X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fappletgui%2FIdPanel.js;h=b8695b5eb0a121729fc4b5755e7c338135d3c8d4;hp=48705bef436e33b7bc0cec6e2ed5d6652d6cf6aa;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6

diff --git a/site/j2s/jalview/appletgui/IdPanel.js b/site/j2s/jalview/appletgui/IdPanel.js
index 48705be..b8695b5 100644
--- a/site/j2s/jalview/appletgui/IdPanel.js
+++ b/site/j2s/jalview/appletgui/IdPanel.js
@@ -1,285 +1,285 @@
-Clazz.declarePackage ("jalview.appletgui");
-Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.lang.Thread", "java.util.Vector"], "jalview.appletgui.IdPanel", ["jalview.appletgui.APopupMenu", "$.IdCanvas", "$.PaintRefresher", "$.Tooltip", "jalview.datamodel.SequenceGroup", "jalview.util.UrlLink", "java.awt.BorderLayout", "java.lang.Float", "$.StringBuffer"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.idCanvas = null;
-this.av = null;
-this.alignPanel = null;
-this.scrollThread = null;
-this.lastid = -1;
-this.mouseDragging = false;
-this.links = null;
-this.tooltip = null;
-if (!Clazz.isClassDefined ("jalview.appletgui.IdPanel.ScrollThread")) {
-jalview.appletgui.IdPanel.$IdPanel$ScrollThread$ ();
-}
-Clazz.instantialize (this, arguments);
-}, jalview.appletgui, "IdPanel", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener]);
-Clazz.prepareFields (c$, function () {
-this.links =  new java.util.Vector ();
-});
-Clazz.makeConstructor (c$, 
-function (av, parent) {
-Clazz.superConstructor (this, jalview.appletgui.IdPanel, []);
-this.setName ("idPanel");
-this.av = av;
-this.alignPanel = parent;
-this.idCanvas =  new jalview.appletgui.IdCanvas (av);
-this.setLayout ( new java.awt.BorderLayout ());
-this.add (this.idCanvas, "Center");
-this.idCanvas.addMouseListener (this);
-this.idCanvas.addMouseMotionListener (this);
-if (av.applet != null) {
-av.applet.getLinkParams (this.links);
-}{
-var srsPos = this.links.indexOf ("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
-if (srsPos > -1) {
-this.links.setElementAt ("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$", srsPos);
-}}if (this.links.size () < 1) {
-this.links =  new java.util.Vector ();
-this.links.addElement ("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
-}}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel");
-Clazz.overrideMethod (c$, "mouseMoved", 
-function (e) {
-var seq = this.alignPanel.seqPanel.findSeq (e);
-var sequence = this.av.getAlignment ().getSequenceAt (seq);
-var tooltiptext =  new StringBuffer ();
-if (sequence != null) {
-if (sequence.getDescription () != null) {
-tooltiptext.append (sequence.getDescription ());
-tooltiptext.append ("\n");
-}var sf = sequence.getSequenceFeatures ();
-for (var sl = 0; sf != null && sl < sf.length; sl++) {
-if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) {
-var nl = false;
-if (sf[sl].getFeatureGroup () != null) {
-tooltiptext.append (sf[sl].getFeatureGroup ());
-nl = true;
-};if (sf[sl].getType () != null) {
-tooltiptext.append (" ");
-tooltiptext.append (sf[sl].getType ());
-nl = true;
-};if (sf[sl].getDescription () != null) {
-tooltiptext.append (" ");
-tooltiptext.append (sf[sl].getDescription ());
-nl = true;
-};if (!Float.isNaN (sf[sl].getScore ()) && sf[sl].getScore () != 0) {
-tooltiptext.append (" Score = ");
-tooltiptext.append (sf[sl].getScore ());
-nl = true;
-};if (sf[sl].getStatus () != null && sf[sl].getStatus ().length > 0) {
-tooltiptext.append (" (");
-tooltiptext.append (sf[sl].getStatus ());
-tooltiptext.append (")");
-nl = true;
-};if (nl) {
