
+var i = 0;
+field = st.nextToken (":");
+do {
+if (this.seqTypes[i].equalsIgnoreCase (field)) {
+break;
+}} while (++i < this.seqTypes.length);
+if (i < this.seqTypes.length) {
+st.nextToken ();
+type = i;
+i = 1;
+while (i < 9 && st.hasMoreTokens ()) {
+if ((field = st.nextToken (":")) != null) {
+if (!field.equals (":")) {
+if (this.Types[i] == 1) {
+var val = this.validResidueCode (field);
+if (val != null) {
+fields.put ( String.instantialize (this.Fields[i] + "num"), val);
+} else {
+type = -1;
+};}fields.put (this.Fields[i++], field);
+if (st.hasMoreTokens ()) {
+st.nextToken ();
+}} else {
+i++;
+}}}
+if (i == 9) {
+while (st.hasMoreTokens ()) {
+var tl = st.nextToken (":");
+field += tl.equals (":") ? tl : (":" + tl);
+}
+fields.put (this.Fields[9], field);
+}}}if (type == -1) {
+fields =  new java.util.Hashtable ();
+fields.put (this.Fields[9],  String.instantialize (desc));
+} else {
+fields.put (this.Fields[0], this.seqTypes[type]);
+}return fields;
+}, $fz.isPrivate = true, $fz), "~S");
+Clazz.makeConstructor (c$, 
+function (desc) {
+if (desc == null) {
+desc = "";
+}this.fields = this.parseDescription (desc);
+}, "~S");
+Clazz.defineMethod (c$, "setStartCode", 
+function (v) {
+var r;
+this.fields.put (this.Fields[2] + "num", r = Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, v));
+this.fields.put (this.Fields[2], r.field);
+}, "~N");
+Clazz.defineMethod (c$, "setEndCode", 
+function (v) {
+var r;
+this.fields.put (this.Fields[4] + "num", r = Clazz.innerTypeInstance (jalview.io.ModellerDescription.resCode, this, null, v));
+this.fields.put (this.Fields[4], r.field);
+}, "~N");
+Clazz.makeConstructor (c$, 
+function (seq) {
+if (seq.getDescription () != null) {
+this.fields = this.parseDescription (seq.getDescription ());
+}if (this.isModellerFieldset ()) {
+if (this.getStartCode () == null || (this.getStartNum () != seq.getStart () && this.getStartCode ().val != null)) {
+this.setStartCode (seq.getStart ());
+}if (this.getEndCode () == null || (this.getEndNum () != seq.getEnd () && this.getStartCode () != null && this.getStartCode ().val != null)) {
+this.setEndCode (seq.getEnd ());
+}} else {
+this.setStartCode (seq.getStart ());
+this.setEndCode (seq.getEnd ());
+this.fields.put (this.Fields[1], seq.getName ());
+var t = 0;
+if (seq.getDatasetSequence () != null && seq.getDatasetSequence ().getDBRef () != null) {
+var dbr = seq.getDatasetSequence ().getDBRef ();
+var i;
+var j;
+for (i = 0, j = dbr.length; i < j; i++) {
+if (dbr[i] != null) {
+if (dbr[i].getSource ().equals (jalview.datamodel.DBRefSource.PDB)) {
+this.fields.put (this.Fields[1], dbr[i].getAccessionId ());
+t = 2;
+break;
+}}}
+}this.fields.put (this.Fields[0], this.seqTypes[t]);
+}}, "jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "isModellerFieldset", 
+function () {
+return (this.fields.containsKey (this.Fields[0]));
+});
+Clazz.defineMethod (c$, "getDescriptionLine", 
+function () {
+var desc = "";
+var lastfield = this.Fields.length - 1;
+if (this.isModellerFieldset ()) {
+var value;
+for (; lastfield > 6; lastfield--) {
+if (this.fields.containsKey (this.Fields[lastfield])) {
+break;
+}}
+for (var i = 0; i < lastfield; i++) {
+value = this.fields.get (this.Fields[i]);
+if (value != null && value.length > 0) {
+desc += (this.fields.get (this.Fields[i])) + ":";
+} else {
+desc += this.Padding[i] + ":";
+}}
+}if (this.fields.containsKey (this.Fields[lastfield])) {
+desc += this.fields.get (this.Fields[lastfield]);
+} else {
+desc += ".";
+}return desc;
+});
+Clazz.defineMethod (c$, "getStartNum", 
+function () {
+var start = 0;
+var val = this.getStartCode ();
+if (val != null && val.val != null) {
+return val.val.intValue ();
+}return start;
+});
+Clazz.defineMethod (c$, "getStartCode", 
+function () {
+if (this.isModellerFieldset () && this.fields.containsKey (this.Fields[2] + "num")) {
+return this.fields.get (this.Fields[2] + "num");
+}return null;
+});
+Clazz.defineMethod (c$, "getEndCode", 
+function () {
+if (this.isModellerFieldset () && this.fields.containsKey (this.Fields[4] + "num")) {
+return this.fields.get (this.Fields[4] + "num");
+}return null;
+});
+Clazz.defineMethod (c$, "getEndNum", 
+function () {
+var end = 0;
+var val = this.getEndCode ();
+if (val != null && val.val != null) {
+return val.val.intValue ();
+}return end;
+});
+Clazz.defineMethod (c$, "updateSequenceI", 
+function (newSeq) {
+if (this.isModellerFieldset ()) {
+var rc = this.getStartCode ();
+if (rc != null && rc.val != null) {
+newSeq.setStart (this.getStartNum ());
+} else {
+newSeq.setStart (1);
+}rc = this.getEndCode ();
+if (rc != null && rc.val != null) {
+newSeq.setEnd (this.getEndNum ());
+} else {
+newSeq.setEnd (newSeq.getStart () + newSeq.getLength ());
+}return true;
+}return false;
+}, "jalview.datamodel.SequenceI");
+c$.$ModellerDescription$resCode$ = function () {
+Clazz.pu$h ();
+c$ = Clazz.decorateAsClass (function () {
+Clazz.prepareCallback (this, arguments);
+this.val = null;
+this.field = null;
+Clazz.instantialize (this, arguments);
+}, jalview.io.ModellerDescription, "resCode");
+Clazz.makeConstructor (c$, 
+function (a, b) {
+this.val = b;
+this.field = a;
+}, "~S,Integer");
+Clazz.makeConstructor (c$, 
+function (a) {
+this.val =  new Integer (a);
+this.field = this.val.toString ();
+}, "~N");
+c$ = Clazz.p0p ();
+};
+});