X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=f965ff4686b41d79f7209b7e2b36e76c61736447;hb=58735c979dbb573eb12d57e33ef7d6e3f3a82c8e;hp=e30879cb8efef0e90fe3238fa6a7026288abfaa2;hpb=4f094851cd2247ea2d982e7829a6f5b663042573;p=jalview.git diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index e30879c..f965ff4 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -21,8 +21,9 @@ package jalview.appletgui; import jalview.analysis.Conservation; -import jalview.analysis.NJTree; +import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; +import jalview.datamodel.BinaryNode; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; @@ -48,12 +49,13 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.util.Enumeration; import java.util.Hashtable; +import java.util.List; import java.util.Vector; -public class TreeCanvas extends Panel implements MouseListener, - MouseMotionListener +public class TreeCanvas extends Panel + implements MouseListener, MouseMotionListener { - NJTree tree; + TreeModel tree; ScrollPane scrollPane; @@ -85,7 +87,7 @@ public class TreeCanvas extends Panel implements MouseListener, Hashtable nodeHash = new Hashtable(); - SequenceNode highlightNode; + BinaryNode highlightNode; AlignmentPanel ap; @@ -115,21 +117,21 @@ public class TreeCanvas extends Panel implements MouseListener, selected.addOrRemove(sequence, true); } - public void setTree(NJTree tree) + public void setTree(TreeModel tree2) { - this.tree = tree; - tree.findHeight(tree.getTopNode()); + this.tree = tree2; + tree2.findHeight(tree2.getTopNode()); // Now have to calculate longest name based on the leaves - Vector leaves = tree.findLeaves(tree.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; } @@ -145,8 +147,8 @@ public class TreeCanvas extends Panel implements MouseListener, setMarkPlaceholders(has_placeholders); } - public void drawNode(Graphics g, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) + public void drawNode(Graphics g, BinaryNode node, float chunk, + double scale, int width, int offx, int offy) { if (node == null) { @@ -157,8 +159,8 @@ public class TreeCanvas extends Panel implements MouseListener, { // Drawing leaf node - float height = node.height; - float dist = node.dist; + double height = node.height; + double dist = node.dist; int xstart = (int) ((height - dist) * scale) + offx; int xend = (int) (height * scale) + offx; @@ -209,8 +211,10 @@ public class TreeCanvas extends Panel implements MouseListener, 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(); @@ -235,13 +239,13 @@ public class TreeCanvas extends Panel implements MouseListener, } 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); - float height = node.height; - float dist = node.dist; + double height = node.height; + double dist = node.dist; int xstart = (int) ((height - dist) * scale) + offx; int xend = (int) (height * scale) + offx; @@ -260,10 +264,10 @@ public class TreeCanvas extends Panel implements MouseListener, g.fillRect(xend - 2, ypos - 2, 4, 4); } - int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) - + offy; - int yend = (int) (((SequenceNode) node.right()).ycount * chunk) - + offy; + int ystart = (int) (node.left() == null ? 0 + : (((BinaryNode) node.left()).ycount * chunk)) + offy; + int yend = (int) (node.right() == null ? 0 + : (((BinaryNode) node.right()).ycount * chunk)) + offy; Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); nodeHash.put(node, pos); @@ -336,21 +340,21 @@ public class TreeCanvas extends Panel implements MouseListener, int width = getSize().width; int height = getSize().height; - SequenceNode top = tree.getTopNode(); + BinaryNode top = tree.getTopNode(); - float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight(); + 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, - float scale, int width, int offx, int offy) + public void pickNode(Rectangle pickBox, BinaryNode node, float chunk, + double scale, int width, int offx, int offy) { if (node == null) { @@ -359,7 +363,7 @@ public class TreeCanvas extends Panel implements MouseListener, if (node.left() == null && node.right() == null) { - float height = node.height; + double height = node.height; // float dist = node.dist; // int xstart = (int) ( (height - dist) * scale) + offx; @@ -382,14 +386,14 @@ public class TreeCanvas extends Panel implements MouseListener, } 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) { @@ -408,8 +412,8 @@ public class TreeCanvas extends Panel implements MouseListener, else { node.color = c; - setColor((SequenceNode) node.left(), c); - setColor((SequenceNode) node.right(), c); + setColor((BinaryNode) node.left(), c); + setColor((BinaryNode) node.right(), c); } } @@ -465,14 +469,14 @@ public class TreeCanvas extends Panel implements MouseListener, // for // scrollbar - float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight(); + 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; @@ -489,7 +493,8 @@ public class TreeCanvas extends Panel implements MouseListener, g.setColor(Color.gray); } - int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx); + int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + + offx); g.drawLine(x, 0, x, getSize().height); } @@ -524,7 +529,7 @@ public class TreeCanvas extends Panel implements MouseListener, } else { - Vector leaves = tree.findLeaves(highlightNode); + Vector leaves = tree.findLeaves(highlightNode); for (int i = 0; i < leaves.size(); i++) { @@ -551,9 +556,9 @@ public class TreeCanvas extends Panel implements MouseListener, Object ob = findElement(evt.getX(), evt.getY()); - if (ob instanceof SequenceNode) + if (ob instanceof BinaryNode) { - highlightNode = (SequenceNode) ob; + highlightNode = (BinaryNode) ob; repaint(); } else @@ -593,8 +598,7 @@ public class TreeCanvas extends Panel implements MouseListener, threshold = (float) (x - offx) / (float) (getSize().width - labelLength - 2 * offx); - tree.getGroups().removeAllElements(); - tree.groupNodes(tree.getTopNode(), threshold); + List groups = tree.groupNodes(threshold); setColor(tree.getTopNode(), Color.black); av.setSelectionGroup(null); @@ -608,7 +612,7 @@ public class TreeCanvas extends Panel implements MouseListener, codingComplement.clearSequenceColours(); } - colourGroups(); + colourGroups(groups); } } @@ -618,19 +622,18 @@ public class TreeCanvas extends Panel implements MouseListener, } - void colourGroups() + void colourGroups(List groups) { - for (int i = 0; i < tree.getGroups().size(); i++) + for (int i = 0; i < groups.size(); i++) { Color col = new Color((int) (Math.random() * 255), (int) (Math.random() * 255), (int) (Math.random() * 255)); - setColor(tree.getGroups().elementAt(i), col.brighter()); + setColor(groups.get(i), col.brighter()); - Vector l = tree.findLeaves(tree.getGroups() - .elementAt(i)); + Vector l = tree.findLeaves(groups.get(i)); - Vector sequences = new Vector(); + Vector sequences = new Vector<>(); for (int j = 0; j < l.size(); j++) { SequenceI s1 = (SequenceI) l.elementAt(j).element(); @@ -656,9 +659,9 @@ public class TreeCanvas extends Panel implements MouseListener, } else { - cs = ColourSchemeProperty.getColourScheme(sg, - ColourSchemeProperty.getColourName(av - .getGlobalColourScheme())); + cs = ColourSchemeProperty.getColourScheme(av, sg, + ColourSchemeProperty + .getColourName(av.getGlobalColourScheme())); } // cs is null if shading is an annotationColourGradient // if (cs != null)