-tooltiptext.append ("\n");
-}}}
-}if (tooltiptext.length () == 0) {
-if (this.tooltip != null) {
-this.tooltip.setVisible (false);
-}this.tooltip = null;
-tooltiptext = null;
-return;
-}if (this.tooltip == null) {
-this.tooltip =  new jalview.appletgui.Tooltip (sequence.getDisplayId (true) + "\n" + tooltiptext.toString (), this.idCanvas);
-} else {
-this.tooltip.setTip (sequence.getDisplayId (true) + "\n" + tooltiptext.toString ());
-}tooltiptext = null;
-}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mouseDragged", 
-function (e) {
-this.mouseDragging = true;
-var seq = Math.max (0, this.alignPanel.seqPanel.findSeq (e));
-if (seq < this.lastid) {
-this.selectSeqs (this.lastid - 1, seq);
-} else if (seq > this.lastid) {
-this.selectSeqs (this.lastid + 1, seq);
-}this.lastid = seq;
-this.alignPanel.paintAlignment (false);
-}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mouseClicked", 
-function (e) {
-if (e.getClickCount () < 2) {
-return;
-}var seq = this.alignPanel.seqPanel.findSeq (e);
-var sq = this.av.getAlignment ().getSequenceAt (seq);
-if (sq == null) {
-return;
-}var id = sq.getName ();
-var target = null;
-var url = null;
-var i = 0;
-while (url == null && i < this.links.size ()) {
-url = this.links.elementAt (i++).toString ();
-var urlLink = null;
-try {
-urlLink =  new jalview.util.UrlLink (url);
-target = urlLink.getTarget ();
-} catch (foo) {
-if (Clazz.exceptionOf (foo, Exception)) {
-System.err.println ("Exception for URLLink '" + url + "'");
-foo.printStackTrace ();
-url = null;
-continue;
-} else {
-throw foo;
-}
-}
-;if (!urlLink.isValid ()) {
-System.err.println (urlLink.getInvalidMessage ());
-url = null;
-continue;
-}var urls = urlLink.makeUrls (id, true);
-if (urls == null || urls[0] == null || urls[0].length < 1) {
-url = null;
-continue;
-}url = urls[1];
-}
-try {
-this.alignPanel.alignFrame.showURL (url, target);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-ex.printStackTrace ();
-} else {
-throw ex;
-}
-}
-}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mouseEntered", 
-function (e) {
-if (this.scrollThread != null) {
-this.scrollThread.running = false;
-}}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mouseExited", 
-function (e) {
-if (this.av.getWrapAlignment ()) {
-return;
-}if (this.mouseDragging && e.getY () < 0 && this.av.getStartSeq () > 0) {
-this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.IdPanel.ScrollThread, this, null, true);
-}if (this.mouseDragging && e.getY () >= this.getSize ().height && this.av.getAlignment ().getHeight () > this.av.getEndSeq ()) {
-this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.IdPanel.ScrollThread, this, null, false);
-}}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mousePressed", 
-function (e) {
-if (e.getClickCount () > 1) {
-return;
-}var y = e.getY ();
-if (this.av.getWrapAlignment ()) {
-y -= 2 * this.av.getCharHeight ();
-}var seq = this.alignPanel.seqPanel.findSeq (e);
-if ((e.getModifiers () & 4) == 4) {
-var sq = this.av.getAlignment ().getSequenceAt (seq);
-var nlinks =  new java.util.Vector ();
-for (var l = 0, lSize = this.links.size (); l < lSize; l++) {
-nlinks.addElement (this.links.elementAt (l));
-}
-var sf = sq == null ? null : sq.getSequenceFeatures ();
-for (var sl = 0; sf != null && sl < sf.length; sl++) {
-if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) {
-if (sf[sl].links != null && sf[sl].links.size () > 0) {
-for (var l = 0, lSize = sf[sl].links.size (); l < lSize; l++) {
