X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fappletgui%2FRedundancyPanel.js;h=647ac1ba201db3fba4e8a8e5b95a404704a6250a;hp=f6b850dc65679546c3ab508fb31bcb16a2fe2fe8;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/appletgui/RedundancyPanel.js b/bin/jalview/appletgui/RedundancyPanel.js
index f6b850d..647ac1b 100644
--- a/bin/jalview/appletgui/RedundancyPanel.js
+++ b/bin/jalview/appletgui/RedundancyPanel.js
@@ -1,165 +1,165 @@
-Clazz.declarePackage ("jalview.appletgui");
-Clazz.load (["jalview.appletgui.SliderPanel", "java.awt.event.WindowListener", "java.util.Stack"], "jalview.appletgui.RedundancyPanel", ["awt2swing.Frame", "jalview.analysis.AlignSeq", "jalview.appletgui.PaintRefresher", "jalview.bin.JalviewLite", "jalview.commands.EditCommand", "jalview.util.MessageManager", "java.awt.event.AdjustmentListener", "java.lang.Thread", "java.util.ArrayList", "$.Vector"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.historyList = null;
-this.redundancy = null;
-this.originalSequences = null;
-this.frame = null;
-this.redundantSeqs = null;
-Clazz.instantialize (this, arguments);
-}, jalview.appletgui, "RedundancyPanel", jalview.appletgui.SliderPanel, [Runnable, java.awt.event.WindowListener]);
-Clazz.prepareFields (c$, function () {
-this.historyList =  new java.util.Stack ();
-});
-Clazz.makeConstructor (c$, 
-function (ap) {
-Clazz.superConstructor (this, jalview.appletgui.RedundancyPanel, [ap, 0, false, null]);
-this.redundantSeqs =  new java.util.Vector ();
-this.ap = ap;
-this.undoButton.setVisible (true);
-this.applyButton.setVisible (true);
-this.allGroupsCheck.setVisible (false);
-this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold"));
-this.valueField.setText ("100");
-this.slider.setVisibleAmount (1);
-this.slider.setMinimum (0);
-this.slider.setMaximum (100 + this.slider.getVisibleAmount ());
-this.slider.setValue (100);
-this.slider.addAdjustmentListener (((Clazz.isClassDefined ("jalview.appletgui.RedundancyPanel$1") ? 0 : jalview.appletgui.RedundancyPanel.$RedundancyPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.RedundancyPanel$1, this, null)));
-this.frame =  new awt2swing.Frame ();
-this.frame.add (this);
-jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.redundancy_threshold_selection"), 400, 100);
-this.frame.addWindowListener (this);
-var worker =  new Thread (this);
-worker.start ();
-}, "jalview.appletgui.AlignmentPanel");
-Clazz.overrideMethod (c$, "run", 
-function () {
-this.label.setText (jalview.util.MessageManager.getString ("label.calculating"));
-this.slider.setVisible (false);
-this.applyButton.setEnabled (false);
-this.valueField.setVisible (false);
-this.validate ();
-var omitHidden = null;
-var sg = this.ap.av.getSelectionGroup ();
-var height;
-var start;
-var end;
-if ((sg != null) && (sg.getSize () >= 1)) {
-this.originalSequences = sg.getSequencesInOrder (this.ap.av.getAlignment ());
-start = sg.getStartRes ();
-end = sg.getEndRes ();
-} else {
-this.originalSequences = this.ap.av.getAlignment ().getSequencesArray ();
-start = 0;
-end = this.ap.av.getAlignment ().getWidth ();
-}height = this.originalSequences.length;
-this.redundancy = jalview.analysis.AlignSeq.computeRedundancyMatrix (this.originalSequences, omitHidden, start, end, false);
-this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold"));
-this.slider.setVisible (true);
-this.applyButton.setEnabled (true);
-this.valueField.setVisible (true);
-this.validate ();
-this.sliderValueChanged ();
-});
-Clazz.defineMethod (c$, "sliderValueChanged", 
-function () {
-if (this.redundancy == null) {
-return;
-}var value = this.slider.getValue ();
-var redundantSequences =  new java.util.ArrayList ();
-for (var i = 0; i < this.redundancy.length; i++) {
-if (value <= this.redundancy[i]) {
-redundantSequences.add (this.originalSequences[i]);
-}}
-this.ap.idPanel.idCanvas.setHighlighted (redundantSequences);
-jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true);
-});
-Clazz.overrideMethod (c$, "applyButton_actionPerformed", 
-function () {
-var del =  new java.util.Vector ();
-this.undoButton.setEnabled (true);
-var value = this.slider.getValue ();
-var sg = this.ap.av.getSelectionGroup ();
-for (var i = 0; i < this.redundancy.length; i++) {
-if (value <= this.redundancy[i]) {
-del.addElement (this.originalSequences[i]);
-}}
-if (del.size () > 0) {
-var deleted =  new Array (del.size ());
-var width = 0;
-for (var i = 0; i < del.size (); i++) {
-deleted[i] = del.elementAt (i);
-if (deleted[i].getLength () > width) {
-width = deleted[i].getLength ();
-}}
