-Clazz.declarePackage ("jalview.appletgui");\r
-Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.util.Hashtable"], "jalview.appletgui.TreeCanvas", ["jalview.analysis.Conservation", "jalview.appletgui.PaintRefresher", "jalview.datamodel.SequenceGroup", "$.SequenceI", "$.SequenceNode", "jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "$.UserColourScheme", "jalview.util.Format", "$.MappingUtils", "java.awt.Color", "$.Dimension", "$.Point", "$.Rectangle", "java.util.Vector"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.tree = null;\r
-this.scrollPane = null;\r
-this.av = null;\r
-this.$font = null;\r
-this.fitToWindow = true;\r
-this.showDistances = false;\r
-this.showBootstrap = false;\r
-this.markPlaceholders = false;\r
-this.offx = 20;\r
-this.offy = 0;\r
-this.threshold = 0;\r
-this.longestName = null;\r
-this.labelLength = -1;\r
-this.nameHash = null;\r
-this.nodeHash = null;\r
-this.highlightNode = null;\r
-this.ap = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.appletgui, "TreeCanvas", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener]);\r
-Clazz.prepareFields (c$, function () {\r
-this.nameHash = new java.util.Hashtable ();\r
-this.nodeHash = new java.util.Hashtable ();\r
-});\r
-Clazz.makeConstructor (c$, \r
-function (ap, scroller) {\r
-Clazz.superConstructor (this, jalview.appletgui.TreeCanvas, []);\r
-this.ap = ap;\r
-this.av = ap.av;\r
-this.$font = this.av.getFont ();\r
-this.scrollPane = scroller;\r
-this.addMouseListener (this);\r
-this.addMouseMotionListener (this);\r
-this.setLayout (null);\r
-jalview.appletgui.PaintRefresher.Register (this, this.av.getSequenceSetId ());\r
-}, "jalview.appletgui.AlignmentPanel,awt2swing.ScrollPane");\r
-Clazz.defineMethod (c$, "treeSelectionChanged", \r
-function (sequence) {\r
-var selected = this.av.getSelectionGroup ();\r
-if (selected == null) {\r
-selected = new jalview.datamodel.SequenceGroup ();\r
-this.av.setSelectionGroup (selected);\r
-}selected.setEndRes (this.av.getAlignment ().getWidth () - 1);\r
-selected.addOrRemove (sequence, true);\r
-}, "jalview.datamodel.SequenceI");\r
-Clazz.defineMethod (c$, "setTree", \r
-function (tree) {\r
-this.tree = tree;\r
-tree.findHeight (tree.getTopNode ());\r
-var leaves = tree.findLeaves (tree.getTopNode (), new java.util.Vector ());\r
-var has_placeholders = false;\r
-this.longestName = "";\r
-for (var i = 0; i < leaves.size (); i++) {\r
-var lf = leaves.elementAt (i);\r
-if (lf.isPlaceholder ()) {\r
-has_placeholders = true;\r
-}if (this.longestName.length < (lf.element ()).getName ().length) {\r
-this.longestName = " * " + (lf.element ()).getName ();\r
-}}\r
-this.setMarkPlaceholders (has_placeholders);\r
-}, "jalview.analysis.NJTree");\r
-Clazz.defineMethod (c$, "drawNode", \r
-function (g, node, chunk, scale, width, offx, offy) {\r
-if (node == null) {\r
-return;\r
-}if (node.left () == null && node.right () == null) {\r
-var height = node.height;\r
-var dist = node.dist;\r
-var xstart = Clazz.floatToInt ((height - dist) * scale) + offx;\r
-var xend = Clazz.floatToInt (height * scale) + offx;\r
-var ypos = Clazz.floatToInt (node.ycount * chunk) + offy;\r
-if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) {\r
-var seq = node.element ();\r
-if (this.av.getSequenceColour (seq) === java.awt.Color.white) {\r
-g.setColor (java.awt.Color.black);\r
-} else {\r
-g.setColor (this.av.getSequenceColour (seq).darker ());\r
-}} else {\r
-g.setColor (java.awt.Color.black);\r
-}g.drawLine (xstart, ypos, xend, ypos);\r
-var nodeLabel = "";\r
-if (this.showDistances && node.dist > 0) {\r
-nodeLabel = new jalview.util.Format ("%-.2f").formDouble (node.dist);\r
-}if (this.showBootstrap) {\r
-var btstrap = node.getBootstrap ();\r
-if (btstrap > -1) {\r
-if (this.showDistances) {\r
-nodeLabel = nodeLabel + " : ";\r
-}nodeLabel = nodeLabel + String.valueOf (node.getBootstrap ());\r
-}}if (!nodeLabel.equals ("")) {\r
-g.drawString (nodeLabel, xstart + 2, ypos - 2);\r
