X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fio%2FMSFfile.js;h=ee2e3af8c13a8a99dd632b7bcab621fa84560563;hp=d80fbdc7346106cf8303b1c755131167f2fc855d;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/io/MSFfile.js b/bin/jalview/io/MSFfile.js
index d80fbdc..ee2e3af 100644
--- a/bin/jalview/io/MSFfile.js
+++ b/bin/jalview/io/MSFfile.js
@@ -1,190 +1,190 @@
-Clazz.declarePackage ("jalview.io");
-Clazz.load (["jalview.io.AlignFile"], "jalview.io.MSFfile", ["jalview.datamodel.Sequence", "jalview.util.Comparison", "$.Format", "java.lang.StringBuffer", "java.util.Hashtable", "$.StringTokenizer", "$.Vector"], function () {
-c$ = Clazz.declareType (jalview.io, "MSFfile", jalview.io.AlignFile);
-Clazz.makeConstructor (c$, 
-function () {
-Clazz.superConstructor (this, jalview.io.MSFfile, []);
-});
-Clazz.overrideMethod (c$, "parse", 
-function () {
-var i = 0;
-var seqFlag = false;
-var key =  String.instantialize ();
-var headers =  new java.util.Vector ();
-var seqhash =  new java.util.Hashtable ();
-var line;
-try {
-while ((line = this.nextLine ()) != null) {
-var str =  new java.util.StringTokenizer (line);
-while (str.hasMoreTokens ()) {
-var inStr = str.nextToken ();
-if (inStr.indexOf ("Name:") != -1) {
-key = str.nextToken ();
-headers.addElement (key);
-}if (inStr.indexOf ("//") != -1) {
-seqFlag = true;
-}if ((inStr.indexOf ("//") == -1) && (seqFlag == true)) {
-key = inStr;
-var tempseq;
-if (seqhash.containsKey (key)) {
-tempseq = seqhash.get (key);
-} else {
-tempseq =  new StringBuffer ();
-seqhash.put (key, tempseq);
-}while (str.hasMoreTokens ()) {
-tempseq.append (str.nextToken ());
-}
-}}
-}
-} catch (e) {
-if (Clazz.exceptionOf (e, java.io.IOException)) {
-System.err.println ("Exception parsing MSFFile " + e);
-e.printStackTrace ();
-} else {
-throw e;
-}
-}
-this.noSeqs = headers.size ();
-for (i = 0; i < headers.size (); i++) {
-if (seqhash.get (headers.elementAt (i)) != null) {
-var head = headers.elementAt (i).toString ();
-var seq = seqhash.get (head).toString ();
-if (this.maxLength < head.length) {
-this.maxLength = head.length;
-}seq = seq.$replace ('~', '-');
-var newSeq = this.parseId (head);
-newSeq.setSequence (seq);
-this.seqs.addElement (newSeq);
-} else {
-System.err.println ("MSFFile Parser: Can't find sequence for " + headers.elementAt (i));
-}}
-});
-Clazz.defineMethod (c$, "checkSum", 
-function (seq) {
-var check = 0;
-var sequence = seq.toUpperCase ();
-for (var i = 0; i < sequence.length; i++) {
-try {
-var value = sequence.charCodeAt (i);
-if (value != -1) {
-check += (i % 57 + 1) * value;
-}} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-System.err.println ("Exception during MSF Checksum calculation");
-e.printStackTrace ();
-} else {
-throw e;
-}
-}
-}
-return check % 10000;
-}, "~S");
-Clazz.defineMethod (c$, "print", 
-function (seqs) {
-var is_NA = jalview.util.Comparison.isNucleotide (seqs);
-var s =  new Array (seqs.length);
-var out =  new StringBuffer ("!!" + (is_NA ? "NA" : "AA") + "_MULTIPLE_ALIGNMENT 1.0");
-out.append (this.newline);
-out.append (this.newline);
-var max = 0;
-var maxid = 0;
-var i = 0;
-while ((i < seqs.length) && (seqs[i] != null)) {
-s[i] =  new jalview.datamodel.Sequence (seqs[i].getName (), seqs[i].getSequenceAsString ().$replace ('-', '.'), seqs[i].getStart (), seqs[i].getEnd ());
-var sb =  new StringBuffer ();
