-Clazz.declarePackage ("jalview.io");\r
-Clazz.load (["jalview.io.AlignFile"], "jalview.io.FastaFile", ["jalview.datamodel.AlignmentAnnotation", "$.Annotation", "java.lang.StringBuffer"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.len = 72;\r
-this.out = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.io, "FastaFile", jalview.io.AlignFile);\r
-Clazz.makeConstructor (c$, \r
-function () {\r
-Clazz.superConstructor (this, jalview.io.FastaFile, []);\r
-});\r
-Clazz.overrideMethod (c$, "parse", \r
-function () {\r
-var sb = new StringBuffer ();\r
-var firstLine = true;\r
-var line;\r
-var uline;\r
-var seq = null;\r
-var annotation = false;\r
-while ((uline = this.nextLine ()) != null) {\r
-line = uline.trim ();\r
-if (line.length > 0) {\r
-if (line.charAt (0) == '>') {\r
-if (line.startsWith (">#_")) {\r
-if (annotation) {\r
-this.annotations.addElement (this.makeAnnotation (seq, sb));\r
-}} else {\r
-annotation = false;\r
-}if (!firstLine) {\r
-seq.setSequence (sb.toString ());\r
-if (!annotation) {\r
-this.seqs.addElement (seq);\r
-}}seq = this.parseId (line.substring (1));\r
-firstLine = false;\r
-sb = new StringBuffer ();\r
-if (line.startsWith (">#_")) {\r
-annotation = true;\r
-}} else {\r
-sb.append (annotation ? uline : line);\r
-}}}\r
-if (annotation) {\r
-this.annotations.addElement (this.makeAnnotation (seq, sb));\r
-} else if (!firstLine) {\r
-seq.setSequence (sb.toString ());\r
-this.seqs.addElement (seq);\r
-}});\r
-Clazz.defineMethod (c$, "makeAnnotation", \r
-($fz = function (seq, sb) {\r
-var anots = new Array (sb.length ());\r
-var cb;\r
-for (var i = 0; i < anots.length; i++) {\r
-var cn = sb.charAt (i);\r
-if (cn != ' ') {\r
-anots[i] = new jalview.datamodel.Annotation ("" + cn, null, ' ', NaN);\r
-}}\r
-var aa = new jalview.datamodel.AlignmentAnnotation (seq.getName ().substring (2), seq.getDescription (), anots);\r
-return aa;\r
-}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,StringBuffer");\r
-Clazz.defineMethod (c$, "addAnnotations", \r
-function (al) {\r
-this.addProperties (al);\r
-for (var i = 0; i < this.annotations.size (); i++) {\r
-var aa = this.annotations.elementAt (i);\r
-aa.setPadGaps (true, al.getGapCharacter ());\r
-al.addAnnotation (aa);\r
-}\r
-}, "jalview.datamodel.Alignment");\r
-Clazz.defineMethod (c$, "print", \r
-function (s) {\r
-this.out = new StringBuffer ();\r
-var i = 0;\r
-while ((i < s.length) && (s[i] != null)) {\r
-this.out.append (">" + this.printId (s[i]));\r
-if (s[i].getDescription () != null) {\r
-this.out.append (" " + s[i].getDescription ());\r
-}this.out.append (this.newline);\r
-var nochunks = (Clazz.doubleToInt (s[i].getLength () / this.len)) + 1;\r
-for (var j = 0; j < nochunks; j++) {\r
-var start = j * this.len;\r
-var end = start + this.len;\r
-if (end < s[i].getLength ()) {\r
-this.out.append (s[i].getSequenceAsString (start, end) + this.newline);\r
-} else if (start < s[i].getLength ()) {\r
-this.out.append (s[i].getSequenceAsString (start, s[i].getLength ()) + this.newline);\r
-}}\r
-i++;\r
-}\r
-return this.out.toString ();\r
-}, "~A");\r
-Clazz.defineMethod (c$, "print", \r
-function () {\r
-return this.print (this.getSeqsAsArray ());\r
-});\r
-});\r
+Clazz.declarePackage ("jalview.io");
+Clazz.load (["jalview.io.AlignFile"], "jalview.io.FastaFile", ["jalview.datamodel.AlignmentAnnotation", "$.Annotation", "java.lang.StringBuffer"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.len = 72;
+this.out = null;
+Clazz.instantialize (this, arguments);
+}, jalview.io, "FastaFile", jalview.io.AlignFile);
+Clazz.makeConstructor (c$,
+function () {
+Clazz.superConstructor (this, jalview.io.FastaFile, []);
+});
+Clazz.overrideMethod (c$, "parse",
+function () {
+var sb = new StringBuffer ();
+var firstLine = true;
+var line;
+var uline;
+var seq = null;
+var annotation = false;
+while ((uline = this.nextLine ()) != null) {
+line = uline.trim ();
+if (line.length > 0) {
+if (line.charAt (0) == '>') {
+if (line.startsWith (">#_")) {
+if (annotation) {
+this.annotations.addElement (this.makeAnnotation (seq, sb));
+}} else {
+annotation = false;
+}if (!firstLine) {
+seq.setSequence (sb.toString ());
+if (!annotation) {
+this.seqs.addElement (seq);
+}}seq = this.parseId (line.substring (1));
+firstLine = false;
+sb = new StringBuffer ();
+if (line.startsWith (">#_")) {
+annotation = true;
+}} else {
+sb.append (annotation ? uline : line);
+}}}
+if (annotation) {
+this.annotations.addElement (this.makeAnnotation (seq, sb));
+} else if (!firstLine) {
+seq.setSequence (sb.toString ());
+this.seqs.addElement (seq);
+}});
+Clazz.defineMethod (c$, "makeAnnotation",
+($fz = function (seq, sb) {
+var anots = new Array (sb.length ());
+var cb;
+for (var i = 0; i < anots.length; i++) {
+var cn = sb.charAt (i);
+if (cn != ' ') {
+anots[i] = new jalview.datamodel.Annotation ("" + cn, null, ' ', NaN);
+}}
+var aa = new jalview.datamodel.AlignmentAnnotation (seq.getName ().substring (2), seq.getDescription (), anots);
+return aa;
+}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,StringBuffer");
+Clazz.defineMethod (c$, "addAnnotations",
+function (al) {
+this.addProperties (al);
+for (var i = 0; i < this.annotations.size (); i++) {
+var aa = this.annotations.elementAt (i);
+aa.setPadGaps (true, al.getGapCharacter ());
+al.addAnnotation (aa);
+}
+}, "jalview.datamodel.Alignment");
+Clazz.defineMethod (c$, "print",
+function (s) {
+this.out = new StringBuffer ();
+var i = 0;
+while ((i < s.length) && (s[i] != null)) {
+this.out.append (">" + this.printId (s[i]));
+if (s[i].getDescription () != null) {
+this.out.append (" " + s[i].getDescription ());
+}this.out.append (this.newline);
+var nochunks = (Clazz.doubleToInt (s[i].getLength () / this.len)) + 1;
+for (var j = 0; j < nochunks; j++) {
+var start = j * this.len;
+var end = start + this.len;
+if (end < s[i].getLength ()) {
+this.out.append (s[i].getSequenceAsString (start, end) + this.newline);
+} else if (start < s[i].getLength ()) {
+this.out.append (s[i].getSequenceAsString (start, s[i].getLength ()) + this.newline);
+}}
+i++;
+}
+return this.out.toString ();
+}, "~A");
+Clazz.defineMethod (c$, "print",
+function () {
+return this.print (this.getSeqsAsArray ());
+});
+});
git://source.jalview.org / jalviewjs.git / blobdiff