-nlinks.addElement (sf[sl].links.elementAt (l));
-}
-}}}
-var popup =  new jalview.appletgui.APopupMenu (this.alignPanel, sq, nlinks);
-this.add (popup);
-popup.show (this, e.getX (), e.getY ());
-return;
-}if ((this.av.getSelectionGroup () == null) || ((!e.isControlDown () && !e.isShiftDown ()) && this.av.getSelectionGroup () != null)) {
-this.av.setSelectionGroup ( new jalview.datamodel.SequenceGroup ());
-this.av.getSelectionGroup ().setStartRes (0);
-this.av.getSelectionGroup ().setEndRes (this.av.getAlignment ().getWidth () - 1);
-}if (e.isShiftDown () && this.lastid != -1) {
-this.selectSeqs (this.lastid, seq);
-} else {
-this.selectSeq (seq);
-}this.alignPanel.paintAlignment (false);
-}, "java.awt.event.MouseEvent");
-Clazz.defineMethod (c$, "selectSeq", 
-function (seq) {
-this.lastid = seq;
-var pickedSeq = this.av.getAlignment ().getSequenceAt (seq);
-this.av.getSelectionGroup ().addOrRemove (pickedSeq, true);
-}, "~N");
-Clazz.defineMethod (c$, "selectSeqs", 
-function (start, end) {
-this.lastid = start;
-if (end >= this.av.getAlignment ().getHeight ()) {
-end = this.av.getAlignment ().getHeight () - 1;
-}if (end < start) {
-var tmp = start;
-start = end;
-end = tmp;
-this.lastid = end;
-}if (this.av.getSelectionGroup () == null) {
-this.av.setSelectionGroup ( new jalview.datamodel.SequenceGroup ());
-}for (var i = start; i <= end; i++) {
-this.av.getSelectionGroup ().addSequence (this.av.getAlignment ().getSequenceAt (i), i == end);
-}
-}, "~N,~N");
-Clazz.overrideMethod (c$, "mouseReleased", 
-function (e) {
-if (this.scrollThread != null) {
-this.scrollThread.running = false;
-}if (this.av.getSelectionGroup () != null) {
-this.av.getSelectionGroup ().recalcConservation ();
-}this.mouseDragging = false;
-jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ());
-this.av.sendSelection ();
-}, "java.awt.event.MouseEvent");
-Clazz.defineMethod (c$, "highlightSearchResults", 
-function (list) {
-this.idCanvas.setHighlighted (list);
-if (list == null) {
-return;
-}var index = this.av.getAlignment ().findIndex (list.get (0));
-if (this.av.getStartSeq () > index || this.av.getEndSeq () < index) {
-this.alignPanel.setScrollValues (this.av.getStartRes (), index);
-}}, "java.util.List");
-c$.$IdPanel$ScrollThread$ = function () {
-Clazz.pu$h(self.c$);
-c$ = Clazz.decorateAsClass (function () {
-Clazz.prepareCallback (this, arguments);
-this.running = false;
-this.up = true;
-Clazz.instantialize (this, arguments);
-}, jalview.appletgui.IdPanel, "ScrollThread", Thread);
-Clazz.makeConstructor (c$, 
-function (a) {
-Clazz.superConstructor (this, jalview.appletgui.IdPanel.ScrollThread, []);
-this.up = a;
-this.start ();
-}, "~B");
-Clazz.defineMethod (c$, "stopScrolling", 
-function () {
-this.running = false;
-});
-Clazz.overrideMethod (c$, "run", 
-function () {
-this.running = true;
-while (this.running) {
-if (this.b$["jalview.appletgui.IdPanel"].alignPanel.scrollUp (this.up)) {
-var a = this.b$["jalview.appletgui.IdPanel"].av.getStartSeq ();
-if (!this.up) {
-a = this.b$["jalview.appletgui.IdPanel"].av.getEndSeq ();
-}if (a < this.b$["jalview.appletgui.IdPanel"].lastid) {
-this.b$["jalview.appletgui.IdPanel"].selectSeqs (this.b$["jalview.appletgui.IdPanel"].lastid - 1, a);
-} else if (a > this.b$["jalview.appletgui.IdPanel"].lastid && a < this.b$["jalview.appletgui.IdPanel"].av.getAlignment ().getHeight ()) {
-this.b$["jalview.appletgui.IdPanel"].selectSeqs (this.b$["jalview.appletgui.IdPanel"].lastid + 1, a);
-}this.b$["jalview.appletgui.IdPanel"].lastid = a;
-} else {
