X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fio%2FAlignFile.js;h=142c507b74827be531cb6e04f2c18e7d0ba8526a;hp=f3247de1799dc989de099564fc21b3b21d39ced6;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/io/AlignFile.js b/site/j2s/jalview/io/AlignFile.js
index f3247de..142c507 100644
--- a/site/j2s/jalview/io/AlignFile.js
+++ b/site/j2s/jalview/io/AlignFile.js
@@ -1,158 +1,158 @@
-Clazz.declarePackage ("jalview.io");
-Clazz.load (["jalview.io.FileParse"], "jalview.io.AlignFile", ["jalview.datamodel.Sequence", "jalview.util.MessageManager", "java.io.IOException", "java.lang.Error", "java.util.ArrayList", "$.Hashtable", "$.Vector"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.noSeqs = 0;
-this.maxLength = 0;
-this.seqs = null;
-this.annotations = null;
-this.seqGroups = null;
-this.properties = null;
-this.start = 0;
-this.end = 0;
-this.jvSuffix = true;
-this.parseCalled = false;
-this.newickStrings = null;
-Clazz.instantialize (this, arguments);
-}, jalview.io, "AlignFile", jalview.io.FileParse);
-Clazz.makeConstructor (c$, 
-function () {
-Clazz.superConstructor (this, jalview.io.AlignFile, []);
-this.initData ();
-});
-Clazz.makeConstructor (c$, 
-function (inFile, type) {
-this.construct (true, inFile, type);
-}, "~S,~S");
-Clazz.makeConstructor (c$, 
-function (parseImmediately, inFile, type) {
-Clazz.superConstructor (this, jalview.io.AlignFile, [inFile, type]);
-this.initData ();
-if (parseImmediately) {
-this.doParse ();
-}}, "~B,~S,~S");
-Clazz.makeConstructor (c$, 
-function (source) {
-this.construct (true, source);
-}, "jalview.io.FileParse");
-Clazz.makeConstructor (c$, 
-function (parseImmediately, source) {
-Clazz.superConstructor (this, jalview.io.AlignFile, [source]);
-this.initData ();
-if (parseImmediately) {
-this.doParse ();
-}}, "~B,jalview.io.FileParse");
-Clazz.defineMethod (c$, "doParse", 
-function () {
-if (this.parseCalled) {
-throw  new java.io.IOException ("Implementation error: Parser called twice for same data.\nNeed to call initData() again before parsing can be reattempted.");
-}this.parseCalled = true;
-this.parse ();
-for (var i = 0, c = this.seqs.size (); i < c; i++) {
-this.seqs.get (i).setIndex (i);
-}
-});
-Clazz.defineMethod (c$, "getSeqs", 
-function () {
-return this.seqs;
-});
-Clazz.defineMethod (c$, "getSeqGroups", 
-function () {
-return this.seqGroups;
-});
-Clazz.defineMethod (c$, "getSeqsAsArray", 
-function () {
-var s =  new Array (this.seqs.size ());
-for (var i = 0; i < this.seqs.size (); i++) {
-s[i] = this.seqs.elementAt (i);
-}
-return s;
-});
-Clazz.defineMethod (c$, "addAnnotations", 
-function (al) {
-this.addProperties (al);
-for (var i = 0; i < this.annotations.size (); i++) {
-var an = this.annotations.elementAt (i);
-an.validateRangeAndDisplay ();
-al.addAnnotation (an);
-}
-}, "jalview.datamodel.AlignmentI");
-Clazz.defineMethod (c$, "addSeqGroups", 
-function (al) {
-this.seqGroups = al.getGroups ();
-}, "jalview.datamodel.AlignmentI");
-Clazz.defineMethod (c$, "addProperties", 
-function (al) {
-if (this.properties != null && this.properties.size () > 0) {
-var keys = this.properties.keys ();
-var vals = this.properties.elements ();
-while (keys.hasMoreElements ()) {
-al.setProperty (keys.nextElement (), vals.nextElement ());
-}
-}}, "jalview.datamodel.AlignmentI");
-Clazz.defineMethod (c$, "setAlignmentProperty", 
-function (key, value) {
-if (key == null) {
-throw  new Error (jalview.util.MessageManager.getString ("error.implementation_error_cannot_have_null_alignment"));
