X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fio%2FPIRFile.js;h=f14a6eacce8bd6abfb7609ecba007c4db923b66f;hp=fe50c34088c34b9741cfc7fe325e6500c76566ac;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/io/PIRFile.js b/site/j2s/jalview/io/PIRFile.js
index fe50c34..f14a6ea 100644
--- a/site/j2s/jalview/io/PIRFile.js
+++ b/site/j2s/jalview/io/PIRFile.js
@@ -1,101 +1,101 @@
-Clazz.declarePackage ("jalview.io");
-Clazz.load (["jalview.io.AlignFile", "java.util.Vector"], "jalview.io.PIRFile", ["jalview.io.ModellerDescription", "jalview.util.Comparison", "java.lang.StringBuffer"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.words = null;
-Clazz.instantialize (this, arguments);
-}, jalview.io, "PIRFile", jalview.io.AlignFile);
-Clazz.prepareFields (c$, function () {
-this.words =  new java.util.Vector ();
-});
-Clazz.makeConstructor (c$, 
-function () {
-Clazz.superConstructor (this, jalview.io.PIRFile, []);
-});
-Clazz.overrideMethod (c$, "parse", 
-function () {
-var sequence;
-var line = null;
-var md;
-while ((line = this.nextLine ()) != null) {
-if (line.length == 0) {
-continue;
-}if (line.indexOf ("C;") == 0 || line.indexOf ("#") == 0) {
-continue;
-}var newSeq = this.parseId (line.substring (line.indexOf (";") + 1));
-sequence =  new StringBuffer ();
-newSeq.setDescription (this.nextLine ());
-var starFound = false;
-while (!starFound) {
-line = this.nextLine ();
-sequence.append (line);
-if (line == null) {
-break;
-}if (line.indexOf ("*") > -1) {
-starFound = true;
-}}
-if (sequence.length () > 0) {
-sequence.setLength (sequence.length () - 1);
-newSeq.setSequence (sequence.toString ());
-this.seqs.addElement (newSeq);
-md =  new jalview.io.ModellerDescription (newSeq.getDescription ());
-md.updateSequenceI (newSeq);
-}}
-});
-Clazz.defineMethod (c$, "print", 
-function () {
-return this.print (this.getSeqsAsArray ());
-});
-Clazz.defineMethod (c$, "print", 
-function (s) {
-var is_NA = jalview.util.Comparison.isNucleotide (s);
-var len = 72;
-var out =  new StringBuffer ();
-var i = 0;
-var md;
-while ((i < s.length) && (s[i] != null)) {
-var seq = s[i].getSequenceAsString ();
-seq = seq + "*";
-if (is_NA) {
-out.append (">N1;" + s[i].getName ());
-out.append (this.newline);
-if (s[i].getDescription () == null) {
-out.append (s[i].getName () + " " + (s[i].getEnd () - s[i].getStart () + 1));
-out.append (is_NA ? " bases" : " residues");
-out.append (this.newline);
-} else {
-out.append (s[i].getDescription ());
-out.append (this.newline);
-}} else {
-if (jalview.io.PIRFile.useModellerOutput) {
-out.append (">P1;" + s[i].getName ());
-out.append (this.newline);
-md =  new jalview.io.ModellerDescription (s[i]);
-out.append (md.getDescriptionLine ());
-out.append (this.newline);
-} else {
-out.append (">P1;" + this.printId (s[i]));
-out.append (this.newline);
-if (s[i].getDescription () != null) {
-out.append (s[i].getDescription ());
-out.append (this.newline);
-} else {
-out.append (s[i].getName () + " " + (s[i].getEnd () - s[i].getStart () + 1) + " residues");
-out.append (this.newline);
-}}}var nochunks = (Clazz.doubleToInt (seq.length / len)) + 1;
-for (var j = 0; j < nochunks; j++) {
-var start = j * len;
-var end = start + len;
-if (end < seq.length) {
-out.append (seq.substring (start, end));
-out.append (this.newline);