-this.running = false;
-}this.b$["jalview.appletgui.IdPanel"].alignPanel.paintAlignment (true);
-try {
-Thread.sleep (100);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-} else {
-throw ex;
-}
-}
-}
-});
-c$ = Clazz.p0p ();
-};
-});
+Clazz.declarePackage ("jalview.appletgui");
+Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.lang.Thread", "java.util.Vector"], "jalview.appletgui.IdPanel", ["jalview.appletgui.APopupMenu", "$.IdCanvas", "$.PaintRefresher", "$.Tooltip", "jalview.datamodel.SequenceGroup", "jalview.util.UrlLink", "java.awt.BorderLayout", "java.lang.Float", "$.StringBuffer"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.idCanvas = null;
+this.av = null;
+this.alignPanel = null;
+this.scrollThread = null;
+this.lastid = -1;
+this.mouseDragging = false;
+this.links = null;
+this.tooltip = null;
+if (!Clazz.isClassDefined ("jalview.appletgui.IdPanel.ScrollThread")) {
+jalview.appletgui.IdPanel.$IdPanel$ScrollThread$ ();
+}
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui, "IdPanel", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener]);
+Clazz.prepareFields (c$, function () {
+this.links =  new java.util.Vector ();
+});
+Clazz.makeConstructor (c$, 
+function (av, parent) {
+Clazz.superConstructor (this, jalview.appletgui.IdPanel, []);
+this.setName ("idPanel");
+this.av = av;
+this.alignPanel = parent;
+this.idCanvas =  new jalview.appletgui.IdCanvas (av);
+this.setLayout ( new java.awt.BorderLayout ());
+this.add (this.idCanvas, "Center");
+this.idCanvas.addMouseListener (this);
+this.idCanvas.addMouseMotionListener (this);
+if (av.applet != null) {
+av.applet.getLinkParams (this.links);
+}{
+var srsPos = this.links.indexOf ("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+if (srsPos > -1) {
+this.links.setElementAt ("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$", srsPos);
+}}if (this.links.size () < 1) {
+this.links =  new java.util.Vector ();
+this.links.addElement ("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
+}}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel");
+Clazz.overrideMethod (c$, "mouseMoved", 
+function (e) {
+var seq = this.alignPanel.seqPanel.findSeq (e);
+var sequence = this.av.getAlignment ().getSequenceAt (seq);
+var tooltiptext =  new StringBuffer ();
+if (sequence != null) {
+if (sequence.getDescription () != null) {
+tooltiptext.append (sequence.getDescription ());
+tooltiptext.append ("\n");
+}var sf = sequence.getSequenceFeatures ();
+for (var sl = 0; sf != null && sl < sf.length; sl++) {
+if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) {
+var nl = false;
+if (sf[sl].getFeatureGroup () != null) {
+tooltiptext.append (sf[sl].getFeatureGroup ());
+nl = true;
+};if (sf[sl].getType () != null) {
+tooltiptext.append (" ");
+tooltiptext.append (sf[sl].getType ());
+nl = true;
+};if (sf[sl].getDescription () != null) {
+tooltiptext.append (" ");
+tooltiptext.append (sf[sl].getDescription ());
+nl = true;
+};if (!Float.isNaN (sf[sl].getScore ()) && sf[sl].getScore () != 0) {
+tooltiptext.append (" Score = ");
+tooltiptext.append (sf[sl].getScore ());
+nl = true;
+};if (sf[sl].getStatus () != null && sf[sl].getStatus ().length > 0) {
+tooltiptext.append (" (");
+tooltiptext.append (sf[sl].getStatus ());
+tooltiptext.append (")");
+nl = true;
+};if (nl) {
+tooltiptext.append ("\n");
+}}}
+}if (tooltiptext.length () == 0) {
+if (this.tooltip != null) {
+this.tooltip.setVisible (false);
+}this.tooltip = null;
+tooltiptext = null;
+return;
+}if (this.tooltip == null) {