-}if (value == null) {
-return;
-}if (this.properties == null) {
-this.properties =  new java.util.Hashtable ();
-}this.properties.put (key, value);
-}, "~O,~O");
-Clazz.defineMethod (c$, "getAlignmentProperty", 
-function (key) {
-if (this.properties != null && key != null) {
-return this.properties.get (key);
-}return null;
-}, "~O");
-Clazz.defineMethod (c$, "initData", 
-function () {
-this.seqs =  new java.util.Vector ();
-this.annotations =  new java.util.Vector ();
-this.seqGroups =  new java.util.ArrayList ();
-this.parseCalled = false;
-});
-Clazz.defineMethod (c$, "setSeqs", 
-function (s) {
-this.seqs =  new java.util.Vector ();
-for (var i = 0; i < s.length; i++) {
-this.seqs.addElement (s[i]);
-}
-}, "~A");
-Clazz.defineMethod (c$, "addJVSuffix", 
-function (b) {
-this.jvSuffix = b;
-}, "~B");
-Clazz.defineMethod (c$, "parseId", 
-function (id) {
-var seq = null;
-id = id.trim ();
-var space = id.indexOf (" ");
-if (space > -1) {
-seq =  new jalview.datamodel.Sequence (id.substring (0, space), "");
-seq.setDescription (id.substring (space + 1));
-} else {
-seq =  new jalview.datamodel.Sequence (id, "");
-}return seq;
-}, "~S");
-Clazz.defineMethod (c$, "printId", 
-function (seq) {
-return seq.getDisplayId (this.jvSuffix);
-}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "addNewickTree", 
-function (treeName, newickString) {
-if (this.newickStrings == null) {
-this.newickStrings =  new java.util.Vector ();
-}this.newickStrings.addElement ( Clazz.newArray (-1, [treeName, newickString]));
-}, "~S,~S");
-Clazz.defineMethod (c$, "getTreeCount", 
-function () {
-return this.newickStrings == null ? 0 : this.newickStrings.size ();
-});
-Clazz.defineMethod (c$, "addGroups", 
-function (al) {
-for (var sg, $sg = this.getSeqGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-al.addGroup (sg);
-}
-}, "jalview.datamodel.AlignmentI");
-});
+Clazz.declarePackage ("jalview.io");
+Clazz.load (["jalview.io.FileParse"], "jalview.io.AlignFile", ["jalview.datamodel.Sequence", "jalview.util.MessageManager", "java.io.IOException", "java.lang.Error", "java.util.ArrayList", "$.Hashtable", "$.Vector"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.noSeqs = 0;
+this.maxLength = 0;
+this.seqs = null;
+this.annotations = null;
+this.seqGroups = null;
+this.properties = null;
+this.start = 0;
+this.end = 0;
+this.jvSuffix = true;
+this.parseCalled = false;
+this.newickStrings = null;
+Clazz.instantialize (this, arguments);
+}, jalview.io, "AlignFile", jalview.io.FileParse);
+Clazz.makeConstructor (c$, 
+function () {
+Clazz.superConstructor (this, jalview.io.AlignFile, []);
+this.initData ();
+});
+Clazz.makeConstructor (c$, 
+function (inFile, type) {
+this.construct (true, inFile, type);
+}, "~S,~S");
+Clazz.makeConstructor (c$, 
+function (parseImmediately, inFile, type) {
+Clazz.superConstructor (this, jalview.io.AlignFile, [inFile, type]);
+this.initData ();
+if (parseImmediately) {
+this.doParse ();
+}}, "~B,~S,~S");
+Clazz.makeConstructor (c$, 
+function (source) {
+this.construct (true, source);
+}, "jalview.io.FileParse");
+Clazz.makeConstructor (c$, 
+function (parseImmediately, source) {
+Clazz.superConstructor (this, jalview.io.AlignFile, [source]);
+this.initData ();
+if (parseImmediately) {
+this.doParse ();
+}}, "~B,jalview.io.FileParse");
+Clazz.defineMethod (c$, "doParse", 
+function () {
+if (this.parseCalled) {
