X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fio%2FFastaFile.js;h=5dc3155d4d9267fe5afe9fef7fa5aba9835db1c9;hp=38f827fb3e17cab52f257357b9b7af426518d2f1;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/io/FastaFile.js b/bin/jalview/io/FastaFile.js
index 38f827f..5dc3155 100644
--- a/bin/jalview/io/FastaFile.js
+++ b/bin/jalview/io/FastaFile.js
@@ -1,94 +1,94 @@
-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 ());
-});
-});
+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 ());
+});
+});