X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.js;h=e91c56dd37fe639b70a75b442dc6ac27c174a4f2;hp=ddb19480177b97ab5e6fa15d8aab1dc72415947e;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/appletgui/PairwiseAlignPanel.js b/bin/jalview/appletgui/PairwiseAlignPanel.js
index ddb1948..e91c56d 100644
--- a/bin/jalview/appletgui/PairwiseAlignPanel.js
+++ b/bin/jalview/appletgui/PairwiseAlignPanel.js
@@ -1,100 +1,100 @@
-Clazz.declarePackage ("jalview.appletgui");
-Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "awt2swing.Button", "$.ScrollPane", "$.TextArea", "java.awt.BorderLayout", "java.util.Vector"], "jalview.appletgui.PairwiseAlignPanel", ["jalview.analysis.AlignSeq", "jalview.appletgui.AlignFrame", "jalview.datamodel.Alignment", "jalview.util.Format", "$.MessageManager", "java.awt.Font"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.sequences = null;
-this.ap = null;
-this.scrollPane = null;
-this.textarea = null;
-this.viewInEditorButton = null;
-this.jPanel1 = null;
-this.borderLayout1 = null;
-Clazz.instantialize (this, arguments);
-}, jalview.appletgui, "PairwiseAlignPanel", awt2swing.Panel, java.awt.event.ActionListener);
-Clazz.prepareFields (c$, function () {
-this.sequences =  new java.util.Vector ();
-this.scrollPane =  new awt2swing.ScrollPane ();
-this.textarea =  new awt2swing.TextArea ();
-this.viewInEditorButton =  new awt2swing.Button ();
-this.jPanel1 =  new awt2swing.Panel ();
-this.borderLayout1 =  new java.awt.BorderLayout ();
-});
-Clazz.makeConstructor (c$, 
-function (ap) {
-Clazz.superConstructor (this, jalview.appletgui.PairwiseAlignPanel, []);
-try {
-this.jbInit ();
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-e.printStackTrace ();
-} else {
-throw e;
-}
-}
-this.ap = ap;
-this.sequences =  new java.util.Vector ();
-var seqs;
-var seqStrings = ap.av.getViewAsString (true);
-if (ap.av.getSelectionGroup () == null) {
-seqs = ap.av.getAlignment ().getSequencesArray ();
-} else {
-seqs = ap.av.getSelectionGroup ().getSequencesInOrder (ap.av.getAlignment ());
-}var scores =  Clazz.newFloatArray (seqs.length, seqs.length, 0);
-var totscore = 0;
-var count = ap.av.getSelectionGroup ().getSize ();
-var type = (ap.av.getAlignment ().isNucleotide ()) ? "dna" : "pep";
-var seq;
-for (var i = 1; i < count; i++) {
-for (var j = 0; j < i; j++) {
-var as =  new jalview.analysis.AlignSeq (seqs[i], seqStrings[i], seqs[j], seqStrings[j], type);
-if (as.s1str.length == 0 || as.s2str.length == 0) {
-continue;
-}as.calcScoreMatrix ();
-as.traceAlignment ();
-as.printAlignment (System.out);
-scores[i][j] = as.getMaxScore () / as.getASeq1 ().length;
-totscore = totscore + scores[i][j];
-this.textarea.append (as.getOutput ());
-this.sequences.add (as.getAlignedSeq1 ());
-this.sequences.add (as.getAlignedSeq1 ());
-}
-}
-if (count > 2) {
-System.out.println ("Pairwise alignment scaled similarity score matrix\n");
-for (var i = 0; i < count; i++) {
-jalview.util.Format.print (System.out, "%s \n", ("" + i) + " " + seqs[i].getName ());
-}
-System.out.println ("\n");
-for (var i = 0; i < count; i++) {
-for (var j = 0; j < i; j++) {
-jalview.util.Format.printDouble (System.out, "%7.3f", scores[i][j] / totscore);
-}
-}
-System.out.println ("\n");
-}}, "jalview.appletgui.AlignmentPanel");
-Clazz.overrideMethod (c$, "actionPerformed", 
-function (evt) {
-if (evt.getSource () === this.viewInEditorButton) {
-this.viewInEditorButton_actionPerformed ();
-}}, "java.awt.event.ActionEvent");
-Clazz.defineMethod (c$, "viewInEditorButton_actionPerformed", 
-function () {
-var seq =  new Array (this.sequences.size ());
-for (var i = 0; i < this.sequences.size (); i++) {
-seq[i] = this.sequences.elementAt (i);
-}
- new jalview.appletgui.AlignFrame ( new jalview.datamodel.Alignment (seq), this.ap.av.applet, "Pairwise Aligned Sequences", false);
-});
-Clazz.defineMethod (c$, "jbInit", 
-($fz = function () {
-this.setLayout (this.borderLayout1);
-this.textarea.setFont ( new java.awt.Font ("Monospaced", 0, 12));
-this.textarea.setText ("");
-this.viewInEditorButton.setFont ( new java.awt.Font ("Verdana", 0, 12));
-this.viewInEditorButton.setLabel (jalview.util.MessageManager.getString ("label.view_alignment_editor"));