-sb.append (s[i].getSequence ());
-for (var ii = 0; ii < sb.length (); ii++) {
-if (sb.charAt (ii) == '.') {
-sb.setCharAt (ii, '~');
-} else {
-break;
-}}
-for (var ii = sb.length () - 1; ii > 0; ii--) {
-if (sb.charAt (ii) == '.') {
-sb.setCharAt (ii, '~');
-} else {
-break;
-}}
-s[i].setSequence (sb.toString ());
-if (s[i].getSequence ().length > max) {
-max = s[i].getSequence ().length;
-}i++;
-}
-var maxLenpad =  new jalview.util.Format ("%" + ( String.instantialize ("" + max)).length + "d");
-var maxChkpad =  new jalview.util.Format ("%" + ( String.instantialize ("1" + max)).length + "d");
-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++;
-}
-var maxNB = 0;
-out.append ("   MSF: " + s[0].getSequence ().length + "   Type: " + (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum % 10000) + "   ..");
-out.append (this.newline);
-out.append (this.newline);
-out.append (this.newline);
-var nameBlock =  new Array (s.length);
-var idBlock =  new Array (s.length);
-i = 0;
-while ((i < s.length) && (s[i] != null)) {
-nameBlock[i] =  String.instantialize ("  Name: " + this.printId (s[i]) + " ");
-idBlock[i] =  String.instantialize ("Len: " + maxLenpad.formLong (s[i].getSequence ().length) + "  Check: " + maxChkpad.formLong (checksums[i]) + "  Weight: 1.00" + this.newline);
-if (s[i].getName ().length > maxid) {
-maxid = s[i].getName ().length;
-}if (nameBlock[i].length > maxNB) {
-maxNB = nameBlock[i].length;
-}i++;
-}
-if (maxid < 10) {
-maxid = 10;
-}if (maxNB < 15) {
-maxNB = 15;
-}var nbFormat =  new jalview.util.Format ("%-" + maxNB + "s");
-for (i = 0; (i < s.length) && (s[i] != null); i++) {
-out.append (nbFormat.form (nameBlock[i]) + idBlock[i]);
-}
-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");
-Clazz.defineMethod (c$, "print", 
-function () {
-return this.print (this.getSeqsAsArray ());
-});
-});
+Clazz.declarePackage ("jalview.io");
+Clazz.load (["jalview.io.AlignFile"], "jalview.io.MSFfile", ["jalview.datamodel.Sequence", "jalview.util.Comparison", "$.Format", "java.lang.StringBuffer", "java.util.Hashtable", "$.StringTokenizer", "$.Vector"], function () {
+c$ = Clazz.declareType (jalview.io, "MSFfile", jalview.io.AlignFile);
+Clazz.makeConstructor (c$, 
+function () {
+Clazz.superConstructor (this, jalview.io.MSFfile, []);
+});
+Clazz.overrideMethod (c$, "parse", 
+function () {
+var i = 0;
+var seqFlag = false;
+var key =  String.instantialize ();
+var headers =  new java.util.Vector ();
+var seqhash =  new java.util.Hashtable ();
+var line;
+try {
+while ((line = this.nextLine ()) != null) {
+var str =  new java.util.StringTokenizer (line);
+while (str.hasMoreTokens ()) {
+var inStr = str.nextToken ();
+if (inStr.indexOf ("Name:") != -1) {
+key = str.nextToken ();
+headers.addElement (key);
+}if (inStr.indexOf ("//") != -1) {
+seqFlag = true;
+}if ((inStr.indexOf ("//") == -1) && (seqFlag == true)) {
+key = inStr;
+var tempseq;
+if (seqhash.containsKey (key)) {
+tempseq = seqhash.get (key);
+} else {
+tempseq =  new StringBuffer ();
+seqhash.put (key, tempseq);
+}while (str.hasMoreTokens ()) {
+tempseq.append (str.nextToken ());
+}
+}}
+}
+} catch (e) {
+if (Clazz.exceptionOf (e, java.io.IOException)) {
+System.err.println ("Exception parsing MSFFile " + e);
+e.printStackTrace ();
+} else {
+throw e;
+}
+}
+this.noSeqs = headers.size ();
