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