-var cut =  new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("action.remove_redundancy"), jalview.commands.EditCommand.Action.CUT, deleted, 0, width, this.ap.av.getAlignment ());
-var alignment = this.ap.av.getAlignment ();
-for (var i = 0; i < del.size (); i++) {
-alignment.deleteSequence (deleted[i]);
-if (sg != null) {
-sg.deleteSequence (deleted[i], false);
-}}
-this.historyList.push (cut);
-this.ap.alignFrame.addHistoryItem (cut);
-jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true);
-this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());
-}});
-Clazz.overrideMethod (c$, "undoButton_actionPerformed", 
-function () {
-var command = this.historyList.pop ();
-command.undoCommand (null);
-if (this.ap.av.getHistoryList ().contains (command)) {
-this.ap.av.getHistoryList ().remove (command);
-this.ap.alignFrame.updateEditMenuBar ();
-this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());
-}this.ap.paintAlignment (true);
-if (this.historyList.size () == 0) {
-this.undoButton.setEnabled (false);
-}});
-Clazz.defineMethod (c$, "valueField_actionPerformed", 
-function (e) {
-try {
-var i = Integer.parseInt (this.valueField.getText ());
-this.slider.setValue (i);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-this.valueField.setText (this.slider.getValue () + "");
-} else {
-throw ex;
-}
-}
-}, "java.awt.event.ActionEvent");
-Clazz.overrideMethod (c$, "windowOpened", 
-function (evt) {
-}, "java.awt.event.WindowEvent");
-Clazz.overrideMethod (c$, "windowClosing", 
-function (evt) {
-this.ap.idPanel.idCanvas.setHighlighted (null);
-}, "java.awt.event.WindowEvent");
-Clazz.overrideMethod (c$, "windowClosed", 
-function (evt) {
-}, "java.awt.event.WindowEvent");
-Clazz.overrideMethod (c$, "windowActivated", 
-function (evt) {
-}, "java.awt.event.WindowEvent");
-Clazz.overrideMethod (c$, "windowDeactivated", 
-function (evt) {
-}, "java.awt.event.WindowEvent");
-Clazz.overrideMethod (c$, "windowIconified", 
-function (evt) {
-}, "java.awt.event.WindowEvent");
-Clazz.overrideMethod (c$, "windowDeiconified", 
-function (evt) {
-}, "java.awt.event.WindowEvent");
-c$.$RedundancyPanel$1$ = function () {
-Clazz.pu$h ();
-c$ = Clazz.declareAnonymous (jalview.appletgui, "RedundancyPanel$1", null, java.awt.event.AdjustmentListener);
-Clazz.overrideMethod (c$, "adjustmentValueChanged", 
-function (evt) {
-this.b$["jalview.appletgui.RedundancyPanel"].valueField.setText (this.b$["jalview.appletgui.RedundancyPanel"].slider.getValue () + "");
-this.b$["jalview.appletgui.RedundancyPanel"].sliderValueChanged ();
-}, "java.awt.event.AdjustmentEvent");
-c$ = Clazz.p0p ();
-};
-});
+Clazz.declarePackage ("jalview.appletgui");
+Clazz.load (["jalview.appletgui.SliderPanel", "java.awt.event.WindowListener", "java.util.Stack"], "jalview.appletgui.RedundancyPanel", ["awt2swing.Frame", "jalview.analysis.AlignSeq", "jalview.appletgui.PaintRefresher", "jalview.bin.JalviewLite", "jalview.commands.EditCommand", "jalview.util.MessageManager", "java.awt.event.AdjustmentListener", "java.lang.Thread", "java.util.ArrayList", "$.Vector"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.historyList = null;
+this.redundancy = null;
+this.originalSequences = null;
+this.frame = null;
+this.redundantSeqs = null;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui, "RedundancyPanel", jalview.appletgui.SliderPanel, [Runnable, java.awt.event.WindowListener]);
+Clazz.prepareFields (c$, function () {
+this.historyList =  new java.util.Stack ();
+});
+Clazz.makeConstructor (c$, 
+function (ap) {
+Clazz.superConstructor (this, jalview.appletgui.RedundancyPanel, [ap, 0, false, null]);
+this.redundantSeqs =  new java.util.Vector ();
+this.ap = ap;
+this.undoButton.setVisible (true);
+this.applyButton.setVisible (true);
+this.allGroupsCheck.setVisible (false);
+this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold"));
+this.valueField.setText ("100");
+this.slider.setVisibleAmount (1);
+this.slider.setMinimum (0);
+this.slider.setMaximum (100 + this.slider.getVisibleAmount ());
+this.slider.setValue (100);
+this.slider.addAdjustmentListener (((Clazz.isClassDefined ("jalview.appletgui.RedundancyPanel$1") ? 0 : jalview.appletgui.RedundancyPanel.$RedundancyPanel$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.RedundancyPanel$1, this, null)));
+this.frame =  new awt2swing.Frame ();
+this.frame.add (this);
+jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.redundancy_threshold_selection"), 400, 100);
+this.frame.addWindowListener (this);
+var worker =  new Thread (this);
+worker.start ();
+}, "jalview.appletgui.AlignmentPanel");
+Clazz.overrideMethod (c$, "run", 
+function () {
+this.label.setText (jalview.util.MessageManager.getString ("label.calculating"));