-}var name = (this.markPlaceholders && node.isPlaceholder ()) ? (" * " + node.getName ()) : node.getName ();\r
-var fm = g.getFontMetrics (this.$font);\r
-var charWidth = fm.stringWidth (name) + 3;\r
-var charHeight = fm.getHeight ();\r
-var rect = new java.awt.Rectangle (xend + 10, ypos - charHeight, charWidth, charHeight);\r
-this.nameHash.put (node.element (), rect);\r
-var selected = this.av.getSelectionGroup ();\r
-if (selected != null && selected.getSequences (null).contains (node.element ())) {\r
-g.setColor (java.awt.Color.gray);\r
-g.fillRect (xend + 10, ypos - charHeight + 3, charWidth, charHeight);\r
-g.setColor (java.awt.Color.white);\r
-}g.drawString (name, xend + 10, ypos);\r
-g.setColor (java.awt.Color.black);\r
-} else {\r
-this.drawNode (g, node.left (), chunk, scale, width, offx, offy);\r
-this.drawNode (g, node.right (), chunk, scale, width, offx, offy);\r
-var height = node.height;\r
-var dist = node.dist;\r
-var xstart = Clazz.floatToInt ((height - dist) * scale) + offx;\r
-var xend = Clazz.floatToInt (height * scale) + offx;\r
-var ypos = Clazz.floatToInt (node.ycount * chunk) + offy;\r
-g.setColor (node.color.darker ());\r
-g.drawLine (xstart, ypos, xend, ypos);\r
-if (node === this.highlightNode) {\r
-g.fillRect (xend - 3, ypos - 3, 6, 6);\r
-} else {\r
-g.fillRect (xend - 2, ypos - 2, 4, 4);\r
-}var ystart = Clazz.floatToInt ((node.left ()).ycount * chunk) + offy;\r
-var yend = Clazz.floatToInt ((node.right ()).ycount * chunk) + offy;\r
-var pos = new java.awt.Rectangle (xend - 2, ypos - 2, 5, 5);\r
-this.nodeHash.put (node, pos);\r
-g.drawLine (Clazz.floatToInt (height * scale) + offx, ystart, Clazz.floatToInt (height * scale) + offx, yend);\r
-var nodeLabel = "";\r
-if (this.showDistances && (node.dist > 0)) {\r
-nodeLabel = new jalview.util.Format ("%-.2f").formDouble (node.dist);\r
-}if (this.showBootstrap) {\r
-var btstrap = node.getBootstrap ();\r
-if (btstrap > -1) {\r
-if (this.showDistances) {\r
-nodeLabel = nodeLabel + " : ";\r
-}nodeLabel = nodeLabel + String.valueOf (node.getBootstrap ());\r
-}}if (!nodeLabel.equals ("")) {\r
-g.drawString (nodeLabel, xstart + 2, ypos - 2);\r
-}}}, "java.awt.Graphics,jalview.datamodel.SequenceNode,~N,~N,~N,~N,~N");\r
-Clazz.defineMethod (c$, "findElement", \r
-function (x, y) {\r
-var keys = this.nameHash.keys ();\r
-while (keys.hasMoreElements ()) {\r
-var ob = keys.nextElement ();\r
-var rect = this.nameHash.get (ob);\r
-if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y && y <= (rect.y + rect.height)) {\r
-return ob;\r
-}}\r
-keys = this.nodeHash.keys ();\r
-while (keys.hasMoreElements ()) {\r
-var ob = keys.nextElement ();\r
-var rect = this.nodeHash.get (ob);\r
-if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y && y <= (rect.y + rect.height)) {\r
-return ob;\r
-}}\r
-return null;\r
-}, "~N,~N");\r
-Clazz.defineMethod (c$, "pickNodes", \r
-function (pickBox) {\r
-var width = this.getSize ().width;\r
-var height = this.getSize ().height;\r
-var top = this.tree.getTopNode ();\r
-var wscale = (width * .8 - this.offx * 2) / this.tree.getMaxHeight ();\r
-if (top.count == 0) {\r
-top.count = (top.left ()).count + (top.right ()).count;\r
-}var chunk = (height - this.offy) / top.count;\r
-this.pickNode (pickBox, top, chunk, wscale, width, this.offx, this.offy);\r
-}, "java.awt.Rectangle");\r
-Clazz.defineMethod (c$, "pickNode", \r
-function (pickBox, node, chunk, scale, width, offx, offy) {\r
-if (node == null) {\r
-return;\r
-}if (node.left () == null && node.right () == null) {\r
-var height = node.height;\r
-var xend = Clazz.floatToInt (height * scale) + offx;\r
-var ypos = Clazz.floatToInt (node.ycount * chunk) + offy;\r
-if (pickBox.contains ( new java.awt.Point (xend, ypos))) {\r
-if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) {\r
-var seq = node.element ();\r
-var sg = this.av.getSelectionGroup ();\r
-if (sg != null) {\r
-sg.addOrRemove (seq, true);\r
