X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fio%2FAlignmentProperties.js;h=6030bea84a4bf206cd8128896a6ee05c61dbfc42;hp=009258905497aaa3d2bb3d7b37eea3f993beb0f2;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/io/AlignmentProperties.js b/bin/jalview/io/AlignmentProperties.js
index 0092589..6030bea 100644
--- a/bin/jalview/io/AlignmentProperties.js
+++ b/bin/jalview/io/AlignmentProperties.js
@@ -1,78 +1,78 @@
-Clazz.declarePackage ("jalview.io");
-Clazz.load (null, "jalview.io.AlignmentProperties", ["java.lang.StringBuffer"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.alignment = null;
-Clazz.instantialize (this, arguments);
-}, jalview.io, "AlignmentProperties");
-Clazz.makeConstructor (c$, 
-function (alignment) {
-this.alignment = alignment;
-}, "jalview.datamodel.AlignmentI");
-Clazz.defineMethod (c$, "writeProperties", 
-function (sb, html) {
-var nl = html ? "<br>" : System.getProperty ("line.separator");
-var avg = 0;
-var min = 2147483647;
-var max = 0;
-for (var i = 0; i < this.alignment.getHeight (); i++) {
-var size = 1 + this.alignment.getSequenceAt (i).getEnd () - this.alignment.getSequenceAt (i).getStart ();
-avg += size;
-if (size > max) {
-max = size;
-}if (size < min) {
-min = size;
-}}
-avg = avg / this.alignment.getHeight ();
-sb.append (nl);
-sb.append ("Sequences: " + this.alignment.getHeight ());
-sb.append (nl);
-sb.append ("Minimum Sequence Length: " + min);
-sb.append (nl);
-sb.append ("Maximum Sequence Length: " + max);
-sb.append (nl);
-sb.append ("Average Length: " + Clazz.floatToInt (avg));
-if ((this.alignment).alignmentProperties != null) {
-sb.append (nl);
-sb.append (nl);
-if (html) {
-sb.append ("<table border=\"1\">");
-}var props = (this.alignment).alignmentProperties;
-var en = props.keys ();
-while (en.hasMoreElements ()) {
-var key = en.nextElement ().toString ();
-var vals = props.get (key).toString ();
-if (html) {
-var val =  new StringBuffer ();
-var pos = 0;
-var npos;
-do {
-npos = vals.indexOf ("\n", pos);
-if (npos == -1) {
-val.append (vals.substring (pos));
-} else {
-val.append (vals.substring (pos, npos));
-val.append ("<br>");
-}pos = npos + 1;
-} while (npos != -1);
-sb.append ("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
-} else {
-sb.append (nl + key + "\t" + vals);
-}}
-if (html) {
-sb.append ("</table>");
-}}}, "StringBuffer,~B");
-Clazz.defineMethod (c$, "formatAsString", 
-function () {
-return this.formatReport (false);
-});
-Clazz.defineMethod (c$, "formatReport", 
-function (html) {
-var sb =  new StringBuffer ();
-this.writeProperties (sb, html);
-return sb;
-}, "~B");
-Clazz.defineMethod (c$, "formatAsHtml", 
-function () {
-return this.formatReport (true);
-});
-});
+Clazz.declarePackage ("jalview.io");
+Clazz.load (null, "jalview.io.AlignmentProperties", ["java.lang.StringBuffer"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.alignment = null;
+Clazz.instantialize (this, arguments);
+}, jalview.io, "AlignmentProperties");
+Clazz.makeConstructor (c$, 
+function (alignment) {
+this.alignment = alignment;
+}, "jalview.datamodel.AlignmentI");
+Clazz.defineMethod (c$, "writeProperties", 
+function (sb, html) {
+var nl = html ? "<br>" : System.getProperty ("line.separator");
+var avg = 0;
+var min = 2147483647;
+var max = 0;
+for (var i = 0; i < this.alignment.getHeight (); i++) {
+var size = 1 + this.alignment.getSequenceAt (i).getEnd () - this.alignment.getSequenceAt (i).getStart ();
+avg += size;
+if (size > max) {
+max = size;
+}if (size < min) {
+min = size;
+}}
+avg = avg / this.alignment.getHeight ();
+sb.append (nl);
+sb.append ("Sequences: " + this.alignment.getHeight ());
+sb.append (nl);
+sb.append ("Minimum Sequence Length: " + min);
+sb.append (nl);
+sb.append ("Maximum Sequence Length: " + max);
+sb.append (nl);
+sb.append ("Average Length: " + Clazz.floatToInt (avg));
+if ((this.alignment).alignmentProperties != null) {
+sb.append (nl);
+sb.append (nl);
+if (html) {
+sb.append ("<table border=\"1\">");
+}var props = (this.alignment).alignmentProperties;
+var en = props.keys ();
+while (en.hasMoreElements ()) {
+var key = en.nextElement ().toString ();
+var vals = props.get (key).toString ();
+if (html) {
+var val =  new StringBuffer ();
+var pos = 0;
+var npos;
+do {
+npos = vals.indexOf ("\n", pos);
+if (npos == -1) {
+val.append (vals.substring (pos));
+} else {
+val.append (vals.substring (pos, npos));
+val.append ("<br>");
+}pos = npos + 1;
+} while (npos != -1);
+sb.append ("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
+} else {
+sb.append (nl + key + "\t" + vals);
+}}
+if (html) {
+sb.append ("</table>");
+}}}, "StringBuffer,~B");
+Clazz.defineMethod (c$, "formatAsString", 
+function () {
+return this.formatReport (false);
+});
+Clazz.defineMethod (c$, "formatReport", 
+function (html) {
+var sb =  new StringBuffer ();
+this.writeProperties (sb, html);
+return sb;
+}, "~B");
+Clazz.defineMethod (c$, "formatAsHtml", 
+function () {
+return this.formatReport (true);
+});
+});