JAL-1807 includes ?j2sdebug flag and DebugJS._(msg)

[jalviewjs.git] / bin / jalview / io / PileUpfile.js

diff --git a/bin/jalview/io/PileUpfile.js b/bin/jalview/io/PileUpfile.js
index b8bb68c..a6effa1 100644 (file)
--- a/bin/jalview/io/PileUpfile.js
+++ b/bin/jalview/io/PileUpfile.js
@@ -1,82 +1,82 @@
-Clazz.declarePackage ("jalview.io");\r
-Clazz.load (["jalview.io.MSFfile"], "jalview.io.PileUpfile", ["jalview.util.Format", "java.lang.StringBuffer"], function () {\r
-c$ = Clazz.declareType (jalview.io, "PileUpfile", jalview.io.MSFfile);\r
-Clazz.makeConstructor (c$, \r
-function () {\r
-Clazz.superConstructor (this, jalview.io.PileUpfile, []);\r
-});\r
-Clazz.defineMethod (c$, "print", \r
-function () {\r
-return this.print (this.getSeqsAsArray ());\r
-});\r
-Clazz.defineMethod (c$, "print", \r
-function (s) {\r
-var out =  new StringBuffer ("PileUp");\r
-out.append (this.newline);\r
-out.append (this.newline);\r
-var max = 0;\r
-var maxid = 0;\r
-var i = 0;\r
-var bigChecksum = 0;\r
-var checksums =  Clazz.newIntArray (s.length, 0);\r
-while (i < s.length) {\r
-checksums[i] = this.checkSum (s[i].getSequenceAsString ());\r
-bigChecksum += checksums[i];\r
-i++;\r
-}\r
-out.append ("   MSF: " + s[0].getSequence ().length + "   Type: P    Check:  " + bigChecksum % 10000 + "   ..");\r
-out.append (this.newline);\r
-out.append (this.newline);\r
-out.append (this.newline);\r
-i = 0;\r
-while ((i < s.length) && (s[i] != null)) {\r
-var seq = s[i].getSequenceAsString ();\r
-out.append (" Name: " + this.printId (s[i]) + " oo  Len:  " + seq.length + "  Check:  " + checksums[i] + "  Weight:  1.00");\r
-out.append (this.newline);\r
-if (seq.length > max) {\r
-max = seq.length;\r
-}if (s[i].getName ().length > maxid) {\r
-maxid = s[i].getName ().length;\r
-}i++;\r
-}\r
-if (maxid < 10) {\r
-maxid = 10;\r
-}maxid++;\r
-out.append (this.newline);\r
-out.append (this.newline);\r
-out.append ("//");\r
-out.append (this.newline);\r
-out.append (this.newline);\r
-var len = 50;\r
-var nochunks = (Clazz.doubleToInt (max / len)) + 1;\r
-if ((max % len) == 0) {\r
-nochunks--;\r
-}for (i = 0; i < nochunks; i++) {\r
-var j = 0;\r
-while ((j < s.length) && (s[j] != null)) {\r
-var name = this.printId (s[j]);\r
-out.append ( new jalview.util.Format ("%-" + maxid + "s").form (name + " "));\r
-for (var k = 0; k < 5; k++) {\r
-var start = (i * 50) + (k * 10);\r
-var end = start + 10;\r
-if ((end < s[j].getSequence ().length) && (start < s[j].getSequence ().length)) {\r
-out.append (s[j].getSequence (start, end));\r
-if (k < 4) {\r
-out.append (" ");\r
-} else {\r
-out.append (this.newline);\r
-}} else {\r
-if (start < s[j].getSequence ().length) {\r
-out.append (s[j].getSequenceAsString ().substring (start));\r
-out.append (this.newline);\r
-} else {\r
-if (k == 0) {\r
-out.append (this.newline);\r
-}}}}\r
-j++;\r
-}\r
-out.append (this.newline);\r
-}\r
-return out.toString ();\r
-}, "~A");\r
-});\r
+Clazz.declarePackage ("jalview.io");
+Clazz.load (["jalview.io.MSFfile"], "jalview.io.PileUpfile", ["jalview.util.Format", "java.lang.StringBuffer"], function () {
+c$ = Clazz.declareType (jalview.io, "PileUpfile", jalview.io.MSFfile);
+Clazz.makeConstructor (c$, 
+function () {
+Clazz.superConstructor (this, jalview.io.PileUpfile, []);
+});
+Clazz.defineMethod (c$, "print", 
+function () {
+return this.print (this.getSeqsAsArray ());
+});
+Clazz.defineMethod (c$, "print", 
+function (s) {
+var out =  new StringBuffer ("PileUp");
+out.append (this.newline);
+out.append (this.newline);
+var max = 0;
+var maxid = 0;
+var i = 0;
+var bigChecksum = 0;
+var checksums =  Clazz.newIntArray (s.length, 0);
+while (i < s.length) {
+checksums[i] = this.checkSum (s[i].getSequenceAsString ());
+bigChecksum += checksums[i];
+i++;
+}
+out.append ("   MSF: " + s[0].getSequence ().length + "   Type: P    Check:  " + bigChecksum % 10000 + "   ..");
+out.append (this.newline);
+out.append (this.newline);
+out.append (this.newline);
+i = 0;
+while ((i < s.length) && (s[i] != null)) {
+var seq = s[i].getSequenceAsString ();
+out.append (" Name: " + this.printId (s[i]) + " oo  Len:  " + seq.length + "  Check:  " + checksums[i] + "  Weight:  1.00");
+out.append (this.newline);
+if (seq.length > max) {
+max = seq.length;
+}if (s[i].getName ().length > maxid) {
+maxid = s[i].getName ().length;
+}i++;
+}
+if (maxid < 10) {
+maxid = 10;
+}maxid++;
+out.append (this.newline);
+out.append (this.newline);
+out.append ("//");
+out.append (this.newline);
+out.append (this.newline);
+var len = 50;
+var nochunks = (Clazz.doubleToInt (max / len)) + 1;
+if ((max % len) == 0) {
+nochunks--;
+}for (i = 0; i < nochunks; i++) {
+var j = 0;
+while ((j < s.length) && (s[j] != null)) {
+var name = this.printId (s[j]);
+out.append ( new jalview.util.Format ("%-" + maxid + "s").form (name + " "));
+for (var k = 0; k < 5; k++) {
+var start = (i * 50) + (k * 10);
+var end = start + 10;
+if ((end < s[j].getSequence ().length) && (start < s[j].getSequence ().length)) {
+out.append (s[j].getSequence (start, end));
+if (k < 4) {
+out.append (" ");
+} else {
+out.append (this.newline);
+}} else {
+if (start < s[j].getSequence ().length) {
+out.append (s[j].getSequenceAsString ().substring (start));
+out.append (this.newline);
+} else {
+if (k == 0) {
+out.append (this.newline);
+}}}}
+j++;
+}
+out.append (this.newline);
+}
+return out.toString ();
+}, "~A");
+});