X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=f965ff4686b41d79f7209b7e2b36e76c61736447;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=cb26fb5dc5374aceb1383e45a84194cf90558d31;hpb=1d0f5219658cdf6ad5e1a1cbe6e1bb8cd12e6d85;p=jalview.git diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index cb26fb5..f965ff4 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -23,6 +23,7 @@ package jalview.appletgui; import jalview.analysis.Conservation; import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; +import jalview.datamodel.BinaryNode; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; @@ -86,7 +87,7 @@ public class TreeCanvas extends Panel Hashtable nodeHash = new Hashtable(); - SequenceNode highlightNode; + BinaryNode highlightNode; AlignmentPanel ap; @@ -122,15 +123,15 @@ public class TreeCanvas extends Panel tree2.findHeight(tree2.getTopNode()); // Now have to calculate longest name based on the leaves - Vector leaves = tree2.findLeaves(tree2.getTopNode()); + Vector leaves = tree2.findLeaves(tree2.getTopNode()); boolean has_placeholders = false; longestName = ""; for (int i = 0; i < leaves.size(); i++) { - SequenceNode lf = leaves.elementAt(i); + BinaryNode lf = leaves.elementAt(i); - if (lf.isPlaceholder()) + if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder()) { has_placeholders = true; } @@ -146,7 +147,7 @@ public class TreeCanvas extends Panel setMarkPlaceholders(has_placeholders); } - public void drawNode(Graphics g, SequenceNode node, float chunk, + public void drawNode(Graphics g, BinaryNode node, float chunk, double scale, int width, int offx, int offy) { if (node == null) @@ -210,9 +211,10 @@ public class TreeCanvas extends Panel g.drawString(nodeLabel, xstart + 2, ypos - 2); } - String name = (markPlaceholders && node.isPlaceholder()) - ? (PLACEHOLDER + node.getName()) - : node.getName(); + String name = (markPlaceholders && node instanceof SequenceNode + && ((SequenceNode) node).isPlaceholder()) + ? (PLACEHOLDER + node.getName()) + : node.getName(); FontMetrics fm = g.getFontMetrics(font); int charWidth = fm.stringWidth(name) + 3; int charHeight = fm.getHeight(); @@ -237,9 +239,9 @@ public class TreeCanvas extends Panel } else { - drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, + drawNode(g, (BinaryNode) node.left(), chunk, scale, width, offx, offy); - drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, + drawNode(g, (BinaryNode) node.right(), chunk, scale, width, offx, offy); double height = node.height; @@ -263,9 +265,9 @@ public class TreeCanvas extends Panel } int ystart = (int) (node.left() == null ? 0 - : (((SequenceNode) node.left()).ycount * chunk)) + offy; + : (((BinaryNode) node.left()).ycount * chunk)) + offy; int yend = (int) (node.right() == null ? 0 - : (((SequenceNode) node.right()).ycount * chunk)) + offy; + : (((BinaryNode) node.right()).ycount * chunk)) + offy; Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); nodeHash.put(node, pos); @@ -338,20 +340,20 @@ public class TreeCanvas extends Panel int width = getSize().width; int height = getSize().height; - SequenceNode top = tree.getTopNode(); + BinaryNode top = tree.getTopNode(); double wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight(); if (top.count == 0) { - top.count = ((SequenceNode) top.left()).count - + ((SequenceNode) top.right()).count; + top.count = ((BinaryNode) top.left()).count + + ((BinaryNode) top.right()).count; } float chunk = (float) (height - offy) / top.count; pickNode(pickBox, top, chunk, wscale, width, offx, offy); } - public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, + public void pickNode(Rectangle pickBox, BinaryNode node, float chunk, double scale, int width, int offx, int offy) { if (node == null) @@ -384,14 +386,14 @@ public class TreeCanvas extends Panel } else { - pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, - offx, offy); - pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, + pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width, offx, + offy); + pickNode(pickBox, (BinaryNode) node.right(), chunk, scale, width, offx, offy); } } - public void setColor(SequenceNode node, Color c) + public void setColor(BinaryNode node, Color c) { if (node == null) { @@ -410,8 +412,8 @@ public class TreeCanvas extends Panel else { node.color = c; - setColor((SequenceNode) node.left(), c); - setColor((SequenceNode) node.right(), c); + setColor((BinaryNode) node.left(), c); + setColor((BinaryNode) node.right(), c); } } @@ -469,12 +471,12 @@ public class TreeCanvas extends Panel double wscale = (width - labelLength - offx * 2) / tree.getMaxHeight(); - SequenceNode top = tree.getTopNode(); + BinaryNode top = tree.getTopNode(); if (top.count == 0) { - top.count = ((SequenceNode) top.left()).count - + ((SequenceNode) top.right()).count; + top.count = ((BinaryNode) top.left()).count + + ((BinaryNode) top.right()).count; } float chunk = (float) (height - offy) / top.count; @@ -527,7 +529,7 @@ public class TreeCanvas extends Panel } else { - Vector leaves = tree.findLeaves(highlightNode); + Vector leaves = tree.findLeaves(highlightNode); for (int i = 0; i < leaves.size(); i++) { @@ -554,9 +556,9 @@ public class TreeCanvas extends Panel Object ob = findElement(evt.getX(), evt.getY()); - if (ob instanceof SequenceNode) + if (ob instanceof BinaryNode) { - highlightNode = (SequenceNode) ob; + highlightNode = (BinaryNode) ob; repaint(); } else @@ -596,7 +598,7 @@ public class TreeCanvas extends Panel threshold = (float) (x - offx) / (float) (getSize().width - labelLength - 2 * offx); - List groups = tree.groupNodes(threshold); + List groups = tree.groupNodes(threshold); setColor(tree.getTopNode(), Color.black); av.setSelectionGroup(null); @@ -620,7 +622,7 @@ public class TreeCanvas extends Panel } - void colourGroups(List groups) + void colourGroups(List groups) { for (int i = 0; i < groups.size(); i++) { @@ -629,7 +631,7 @@ public class TreeCanvas extends Panel (int) (Math.random() * 255), (int) (Math.random() * 255)); setColor(groups.get(i), col.brighter()); - Vector l = tree.findLeaves(groups.get(i)); + Vector l = tree.findLeaves(groups.get(i)); Vector sequences = new Vector<>(); for (int j = 0; j < l.size(); j++) @@ -659,7 +661,7 @@ public class TreeCanvas extends Panel { cs = ColourSchemeProperty.getColourScheme(av, sg, ColourSchemeProperty - .getColourName(av.getGlobalColourScheme())); + .getColourName(av.getGlobalColourScheme())); } // cs is null if shading is an annotationColourGradient // if (cs != null)