-this.viewInEditorButton.addActionListener (this);
-this.add (this.scrollPane, "Center");
-this.scrollPane.add (this.textarea);
-this.add (this.jPanel1, "South");
-this.jPanel1.add (this.viewInEditorButton, null);
-}, $fz.isPrivate = true, $fz));
-});
+Clazz.declarePackage ("jalview.appletgui");
+Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "awt2swing.Button", "$.ScrollPane", "$.TextArea", "java.awt.BorderLayout", "java.util.Vector"], "jalview.appletgui.PairwiseAlignPanel", ["jalview.analysis.AlignSeq", "jalview.appletgui.AlignFrame", "jalview.datamodel.Alignment", "jalview.util.Format", "$.MessageManager", "java.awt.Font"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.sequences = null;
+this.ap = null;
+this.scrollPane = null;
+this.textarea = null;
+this.viewInEditorButton = null;
+this.jPanel1 = null;
+this.borderLayout1 = null;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui, "PairwiseAlignPanel", awt2swing.Panel, java.awt.event.ActionListener);
+Clazz.prepareFields (c$, function () {
+this.sequences =  new java.util.Vector ();
+this.scrollPane =  new awt2swing.ScrollPane ();
+this.textarea =  new awt2swing.TextArea ();
+this.viewInEditorButton =  new awt2swing.Button ();
+this.jPanel1 =  new awt2swing.Panel ();
+this.borderLayout1 =  new java.awt.BorderLayout ();
+});
+Clazz.makeConstructor (c$, 
+function (ap) {
+Clazz.superConstructor (this, jalview.appletgui.PairwiseAlignPanel, []);
+try {
+this.jbInit ();
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+} else {
+throw e;
+}
+}
+this.ap = ap;
+this.sequences =  new java.util.Vector ();
+var seqs;
+var seqStrings = ap.av.getViewAsString (true);
+if (ap.av.getSelectionGroup () == null) {
+seqs = ap.av.getAlignment ().getSequencesArray ();
+} else {
+seqs = ap.av.getSelectionGroup ().getSequencesInOrder (ap.av.getAlignment ());
+}var scores =  Clazz.newFloatArray (seqs.length, seqs.length, 0);
+var totscore = 0;
+var count = ap.av.getSelectionGroup ().getSize ();
+var type = (ap.av.getAlignment ().isNucleotide ()) ? "dna" : "pep";
+var seq;
+for (var i = 1; i < count; i++) {
+for (var j = 0; j < i; j++) {
+var as =  new jalview.analysis.AlignSeq (seqs[i], seqStrings[i], seqs[j], seqStrings[j], type);
+if (as.s1str.length == 0 || as.s2str.length == 0) {
+continue;
+}as.calcScoreMatrix ();
+as.traceAlignment ();
+as.printAlignment (System.out);
+scores[i][j] = as.getMaxScore () / as.getASeq1 ().length;
+totscore = totscore + scores[i][j];
+this.textarea.append (as.getOutput ());
+this.sequences.add (as.getAlignedSeq1 ());
+this.sequences.add (as.getAlignedSeq1 ());
+}
+}
+if (count > 2) {
+System.out.println ("Pairwise alignment scaled similarity score matrix\n");
+for (var i = 0; i < count; i++) {
+jalview.util.Format.print (System.out, "%s \n", ("" + i) + " " + seqs[i].getName ());
+}
+System.out.println ("\n");
+for (var i = 0; i < count; i++) {
+for (var j = 0; j < i; j++) {
+jalview.util.Format.printDouble (System.out, "%7.3f", scores[i][j] / totscore);
+}
+}
+System.out.println ("\n");
+}}, "jalview.appletgui.AlignmentPanel");
+Clazz.overrideMethod (c$, "actionPerformed", 
+function (evt) {
+if (evt.getSource () === this.viewInEditorButton) {
+this.viewInEditorButton_actionPerformed ();
+}}, "java.awt.event.ActionEvent");
+Clazz.defineMethod (c$, "viewInEditorButton_actionPerformed", 
+function () {
+var seq =  new Array (this.sequences.size ());
+for (var i = 0; i < this.sequences.size (); i++) {
+seq[i] = this.sequences.elementAt (i);
+}
+ new jalview.appletgui.AlignFrame ( new jalview.datamodel.Alignment (seq), this.ap.av.applet, "Pairwise Aligned Sequences", false);
+});
+Clazz.defineMethod (c$, "jbInit", 
+($fz = function () {
+this.setLayout (this.borderLayout1);
+this.textarea.setFont ( new java.awt.Font ("Monospaced", 0, 12));
+this.textarea.setText ("");
+this.viewInEditorButton.setFont ( new java.awt.Font ("Verdana", 0, 12));
+this.viewInEditorButton.setLabel (jalview.util.MessageManager.getString ("label.view_alignment_editor"));
+this.viewInEditorButton.addActionListener (this);
+this.add (this.scrollPane, "Center");
+this.scrollPane.add (this.textarea);
+this.add (this.jPanel1, "South");
+this.jPanel1.add (this.viewInEditorButton, null);
+}, $fz.isPrivate = true, $fz));
+});