+this.tooltip =  new jalview.appletgui.Tooltip (sequence.getDisplayId (true) + "\n" + tooltiptext.toString (), this.idCanvas);
+} else {
+this.tooltip.setTip (sequence.getDisplayId (true) + "\n" + tooltiptext.toString ());
+}tooltiptext = null;
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseDragged", 
+function (e) {
+this.mouseDragging = true;
+var seq = Math.max (0, this.alignPanel.seqPanel.findSeq (e));
+if (seq < this.lastid) {
+this.selectSeqs (this.lastid - 1, seq);
+} else if (seq > this.lastid) {
+this.selectSeqs (this.lastid + 1, seq);
+}this.lastid = seq;
+this.alignPanel.paintAlignment (false);
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseClicked", 
+function (e) {
+if (e.getClickCount () < 2) {
+return;
+}var seq = this.alignPanel.seqPanel.findSeq (e);
+var sq = this.av.getAlignment ().getSequenceAt (seq);
+if (sq == null) {
+return;
+}var id = sq.getName ();
+var target = null;
+var url = null;
+var i = 0;
+while (url == null && i < this.links.size ()) {
+url = this.links.elementAt (i++).toString ();
+var urlLink = null;
+try {
+urlLink =  new jalview.util.UrlLink (url);
+target = urlLink.getTarget ();
+} catch (foo) {
+if (Clazz.exceptionOf (foo, Exception)) {
+System.err.println ("Exception for URLLink '" + url + "'");
+foo.printStackTrace ();
+url = null;
+continue;
+} else {
+throw foo;
+}
+}
+;if (!urlLink.isValid ()) {
+System.err.println (urlLink.getInvalidMessage ());
+url = null;
+continue;
+}var urls = urlLink.makeUrls (id, true);
+if (urls == null || urls[0] == null || urls[0].length < 1) {
+url = null;
+continue;
+}url = urls[1];
+}
+try {
+this.alignPanel.alignFrame.showURL (url, target);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+ex.printStackTrace ();
+} else {
+throw ex;
+}
+}
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseEntered", 
+function (e) {
+if (this.scrollThread != null) {
+this.scrollThread.running = false;
+}}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseExited", 
+function (e) {
+if (this.av.getWrapAlignment ()) {
+return;
+}if (this.mouseDragging && e.getY () < 0 && this.av.getStartSeq () > 0) {
+this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.IdPanel.ScrollThread, this, null, true);
+}if (this.mouseDragging && e.getY () >= this.getSize ().height && this.av.getAlignment ().getHeight () > this.av.getEndSeq ()) {
+this.scrollThread = Clazz.innerTypeInstance (jalview.appletgui.IdPanel.ScrollThread, this, null, false);
+}}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mousePressed", 
+function (e) {
+if (e.getClickCount () > 1) {
+return;
+}var y = e.getY ();
+if (this.av.getWrapAlignment ()) {
+y -= 2 * this.av.getCharHeight ();
+}var seq = this.alignPanel.seqPanel.findSeq (e);
+if ((e.getModifiers () & 4) == 4) {
+var sq = this.av.getAlignment ().getSequenceAt (seq);
+var nlinks =  new java.util.Vector ();
+for (var l = 0, lSize = this.links.size (); l < lSize; l++) {
+nlinks.addElement (this.links.elementAt (l));
+}
+var sf = sq == null ? null : sq.getSequenceFeatures ();
+for (var sl = 0; sf != null && sl < sf.length; sl++) {
+if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) {
+if (sf[sl].links != null && sf[sl].links.size () > 0) {
+for (var l = 0, lSize = sf[sl].links.size (); l < lSize; l++) {
+nlinks.addElement (sf[sl].links.elementAt (l));
+}
+}}}
+var popup =  new jalview.appletgui.APopupMenu (this.alignPanel, sq, nlinks);
+this.add (popup);
+popup.show (this, e.getX (), e.getY ());
+return;