-}}}} else {\r
-this.pickNode (pickBox, node.left (), chunk, scale, width, offx, offy);\r
-this.pickNode (pickBox, node.right (), chunk, scale, width, offx, offy);\r
-}}, "java.awt.Rectangle,jalview.datamodel.SequenceNode,~N,~N,~N,~N,~N");\r
-Clazz.defineMethod (c$, "setColor", \r
-function (node, c) {\r
-if (node == null) {\r
-return;\r
-}if (node.left () == null && node.right () == null) {\r
-node.color = c;\r
-if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) {\r
-this.av.setSequenceColour (node.element (), c);\r
-}} else {\r
-node.color = c;\r
-this.setColor (node.left (), c);\r
-this.setColor (node.right (), c);\r
-}}, "jalview.datamodel.SequenceNode,java.awt.Color");\r
-Clazz.overrideMethod (c$, "update", \r
-function (g) {\r
-this.paint (g);\r
-}, "java.awt.Graphics");\r
-Clazz.overrideMethod (c$, "paintComponent", \r
-function (g) {\r
-if (this.tree == null) {\r
-return;\r
-}if (this.nameHash.size () == 0) {\r
-this.repaint ();\r
-}var width = this.scrollPane.getSize ().width;\r
-var height = this.scrollPane.getSize ().height;\r
-if (!this.fitToWindow) {\r
-height = g.getFontMetrics (this.$font).getHeight () * this.nameHash.size ();\r
-}if (this.getSize ().width > width) {\r
-this.setSize ( new java.awt.Dimension (width, height));\r
-this.scrollPane.validate ();\r
-return;\r
-}this.setSize ( new java.awt.Dimension (width, height));\r
-g.setFont (this.$font);\r
-this.draw (g, width, height);\r
-this.validate ();\r
-}, "java.awt.Graphics");\r
-Clazz.defineMethod (c$, "draw", \r
-function (g, width, height) {\r
-this.offy = this.$font.getSize () + 10;\r
-g.setColor (java.awt.Color.white);\r
-g.fillRect (0, 0, width, height);\r
-this.labelLength = g.getFontMetrics (this.$font).stringWidth (this.longestName) + 20;\r
-var wscale = (width - this.labelLength - this.offx * 2) / this.tree.getMaxHeight ();\r
-var top = this.tree.getTopNode ();\r
-if (top.count == 0) {\r
-top.count = (top.left ()).count + (top.right ()).count;\r
-}var chunk = (height - this.offy) / top.count;\r
-this.drawNode (g, this.tree.getTopNode (), chunk, wscale, width, this.offx, this.offy);\r
-if (this.threshold != 0) {\r
-if (this.av.getCurrentTree () === this.tree) {\r
-g.setColor (java.awt.Color.red);\r
-} else {\r
-g.setColor (java.awt.Color.gray);\r
-}var x = Clazz.floatToInt (this.threshold * (this.getSize ().width - this.labelLength - 2 * this.offx) + this.offx);\r
-g.drawLine (x, 0, x, this.getSize ().height);\r
-}}, "java.awt.Graphics,~N,~N");\r
-Clazz.overrideMethod (c$, "mouseReleased", \r
-function (e) {\r
-}, "java.awt.event.MouseEvent");\r
-Clazz.overrideMethod (c$, "mouseEntered", \r
-function (e) {\r
-}, "java.awt.event.MouseEvent");\r
-Clazz.overrideMethod (c$, "mouseExited", \r
-function (e) {\r
-}, "java.awt.event.MouseEvent");\r
-Clazz.overrideMethod (c$, "mouseClicked", \r
-function (evt) {\r
-if (this.highlightNode != null) {\r
-if (evt.getClickCount () > 1) {\r
-this.tree.swapNodes (this.highlightNode);\r
-this.tree.reCount (this.tree.getTopNode ());\r
-this.tree.findHeight (this.tree.getTopNode ());\r
-} else {\r
-var leaves = new java.util.Vector ();\r
-this.tree.findLeaves (this.highlightNode, leaves);\r
-for (var i = 0; i < leaves.size (); i++) {\r
-var seq = (leaves.elementAt (i)).element ();\r
-this.treeSelectionChanged (seq);\r
-}\r
-}jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ());\r
-this.repaint ();\r
-this.av.sendSelection ();\r
-}}, "java.awt.event.MouseEvent");\r
-Clazz.overrideMethod (c$, "mouseDragged", \r
-function (ect) {\r
-}, "java.awt.event.MouseEvent");\r
-Clazz.overrideMethod (c$, "mouseMoved", \r
-function (evt) {\r
-this.av.setCurrentTree (this.tree);\r
-var ob = this.findElement (evt.getX (), evt.getY ());\r
-if (Clazz.instanceOf (ob, jalview.datamodel.SequenceNode)) {\r
-this.highlightNode = ob;\r
-this.repaint ();\r
-} else {\r
-if (this.highlightNode != null) {\r
-this.highlightNode = null;\r
-this.repaint ();\r