+for (i = 0; i < headers.size (); i++) {
+if (seqhash.get (headers.elementAt (i)) != null) {
+var head = headers.elementAt (i).toString ();
+var seq = seqhash.get (head).toString ();
+if (this.maxLength < head.length) {
+this.maxLength = head.length;
+}seq = seq.$replace ('~', '-');
+var newSeq = this.parseId (head);
+newSeq.setSequence (seq);
+this.seqs.addElement (newSeq);
+} else {
+System.err.println ("MSFFile Parser: Can't find sequence for " + headers.elementAt (i));
+}}
+});
+Clazz.defineMethod (c$, "checkSum", 
+function (seq) {
+var check = 0;
+var sequence = seq.toUpperCase ();
+for (var i = 0; i < sequence.length; i++) {
+try {
+var value = sequence.charCodeAt (i);
+if (value != -1) {
+check += (i % 57 + 1) * value;
+}} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+System.err.println ("Exception during MSF Checksum calculation");
+e.printStackTrace ();
+} else {
+throw e;
+}
+}
+}
+return check % 10000;
+}, "~S");
+Clazz.defineMethod (c$, "print", 
+function (seqs) {
+var is_NA = jalview.util.Comparison.isNucleotide (seqs);
+var s =  new Array (seqs.length);
+var out =  new StringBuffer ("!!" + (is_NA ? "NA" : "AA") + "_MULTIPLE_ALIGNMENT 1.0");
+out.append (this.newline);
+out.append (this.newline);
+var max = 0;
+var maxid = 0;
+var i = 0;
+while ((i < seqs.length) && (seqs[i] != null)) {
+s[i] =  new jalview.datamodel.Sequence (seqs[i].getName (), seqs[i].getSequenceAsString ().$replace ('-', '.'), seqs[i].getStart (), seqs[i].getEnd ());
+var sb =  new StringBuffer ();
+sb.append (s[i].getSequence ());
+for (var ii = 0; ii < sb.length (); ii++) {
+if (sb.charAt (ii) == '.') {
+sb.setCharAt (ii, '~');
+} else {
+break;
+}}
+for (var ii = sb.length () - 1; ii > 0; ii--) {
+if (sb.charAt (ii) == '.') {
+sb.setCharAt (ii, '~');
+} else {
+break;
+}}
+s[i].setSequence (sb.toString ());
+if (s[i].getSequence ().length > max) {
+max = s[i].getSequence ().length;
+}i++;
+}
+var maxLenpad =  new jalview.util.Format ("%" + ( String.instantialize ("" + max)).length + "d");
+var maxChkpad =  new jalview.util.Format ("%" + ( String.instantialize ("1" + max)).length + "d");
+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++;
+}
+var maxNB = 0;
+out.append ("   MSF: " + s[0].getSequence ().length + "   Type: " + (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum % 10000) + "   ..");
+out.append (this.newline);
+out.append (this.newline);
+out.append (this.newline);
+var nameBlock =  new Array (s.length);
+var idBlock =  new Array (s.length);
+i = 0;
+while ((i < s.length) && (s[i] != null)) {
+nameBlock[i] =  String.instantialize ("  Name: " + this.printId (s[i]) + " ");
+idBlock[i] =  String.instantialize ("Len: " + maxLenpad.formLong (s[i].getSequence ().length) + "  Check: " + maxChkpad.formLong (checksums[i]) + "  Weight: 1.00" + this.newline);
+if (s[i].getName ().length > maxid) {
+maxid = s[i].getName ().length;
+}if (nameBlock[i].length > maxNB) {
+maxNB = nameBlock[i].length;
+}i++;
+}
+if (maxid < 10) {
+maxid = 10;
+}if (maxNB < 15) {
+maxNB = 15;
+}var nbFormat =  new jalview.util.Format ("%-" + maxNB + "s");
+for (i = 0; (i < s.length) && (s[i] != null); i++) {
+out.append (nbFormat.form (nameBlock[i]) + idBlock[i]);
+}
+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");
+Clazz.defineMethod (c$, "print", 
+function () {
+return this.print (this.getSeqsAsArray ());
+});
+});