-} else if (start < seq.length) {
-out.append (seq.substring (start));
-out.append (this.newline);
-}}
-i++;
-}
-return out.toString ();
-}, "~A");
-Clazz.defineStatics (c$,
-"useModellerOutput", false);
-});
+Clazz.declarePackage ("jalview.io");
+Clazz.load (["jalview.io.AlignFile", "java.util.Vector"], "jalview.io.PIRFile", ["jalview.io.ModellerDescription", "jalview.util.Comparison", "java.lang.StringBuffer"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.words = null;
+Clazz.instantialize (this, arguments);
+}, jalview.io, "PIRFile", jalview.io.AlignFile);
+Clazz.prepareFields (c$, function () {
+this.words =  new java.util.Vector ();
+});
+Clazz.makeConstructor (c$, 
+function () {
+Clazz.superConstructor (this, jalview.io.PIRFile, []);
+});
+Clazz.overrideMethod (c$, "parse", 
+function () {
+var sequence;
+var line = null;
+var md;
+while ((line = this.nextLine ()) != null) {
+if (line.length == 0) {
+continue;
+}if (line.indexOf ("C;") == 0 || line.indexOf ("#") == 0) {
+continue;
+}var newSeq = this.parseId (line.substring (line.indexOf (";") + 1));
+sequence =  new StringBuffer ();
+newSeq.setDescription (this.nextLine ());
+var starFound = false;
+while (!starFound) {
+line = this.nextLine ();
+sequence.append (line);
+if (line == null) {
+break;
+}if (line.indexOf ("*") > -1) {
+starFound = true;
+}}
+if (sequence.length () > 0) {
+sequence.setLength (sequence.length () - 1);
+newSeq.setSequence (sequence.toString ());
+this.seqs.addElement (newSeq);
+md =  new jalview.io.ModellerDescription (newSeq.getDescription ());
+md.updateSequenceI (newSeq);
+}}
+});
+Clazz.defineMethod (c$, "print", 
+function () {
+return this.print (this.getSeqsAsArray ());
+});
+Clazz.defineMethod (c$, "print", 
+function (s) {
+var is_NA = jalview.util.Comparison.isNucleotide (s);
+var len = 72;
+var out =  new StringBuffer ();
+var i = 0;
+var md;
+while ((i < s.length) && (s[i] != null)) {
+var seq = s[i].getSequenceAsString ();
+seq = seq + "*";
+if (is_NA) {
+out.append (">N1;" + s[i].getName ());
+out.append (this.newline);
+if (s[i].getDescription () == null) {
+out.append (s[i].getName () + " " + (s[i].getEnd () - s[i].getStart () + 1));
+out.append (is_NA ? " bases" : " residues");
+out.append (this.newline);
+} else {
+out.append (s[i].getDescription ());
+out.append (this.newline);
+}} else {
+if (jalview.io.PIRFile.useModellerOutput) {
+out.append (">P1;" + s[i].getName ());
+out.append (this.newline);
+md =  new jalview.io.ModellerDescription (s[i]);
+out.append (md.getDescriptionLine ());
+out.append (this.newline);
+} else {
+out.append (">P1;" + this.printId (s[i]));
+out.append (this.newline);
+if (s[i].getDescription () != null) {
+out.append (s[i].getDescription ());
+out.append (this.newline);
+} else {
+out.append (s[i].getName () + " " + (s[i].getEnd () - s[i].getStart () + 1) + " residues");
+out.append (this.newline);
+}}}var nochunks = (Clazz.doubleToInt (seq.length / len)) + 1;
+for (var j = 0; j < nochunks; j++) {
+var start = j * len;
+var end = start + len;
+if (end < seq.length) {
+out.append (seq.substring (start, end));
+out.append (this.newline);
+} else if (start < seq.length) {
+out.append (seq.substring (start));
+out.append (this.newline);
+}}
+i++;
+}
+return out.toString ();
+}, "~A");
+Clazz.defineStatics (c$,
+"useModellerOutput", false);
+});