-}}}, "java.awt.event.MouseEvent");\r
-Clazz.overrideMethod (c$, "mousePressed", \r
-function (e) {\r
-this.av.setCurrentTree (this.tree);\r
-var x = e.getX ();\r
-var y = e.getY ();\r
-var ob = this.findElement (x, y);\r
-if (Clazz.instanceOf (ob, jalview.datamodel.SequenceI)) {\r
-this.treeSelectionChanged (ob);\r
-jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ());\r
-this.repaint ();\r
-this.av.sendSelection ();\r
-return;\r
-} else if (!(Clazz.instanceOf (ob, jalview.datamodel.SequenceNode))) {\r
-if (this.tree.getMaxHeight () != 0) {\r
-this.threshold = (x - this.offx) / (this.getSize ().width - this.labelLength - 2 * this.offx);\r
-this.tree.getGroups ().removeAllElements ();\r
-this.tree.groupNodes (this.tree.getTopNode (), this.threshold);\r
-this.setColor (this.tree.getTopNode (), java.awt.Color.black);\r
-this.av.setSelectionGroup (null);\r
-this.av.getAlignment ().deleteAllGroups ();\r
-this.av.clearSequenceColours ();\r
-var codingComplement = this.av.getCodingComplement ();\r
-if (codingComplement != null) {\r
-codingComplement.setSelectionGroup (null);\r
-codingComplement.getAlignment ().deleteAllGroups ();\r
-codingComplement.clearSequenceColours ();\r
-}this.colourGroups ();\r
-}}jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ());\r
-this.repaint ();\r
-}, "java.awt.event.MouseEvent");\r
-Clazz.defineMethod (c$, "colourGroups", \r
-function () {\r
-for (var i = 0; i < this.tree.getGroups ().size (); i++) {\r
-var col = new java.awt.Color (Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255));\r
-this.setColor (this.tree.getGroups ().elementAt (i), col.brighter ());\r
-var l = this.tree.findLeaves (this.tree.getGroups ().elementAt (i), new java.util.Vector ());\r
-var sequences = new java.util.Vector ();\r
-for (var j = 0; j < l.size (); j++) {\r
-var s1 = (l.elementAt (j)).element ();\r
-if (!sequences.contains (s1)) {\r
-sequences.addElement (s1);\r
-}}\r
-var cs = null;\r
-var sg = new jalview.datamodel.SequenceGroup (sequences, "", cs, true, true, false, 0, this.av.getAlignment ().getWidth () - 1);\r
-if (this.av.getGlobalColourScheme () != null) {\r
-if (Clazz.instanceOf (this.av.getGlobalColourScheme (), jalview.schemes.UserColourScheme)) {\r
-cs = new jalview.schemes.UserColourScheme ((this.av.getGlobalColourScheme ()).getColours ());\r
-} else {\r
-cs = jalview.schemes.ColourSchemeProperty.getColour (sg, jalview.schemes.ColourSchemeProperty.getColourName (this.av.getGlobalColourScheme ()));\r
-}if (cs != null) {\r
-cs.setThreshold (this.av.getGlobalColourScheme ().getThreshold (), this.av.isIgnoreGapsConsensus ());\r
-}}sg.cs = cs;\r
-sg.setName ("JTreeGroup:" + sg.hashCode ());\r
-sg.setIdColour (col);\r
-if (this.av.getGlobalColourScheme () != null && this.av.getGlobalColourScheme ().conservationApplied ()) {\r
-var c = new jalview.analysis.Conservation ("Group", jalview.schemes.ResidueProperties.propHash, 3, sg.getSequences (null), sg.getStartRes (), sg.getEndRes ());\r
-c.calculate ();\r
-c.verdict (false, this.av.getConsPercGaps ());\r
-cs.setConservation (c);\r
-sg.cs = cs;\r
-}this.av.getAlignment ().addGroup (sg);\r
-this.av.getAlignment ().addGroup (sg);\r
-var codingComplement = this.av.getCodingComplement ();\r
-if (codingComplement != null) {\r
-var mappedGroup = jalview.util.MappingUtils.mapSequenceGroup (sg, this.av, codingComplement);\r
-if (mappedGroup.getSequences ().size () > 0) {\r
-codingComplement.getAlignment ().addGroup (mappedGroup);\r
-for (var seq, $seq = mappedGroup.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {\r
-codingComplement.setSequenceColour (seq, col);\r
-}\r
-}}}\r
-this.ap.updateAnnotation ();\r
-if (this.av.getCodingComplement () != null) {\r
-(this.av.getCodingComplement ()).firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());\r
-}});\r
-Clazz.defineMethod (c$, "setShowDistances", \r
-function (state) {\r
-this.showDistances = state;\r
-this.repaint ();\r
-}, "~B");\r