+}if ((this.av.getSelectionGroup () == null) || ((!e.isControlDown () && !e.isShiftDown ()) && this.av.getSelectionGroup () != null)) {
+this.av.setSelectionGroup ( new jalview.datamodel.SequenceGroup ());
+this.av.getSelectionGroup ().setStartRes (0);
+this.av.getSelectionGroup ().setEndRes (this.av.getAlignment ().getWidth () - 1);
+}if (e.isShiftDown () && this.lastid != -1) {
+this.selectSeqs (this.lastid, seq);
+} else {
+this.selectSeq (seq);
+}this.alignPanel.paintAlignment (false);
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod (c$, "selectSeq", 
+function (seq) {
+this.lastid = seq;
+var pickedSeq = this.av.getAlignment ().getSequenceAt (seq);
+this.av.getSelectionGroup ().addOrRemove (pickedSeq, true);
+}, "~N");
+Clazz.defineMethod (c$, "selectSeqs", 
+function (start, end) {
+this.lastid = start;
+if (end >= this.av.getAlignment ().getHeight ()) {
+end = this.av.getAlignment ().getHeight () - 1;
+}if (end < start) {
+var tmp = start;
+start = end;
+end = tmp;
+this.lastid = end;
+}if (this.av.getSelectionGroup () == null) {
+this.av.setSelectionGroup ( new jalview.datamodel.SequenceGroup ());
+}for (var i = start; i <= end; i++) {
+this.av.getSelectionGroup ().addSequence (this.av.getAlignment ().getSequenceAt (i), i == end);
+}
+}, "~N,~N");
+Clazz.overrideMethod (c$, "mouseReleased", 
+function (e) {
+if (this.scrollThread != null) {
+this.scrollThread.running = false;
+}if (this.av.getSelectionGroup () != null) {
+this.av.getSelectionGroup ().recalcConservation ();
+}this.mouseDragging = false;
+jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ());
+this.av.sendSelection ();
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod (c$, "highlightSearchResults", 
+function (list) {
+this.idCanvas.setHighlighted (list);
+if (list == null) {
+return;
+}var index = this.av.getAlignment ().findIndex (list.get (0));
+if (this.av.getStartSeq () > index || this.av.getEndSeq () < index) {
+this.alignPanel.setScrollValues (this.av.getStartRes (), index);
+}}, "java.util.List");
+c$.$IdPanel$ScrollThread$ = function () {
+Clazz.pu$h(self.c$);
+c$ = Clazz.decorateAsClass (function () {
+Clazz.prepareCallback (this, arguments);
+this.running = false;
+this.up = true;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui.IdPanel, "ScrollThread", Thread);
+Clazz.makeConstructor (c$, 
+function (a) {
+Clazz.superConstructor (this, jalview.appletgui.IdPanel.ScrollThread, []);
+this.up = a;
+this.start ();
+}, "~B");
+Clazz.defineMethod (c$, "stopScrolling", 
+function () {
+this.running = false;
+});
+Clazz.overrideMethod (c$, "run", 
+function () {
+this.running = true;
+while (this.running) {
+if (this.b$["jalview.appletgui.IdPanel"].alignPanel.scrollUp (this.up)) {
+var a = this.b$["jalview.appletgui.IdPanel"].av.getStartSeq ();
+if (!this.up) {
+a = this.b$["jalview.appletgui.IdPanel"].av.getEndSeq ();
+}if (a < this.b$["jalview.appletgui.IdPanel"].lastid) {
+this.b$["jalview.appletgui.IdPanel"].selectSeqs (this.b$["jalview.appletgui.IdPanel"].lastid - 1, a);
+} else if (a > this.b$["jalview.appletgui.IdPanel"].lastid && a < this.b$["jalview.appletgui.IdPanel"].av.getAlignment ().getHeight ()) {
+this.b$["jalview.appletgui.IdPanel"].selectSeqs (this.b$["jalview.appletgui.IdPanel"].lastid + 1, a);
+}this.b$["jalview.appletgui.IdPanel"].lastid = a;
+} else {
+this.running = false;
+}this.b$["jalview.appletgui.IdPanel"].alignPanel.paintAlignment (true);
+try {
+Thread.sleep (100);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+} else {
+throw ex;
+}
+}
+}
+});
+c$ = Clazz.p0p ();
+};
+});