+throw  new java.io.IOException ("Implementation error: Parser called twice for same data.\nNeed to call initData() again before parsing can be reattempted.");
+}this.parseCalled = true;
+this.parse ();
+for (var i = 0, c = this.seqs.size (); i < c; i++) {
+this.seqs.get (i).setIndex (i);
+}
+});
+Clazz.defineMethod (c$, "getSeqs", 
+function () {
+return this.seqs;
+});
+Clazz.defineMethod (c$, "getSeqGroups", 
+function () {
+return this.seqGroups;
+});
+Clazz.defineMethod (c$, "getSeqsAsArray", 
+function () {
+var s =  new Array (this.seqs.size ());
+for (var i = 0; i < this.seqs.size (); i++) {
+s[i] = this.seqs.elementAt (i);
+}
+return s;
+});
+Clazz.defineMethod (c$, "addAnnotations", 
+function (al) {
+this.addProperties (al);
+for (var i = 0; i < this.annotations.size (); i++) {
+var an = this.annotations.elementAt (i);
+an.validateRangeAndDisplay ();
+al.addAnnotation (an);
+}
+}, "jalview.datamodel.AlignmentI");
+Clazz.defineMethod (c$, "addSeqGroups", 
+function (al) {
+this.seqGroups = al.getGroups ();
+}, "jalview.datamodel.AlignmentI");
+Clazz.defineMethod (c$, "addProperties", 
+function (al) {
+if (this.properties != null && this.properties.size () > 0) {
+var keys = this.properties.keys ();
+var vals = this.properties.elements ();
+while (keys.hasMoreElements ()) {
+al.setProperty (keys.nextElement (), vals.nextElement ());
+}
+}}, "jalview.datamodel.AlignmentI");
+Clazz.defineMethod (c$, "setAlignmentProperty", 
+function (key, value) {
+if (key == null) {
+throw  new Error (jalview.util.MessageManager.getString ("error.implementation_error_cannot_have_null_alignment"));
+}if (value == null) {
+return;
+}if (this.properties == null) {
+this.properties =  new java.util.Hashtable ();
+}this.properties.put (key, value);
+}, "~O,~O");
+Clazz.defineMethod (c$, "getAlignmentProperty", 
+function (key) {
+if (this.properties != null && key != null) {
+return this.properties.get (key);
+}return null;
+}, "~O");
+Clazz.defineMethod (c$, "initData", 
+function () {
+this.seqs =  new java.util.Vector ();
+this.annotations =  new java.util.Vector ();
+this.seqGroups =  new java.util.ArrayList ();
+this.parseCalled = false;
+});
+Clazz.defineMethod (c$, "setSeqs", 
+function (s) {
+this.seqs =  new java.util.Vector ();
+for (var i = 0; i < s.length; i++) {
+this.seqs.addElement (s[i]);
+}
+}, "~A");
+Clazz.defineMethod (c$, "addJVSuffix", 
+function (b) {
+this.jvSuffix = b;
+}, "~B");
+Clazz.defineMethod (c$, "parseId", 
+function (id) {
+var seq = null;
+id = id.trim ();
+var space = id.indexOf (" ");
+if (space > -1) {
+seq =  new jalview.datamodel.Sequence (id.substring (0, space), "");
+seq.setDescription (id.substring (space + 1));
+} else {
+seq =  new jalview.datamodel.Sequence (id, "");
+}return seq;
+}, "~S");
+Clazz.defineMethod (c$, "printId", 
+function (seq) {
+return seq.getDisplayId (this.jvSuffix);
+}, "jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "addNewickTree", 
+function (treeName, newickString) {
+if (this.newickStrings == null) {
+this.newickStrings =  new java.util.Vector ();
+}this.newickStrings.addElement ( Clazz.newArray (-1, [treeName, newickString]));
+}, "~S,~S");
+Clazz.defineMethod (c$, "getTreeCount", 
+function () {
+return this.newickStrings == null ? 0 : this.newickStrings.size ();
+});
+Clazz.defineMethod (c$, "addGroups", 
+function (al) {
+for (var sg, $sg = this.getSeqGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+al.addGroup (sg);
+}
+}, "jalview.datamodel.AlignmentI");
+});