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