-Clazz.defineMethod (c$, "setShowBootstrap", \r
-function (state) {\r
-this.showBootstrap = state;\r
-this.repaint ();\r
-}, "~B");\r
-Clazz.defineMethod (c$, "setMarkPlaceholders", \r
-function (state) {\r
-this.markPlaceholders = state;\r
-this.repaint ();\r
-}, "~B");\r
-Clazz.defineStatics (c$,\r
-"PLACEHOLDER", " * ");\r
-});\r
+Clazz.declarePackage ("jalview.appletgui");
+Clazz.load (["awt2swing.Panel", "java.awt.event.MouseListener", "$.MouseMotionListener", "java.util.Hashtable"], "jalview.appletgui.TreeCanvas", ["jalview.analysis.Conservation", "jalview.appletgui.PaintRefresher", "jalview.datamodel.SequenceGroup", "$.SequenceI", "$.SequenceNode", "jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "$.UserColourScheme", "jalview.util.Format", "$.MappingUtils", "java.awt.Color", "$.Dimension", "$.Point", "$.Rectangle", "java.util.Vector"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.tree = null;
+this.scrollPane = null;
+this.av = null;
+this.$font = null;
+this.fitToWindow = true;
+this.showDistances = false;
+this.showBootstrap = false;
+this.markPlaceholders = false;
+this.offx = 20;
+this.offy = 0;
+this.threshold = 0;
+this.longestName = null;
+this.labelLength = -1;
+this.nameHash = null;
+this.nodeHash = null;
+this.highlightNode = null;
+this.ap = null;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui, "TreeCanvas", awt2swing.Panel, [java.awt.event.MouseListener, java.awt.event.MouseMotionListener]);
+Clazz.prepareFields (c$, function () {
+this.nameHash = new java.util.Hashtable ();
+this.nodeHash = new java.util.Hashtable ();
+});
+Clazz.makeConstructor (c$,
+function (ap, scroller) {
+Clazz.superConstructor (this, jalview.appletgui.TreeCanvas, []);
+this.ap = ap;
+this.av = ap.av;
+this.$font = this.av.getFont ();
+this.scrollPane = scroller;
+this.addMouseListener (this);
+this.addMouseMotionListener (this);
+this.setLayout (null);
+jalview.appletgui.PaintRefresher.Register (this, this.av.getSequenceSetId ());
+}, "jalview.appletgui.AlignmentPanel,awt2swing.ScrollPane");
+Clazz.defineMethod (c$, "treeSelectionChanged",
+function (sequence) {
+var selected = this.av.getSelectionGroup ();
+if (selected == null) {
+selected = new jalview.datamodel.SequenceGroup ();
+this.av.setSelectionGroup (selected);
+}selected.setEndRes (this.av.getAlignment ().getWidth () - 1);
+selected.addOrRemove (sequence, true);
+}, "jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "setTree",
+function (tree) {
+this.tree = tree;
+tree.findHeight (tree.getTopNode ());
+var leaves = tree.findLeaves (tree.getTopNode (), new java.util.Vector ());
+var has_placeholders = false;
+this.longestName = "";
+for (var i = 0; i < leaves.size (); i++) {
+var lf = leaves.elementAt (i);
+if (lf.isPlaceholder ()) {
+has_placeholders = true;
+}if (this.longestName.length < (lf.element ()).getName ().length) {
+this.longestName = " * " + (lf.element ()).getName ();
+}}
+this.setMarkPlaceholders (has_placeholders);
+}, "jalview.analysis.NJTree");
+Clazz.defineMethod (c$, "drawNode",
+function (g, node, chunk, scale, width, offx, offy) {
+if (node == null) {
+return;
+}if (node.left () == null && node.right () == null) {
+var height = node.height;
+var dist = node.dist;
+var xstart = Clazz.floatToInt ((height - dist) * scale) + offx;
+var xend = Clazz.floatToInt (height * scale) + offx;
+var ypos = Clazz.floatToInt (node.ycount * chunk) + offy;
+if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) {
+var seq = node.element ();
+if (this.av.getSequenceColour (seq) === java.awt.Color.white) {
+g.setColor (java.awt.Color.black);
+} else {
+g.setColor (this.av.getSequenceColour (seq).darker ());
+}} else {
+g.setColor (java.awt.Color.black);
+}g.drawLine (xstart, ypos, xend, ypos);
+var nodeLabel = "";
+if (this.showDistances && node.dist > 0) {
+nodeLabel = new jalview.util.Format ("%-.2f").formDouble (node.dist);
+}if (this.showBootstrap) {
+var btstrap = node.getBootstrap ();