+this.slider.setVisible (false);
+this.applyButton.setEnabled (false);
+this.valueField.setVisible (false);
+this.validate ();
+var omitHidden = null;
+var sg = this.ap.av.getSelectionGroup ();
+var height;
+var start;
+var end;
+if ((sg != null) && (sg.getSize () >= 1)) {
+this.originalSequences = sg.getSequencesInOrder (this.ap.av.getAlignment ());
+start = sg.getStartRes ();
+end = sg.getEndRes ();
+} else {
+this.originalSequences = this.ap.av.getAlignment ().getSequencesArray ();
+start = 0;
+end = this.ap.av.getAlignment ().getWidth ();
+}height = this.originalSequences.length;
+this.redundancy = jalview.analysis.AlignSeq.computeRedundancyMatrix (this.originalSequences, omitHidden, start, end, false);
+this.label.setText (jalview.util.MessageManager.getString ("label.enter_redundancy_threshold"));
+this.slider.setVisible (true);
+this.applyButton.setEnabled (true);
+this.valueField.setVisible (true);
+this.validate ();
+this.sliderValueChanged ();
+});
+Clazz.defineMethod (c$, "sliderValueChanged", 
+function () {
+if (this.redundancy == null) {
+return;
+}var value = this.slider.getValue ();
+var redundantSequences =  new java.util.ArrayList ();
+for (var i = 0; i < this.redundancy.length; i++) {
+if (value <= this.redundancy[i]) {
+redundantSequences.add (this.originalSequences[i]);
+}}
+this.ap.idPanel.idCanvas.setHighlighted (redundantSequences);
+jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true);
+});
+Clazz.overrideMethod (c$, "applyButton_actionPerformed", 
+function () {
+var del =  new java.util.Vector ();
+this.undoButton.setEnabled (true);
+var value = this.slider.getValue ();
+var sg = this.ap.av.getSelectionGroup ();
+for (var i = 0; i < this.redundancy.length; i++) {
+if (value <= this.redundancy[i]) {
+del.addElement (this.originalSequences[i]);
+}}
+if (del.size () > 0) {
+var deleted =  new Array (del.size ());
+var width = 0;
+for (var i = 0; i < del.size (); i++) {
+deleted[i] = del.elementAt (i);
+if (deleted[i].getLength () > width) {
+width = deleted[i].getLength ();
+}}
+var cut =  new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("action.remove_redundancy"), jalview.commands.EditCommand.Action.CUT, deleted, 0, width, this.ap.av.getAlignment ());
+var alignment = this.ap.av.getAlignment ();
+for (var i = 0; i < del.size (); i++) {
+alignment.deleteSequence (deleted[i]);
+if (sg != null) {
+sg.deleteSequence (deleted[i], false);
+}}
+this.historyList.push (cut);
+this.ap.alignFrame.addHistoryItem (cut);
+jalview.appletgui.PaintRefresher.Refresh (this, this.ap.av.getSequenceSetId (), true, true);
+this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());
+}});
+Clazz.overrideMethod (c$, "undoButton_actionPerformed", 
+function () {
+var command = this.historyList.pop ();
+command.undoCommand (null);
+if (this.ap.av.getHistoryList ().contains (command)) {
+this.ap.av.getHistoryList ().remove (command);
+this.ap.alignFrame.updateEditMenuBar ();
+this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());
+}this.ap.paintAlignment (true);
+if (this.historyList.size () == 0) {
+this.undoButton.setEnabled (false);
+}});
+Clazz.defineMethod (c$, "valueField_actionPerformed", 
+function (e) {
+try {
+var i = Integer.parseInt (this.valueField.getText ());
+this.slider.setValue (i);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+this.valueField.setText (this.slider.getValue () + "");
+} else {
+throw ex;
+}
+}
+}, "java.awt.event.ActionEvent");
+Clazz.overrideMethod (c$, "windowOpened", 
+function (evt) {
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowClosing", 
+function (evt) {
+this.ap.idPanel.idCanvas.setHighlighted (null);
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowClosed", 
+function (evt) {
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowActivated", 
+function (evt) {
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowDeactivated", 
+function (evt) {
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowIconified", 
+function (evt) {
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod (c$, "windowDeiconified", 
+function (evt) {
+}, "java.awt.event.WindowEvent");
+c$.$RedundancyPanel$1$ = function () {
+Clazz.pu$h ();
+c$ = Clazz.declareAnonymous (jalview.appletgui, "RedundancyPanel$1", null, java.awt.event.AdjustmentListener);
+Clazz.overrideMethod (c$, "adjustmentValueChanged", 
+function (evt) {
+this.b$["jalview.appletgui.RedundancyPanel"].valueField.setText (this.b$["jalview.appletgui.RedundancyPanel"].slider.getValue () + "");
+this.b$["jalview.appletgui.RedundancyPanel"].sliderValueChanged ();
+}, "java.awt.event.AdjustmentEvent");
+c$ = Clazz.p0p ();
+};
+});