+if (btstrap > -1) {
+if (this.showDistances) {
+nodeLabel = nodeLabel + " : ";
+}nodeLabel = nodeLabel + String.valueOf (node.getBootstrap ());
+}}if (!nodeLabel.equals ("")) {
+g.drawString (nodeLabel, xstart + 2, ypos - 2);
+}var name = (this.markPlaceholders && node.isPlaceholder ()) ? (" * " + node.getName ()) : node.getName ();
+var fm = g.getFontMetrics (this.$font);
+var charWidth = fm.stringWidth (name) + 3;
+var charHeight = fm.getHeight ();
+var rect = new java.awt.Rectangle (xend + 10, ypos - charHeight, charWidth, charHeight);
+this.nameHash.put (node.element (), rect);
+var selected = this.av.getSelectionGroup ();
+if (selected != null && selected.getSequences (null).contains (node.element ())) {
+g.setColor (java.awt.Color.gray);
+g.fillRect (xend + 10, ypos - charHeight + 3, charWidth, charHeight);
+g.setColor (java.awt.Color.white);
+}g.drawString (name, xend + 10, ypos);
+g.setColor (java.awt.Color.black);
+} else {
+this.drawNode (g, node.left (), chunk, scale, width, offx, offy);
+this.drawNode (g, node.right (), chunk, scale, width, offx, offy);
+var height = node.height;
+var dist = node.dist;
+var xstart = Clazz.floatToInt ((height - dist) * scale) + offx;
+var xend = Clazz.floatToInt (height * scale) + offx;
+var ypos = Clazz.floatToInt (node.ycount * chunk) + offy;
+g.setColor (node.color.darker ());
+g.drawLine (xstart, ypos, xend, ypos);
+if (node === this.highlightNode) {
+g.fillRect (xend - 3, ypos - 3, 6, 6);
+} else {
+g.fillRect (xend - 2, ypos - 2, 4, 4);
+}var ystart = Clazz.floatToInt ((node.left ()).ycount * chunk) + offy;
+var yend = Clazz.floatToInt ((node.right ()).ycount * chunk) + offy;
+var pos = new java.awt.Rectangle (xend - 2, ypos - 2, 5, 5);
+this.nodeHash.put (node, pos);
+g.drawLine (Clazz.floatToInt (height * scale) + offx, ystart, Clazz.floatToInt (height * scale) + offx, yend);
+var nodeLabel = "";
+if (this.showDistances && (node.dist > 0)) {
+nodeLabel = new jalview.util.Format ("%-.2f").formDouble (node.dist);
+}if (this.showBootstrap) {
+var btstrap = node.getBootstrap ();
+if (btstrap > -1) {
+if (this.showDistances) {
+nodeLabel = nodeLabel + " : ";
+}nodeLabel = nodeLabel + String.valueOf (node.getBootstrap ());
+}}if (!nodeLabel.equals ("")) {
+g.drawString (nodeLabel, xstart + 2, ypos - 2);
+}}}, "java.awt.Graphics,jalview.datamodel.SequenceNode,~N,~N,~N,~N,~N");
+Clazz.defineMethod (c$, "findElement",
+function (x, y) {
+var keys = this.nameHash.keys ();
+while (keys.hasMoreElements ()) {
+var ob = keys.nextElement ();
+var rect = this.nameHash.get (ob);
+if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y && y <= (rect.y + rect.height)) {
+return ob;
+}}
+keys = this.nodeHash.keys ();
+while (keys.hasMoreElements ()) {
+var ob = keys.nextElement ();
+var rect = this.nodeHash.get (ob);
+if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y && y <= (rect.y + rect.height)) {
+return ob;
+}}
+return null;
+}, "~N,~N");
+Clazz.defineMethod (c$, "pickNodes",
+function (pickBox) {
+var width = this.getSize ().width;
+var height = this.getSize ().height;
+var top = this.tree.getTopNode ();
+var wscale = (width * .8 - this.offx * 2) / this.tree.getMaxHeight ();
+if (top.count == 0) {
+top.count = (top.left ()).count + (top.right ()).count;
+}var chunk = (height - this.offy) / top.count;
+this.pickNode (pickBox, top, chunk, wscale, width, this.offx, this.offy);
+}, "java.awt.Rectangle");
+Clazz.defineMethod (c$, "pickNode",
+function (pickBox, node, chunk, scale, width, offx, offy) {
+if (node == null) {
+return;
+}if (node.left () == null && node.right () == null) {
+var height = node.height;
+var xend = Clazz.floatToInt (height * scale) + offx;
+var ypos = Clazz.floatToInt (node.ycount * chunk) + offy;
+if (pickBox.contains ( new java.awt.Point (xend, ypos))) {
+if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) {
+var seq = node.element ();
+var sg = this.av.getSelectionGroup ();
+if (sg != null) {
+sg.addOrRemove (seq, true);
+}}}} else {
+this.pickNode (pickBox, node.left (), chunk, scale, width, offx, offy);
+this.pickNode (pickBox, node.right (), chunk, scale, width, offx, offy);
+}}, "java.awt.Rectangle,jalview.datamodel.SequenceNode,~N,~N,~N,~N,~N");
+Clazz.defineMethod (c$, "setColor",
+function (node, c) {
+if (node == null) {
+return;
+}if (node.left () == null && node.right () == null) {
+node.color = c;
+if (Clazz.instanceOf (node.element (), jalview.datamodel.SequenceI)) {
+this.av.setSequenceColour (node.element (), c);
+}} else {
+node.color = c;
+this.setColor (node.left (), c);
+this.setColor (node.right (), c);
+}}, "jalview.datamodel.SequenceNode,java.awt.Color");
+Clazz.overrideMethod (c$, "update",
+function (g) {
+this.paint (g);
+}, "java.awt.Graphics");
+Clazz.overrideMethod (c$, "paintComponent",
+function (g) {
+if (this.tree == null) {
+return;
+}if (this.nameHash.size () == 0) {
+this.repaint ();
+}var width = this.scrollPane.getSize ().width;
+var height = this.scrollPane.getSize ().height;
+if (!this.fitToWindow) {
+height = g.getFontMetrics (this.$font).getHeight () * this.nameHash.size ();
+}if (this.getSize ().width > width) {
+this.setSize ( new java.awt.Dimension (width, height));
+this.scrollPane.validate ();
+return;
+}this.setSize ( new java.awt.Dimension (width, height));
+g.setFont (this.$font);
+this.draw (g, width, height);
+this.validate ();
+}, "java.awt.Graphics");
+Clazz.defineMethod (c$, "draw",
+function (g, width, height) {
+this.offy = this.$font.getSize () + 10;
+g.setColor (java.awt.Color.white);
+g.fillRect (0, 0, width, height);
+this.labelLength = g.getFontMetrics (this.$font).stringWidth (this.longestName) + 20;
+var wscale = (width - this.labelLength - this.offx * 2) / this.tree.getMaxHeight ();
+var top = this.tree.getTopNode ();
+if (top.count == 0) {
+top.count = (top.left ()).count + (top.right ()).count;
+}var chunk = (height - this.offy) / top.count;
+this.drawNode (g, this.tree.getTopNode (), chunk, wscale, width, this.offx, this.offy);
+if (this.threshold != 0) {
+if (this.av.getCurrentTree () === this.tree) {
+g.setColor (java.awt.Color.red);
+} else {
+g.setColor (java.awt.Color.gray);
+}var x = Clazz.floatToInt (this.threshold * (this.getSize ().width - this.labelLength - 2 * this.offx) + this.offx);
+g.drawLine (x, 0, x, this.getSize ().height);
+}}, "java.awt.Graphics,~N,~N");
+Clazz.overrideMethod (c$, "mouseReleased",
+function (e) {
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseEntered",
+function (e) {
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseExited",
+function (e) {
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseClicked",
+function (evt) {
+if (this.highlightNode != null) {
+if (evt.getClickCount () > 1) {
+this.tree.swapNodes (this.highlightNode);
+this.tree.reCount (this.tree.getTopNode ());
+this.tree.findHeight (this.tree.getTopNode ());
+} else {
+var leaves = new java.util.Vector ();
+this.tree.findLeaves (this.highlightNode, leaves);
+for (var i = 0; i < leaves.size (); i++) {
+var seq = (leaves.elementAt (i)).element ();
+this.treeSelectionChanged (seq);
+}
+}jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ());
+this.repaint ();
+this.av.sendSelection ();
+}}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseDragged",
+function (ect) {
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseMoved",
+function (evt) {
+this.av.setCurrentTree (this.tree);
+var ob = this.findElement (evt.getX (), evt.getY ());
+if (Clazz.instanceOf (ob, jalview.datamodel.SequenceNode)) {
+this.highlightNode = ob;
+this.repaint ();
+} else {
+if (this.highlightNode != null) {
+this.highlightNode = null;
+this.repaint ();
+}}}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mousePressed",
+function (e) {
+this.av.setCurrentTree (this.tree);
+var x = e.getX ();
+var y = e.getY ();
+var ob = this.findElement (x, y);
+if (Clazz.instanceOf (ob, jalview.datamodel.SequenceI)) {
+this.treeSelectionChanged (ob);
+jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ());
+this.repaint ();
+this.av.sendSelection ();
+return;
+} else if (!(Clazz.instanceOf (ob, jalview.datamodel.SequenceNode))) {
+if (this.tree.getMaxHeight () != 0) {
+this.threshold = (x - this.offx) / (this.getSize ().width - this.labelLength - 2 * this.offx);
+this.tree.getGroups ().removeAllElements ();
+this.tree.groupNodes (this.tree.getTopNode (), this.threshold);
+this.setColor (this.tree.getTopNode (), java.awt.Color.black);
+this.av.setSelectionGroup (null);
+this.av.getAlignment ().deleteAllGroups ();
+this.av.clearSequenceColours ();
+var codingComplement = this.av.getCodingComplement ();
+if (codingComplement != null) {
+codingComplement.setSelectionGroup (null);
+codingComplement.getAlignment ().deleteAllGroups ();
+codingComplement.clearSequenceColours ();
+}this.colourGroups ();
+}}jalview.appletgui.PaintRefresher.Refresh (this, this.av.getSequenceSetId ());
+this.repaint ();
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod (c$, "colourGroups",
+function () {
+for (var i = 0; i < this.tree.getGroups ().size (); i++) {
+var col = new java.awt.Color (Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255));
+this.setColor (this.tree.getGroups ().elementAt (i), col.brighter ());
+var l = this.tree.findLeaves (this.tree.getGroups ().elementAt (i), new java.util.Vector ());
+var sequences = new java.util.Vector ();
+for (var j = 0; j < l.size (); j++) {
+var s1 = (l.elementAt (j)).element ();
+if (!sequences.contains (s1)) {
+sequences.addElement (s1);
+}}
+var cs = null;
+var sg = new jalview.datamodel.SequenceGroup (sequences, "", cs, true, true, false, 0, this.av.getAlignment ().getWidth () - 1);
+if (this.av.getGlobalColourScheme () != null) {
+if (Clazz.instanceOf (this.av.getGlobalColourScheme (), jalview.schemes.UserColourScheme)) {
+cs = new jalview.schemes.UserColourScheme ((this.av.getGlobalColourScheme ()).getColours ());
+} else {
+cs = jalview.schemes.ColourSchemeProperty.getColour (sg, jalview.schemes.ColourSchemeProperty.getColourName (this.av.getGlobalColourScheme ()));
+}if (cs != null) {
+cs.setThreshold (this.av.getGlobalColourScheme ().getThreshold (), this.av.isIgnoreGapsConsensus ());
+}}sg.cs = cs;
+sg.setName ("JTreeGroup:" + sg.hashCode ());
+sg.setIdColour (col);
+if (this.av.getGlobalColourScheme () != null && this.av.getGlobalColourScheme ().conservationApplied ()) {
+var c = new jalview.analysis.Conservation ("Group", jalview.schemes.ResidueProperties.propHash, 3, sg.getSequences (null), sg.getStartRes (), sg.getEndRes ());
+c.calculate ();
+c.verdict (false, this.av.getConsPercGaps ());
+cs.setConservation (c);
+sg.cs = cs;
+}this.av.getAlignment ().addGroup (sg);
+this.av.getAlignment ().addGroup (sg);
+var codingComplement = this.av.getCodingComplement ();
+if (codingComplement != null) {
+var mappedGroup = jalview.util.MappingUtils.mapSequenceGroup (sg, this.av, codingComplement);
+if (mappedGroup.getSequences ().size () > 0) {
+codingComplement.getAlignment ().addGroup (mappedGroup);
+for (var seq, $seq = mappedGroup.getSequences ().iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
+codingComplement.setSequenceColour (seq, col);
+}
+}}}
+this.ap.updateAnnotation ();
+if (this.av.getCodingComplement () != null) {
+(this.av.getCodingComplement ()).firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());
+}});
+Clazz.defineMethod (c$, "setShowDistances",
+function (state) {
+this.showDistances = state;
+this.repaint ();
+}, "~B");
+Clazz.defineMethod (c$, "setShowBootstrap",
+function (state) {
+this.showBootstrap = state;
+this.repaint ();
+}, "~B");
+Clazz.defineMethod (c$, "setMarkPlaceholders",
+function (state) {
+this.markPlaceholders = state;
+this.repaint ();
+}, "~B");
+Clazz.defineStatics (c$,
+"PLACEHOLDER", " * ");
+});
git://source.jalview.org / jalviewjs.git / blobdiff