X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=a1bcebd25a43917bf7d0561cc58889ee4219638b;hb=948828a5fed141e2ed319586687b80b6d0298268;hp=baaec82a2c4cc26a208f765640df99a1faf3cf04;hpb=080fea8156db2a9fe6126d353e02f0a51942b231;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index baaec82..a1bcebd 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -50,6 +50,7 @@ import javax.swing.ToolTipManager; 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; @@ -106,9 +107,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Map nameHash = new Hashtable<>(); - Map nodeHash = new Hashtable<>(); + Map nodeHash = new Hashtable<>(); - SequenceNode highlightNode; + BinaryNode highlightNode; boolean applyToAllViews = false; @@ -173,15 +174,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, tree.findHeight(tree.getTopNode()); // Now have to calculate longest name based on the leaves - Vector leaves = tree.findLeaves(tree.getTopNode()); + Vector leaves = tree.findLeaves(tree.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; } @@ -215,7 +216,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param offy * DOCUMENT ME! */ - public void drawNode(Graphics g, SequenceNode node, float chunk, + public void drawNode(Graphics g, BinaryNode node, float chunk, double wscale, int width, int offx, int offy) { if (node == null) @@ -259,7 +260,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (showDistances && (node.dist > 0)) { - nodeLabel = new Format("%-.2f").form(node.dist); + nodeLabel = new Format("%g").form(node.dist); } if (showBootstrap && node.bootstrap > -1) @@ -277,7 +278,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g.drawString(nodeLabel, xstart + 2, ypos - 2); } - String name = (markPlaceholders && node.isPlaceholder()) + String name = (markPlaceholders && ((node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder()))) ? (PLACEHOLDER + node.getName()) : node.getName(); @@ -306,9 +307,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - drawNode(g, (SequenceNode) node.left(), chunk, wscale, width, offx, + drawNode(g, (BinaryNode) node.left(), chunk, wscale, width, offx, offy); - drawNode(g, (SequenceNode) node.right(), chunk, wscale, width, offx, + drawNode(g, (BinaryNode) node.right(), chunk, wscale, width, offx, offy); double height = node.height; @@ -332,9 +333,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } int ystart = (node.left() == null ? 0 - : (int) (((SequenceNode) node.left()).ycount * chunk)) + offy; + : (int) (((BinaryNode) node.left()).ycount * chunk)) + offy; int yend = (node.right() == null ? 0 - : (int) (((SequenceNode) node.right()).ycount * chunk)) + : (int) (((BinaryNode) node.right()).ycount * chunk)) + offy; Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); @@ -347,7 +348,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (showDistances && (node.dist > 0)) { - nodeLabel = new Format("%-.2f").form(node.dist); + nodeLabel = new Format("%g").form(node.dist); } if (showBootstrap && node.bootstrap > -1) @@ -381,7 +382,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { for (Entry entry : nameHash.entrySet()) { - Rectangle rect = (Rectangle) nameHash.get(entry.getValue()); + Rectangle rect = entry.getValue(); if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) && (y <= (rect.y + rect.height))) @@ -390,7 +391,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } } - for (Entry entry : nodeHash.entrySet()) + for (Entry entry : nodeHash.entrySet()) { Rectangle rect = entry.getValue(); @@ -415,14 +416,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, int width = getWidth(); int height = getHeight(); - SequenceNode top = tree.getTopNode(); + BinaryNode top = tree.getTopNode(); double wscale = ((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; @@ -448,7 +449,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param offy * DOCUMENT ME! */ - public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, + public void pickNode(Rectangle pickBox, BinaryNode node, float chunk, double wscale, int width, int offx, int offy) { if (node == null) @@ -459,8 +460,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if ((node.left() == null) && (node.right() == null)) { double height = node.height; -// double dist = node.dist; -// int xstart = (int) ((height - dist) * wscale) + offx; + // double dist = node.dist; + // int xstart = (int) ((height - dist) * wscale) + offx; int xend = (int) (height * wscale) + offx; int ypos = (int) (node.ycount * chunk) + offy; @@ -481,9 +482,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - pickNode(pickBox, (SequenceNode) node.left(), chunk, wscale, width, + pickNode(pickBox, (BinaryNode) node.left(), chunk, wscale, width, offx, offy); - pickNode(pickBox, (SequenceNode) node.right(), chunk, wscale, width, + pickNode(pickBox, (BinaryNode) node.right(), chunk, wscale, width, offx, offy); } } @@ -496,7 +497,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param c * DOCUMENT ME! */ - public void setColor(SequenceNode node, Color c) + public void setColor(BinaryNode node, Color c) { if (node == null) { @@ -516,8 +517,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } } } - setColor((SequenceNode) node.left(), c); - setColor((SequenceNode) node.right(), c); + setColor((BinaryNode) node.left(), c); + setColor((BinaryNode) node.right(), c); } /** @@ -713,12 +714,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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; @@ -804,7 +805,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - Vector leaves = tree.findLeaves(highlightNode); + Vector leaves = tree.findLeaves(highlightNode); for (int i = 0; i < leaves.size(); i++) { @@ -826,7 +827,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, void chooseSubtreeColour() { String ttl = MessageManager.getString("label.select_subtree_colour"); - ColourChooserListener listener = new ColourChooserListener() { + ColourChooserListener listener = new ColourChooserListener() + { @Override public void colourSelected(Color c) { @@ -835,7 +837,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, repaint(); } }; - JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color, listener); + JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color, + listener); } @Override @@ -845,9 +848,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Object ob = findElement(evt.getX(), evt.getY()); - if (ob instanceof SequenceNode) + if (ob instanceof BinaryNode) { - highlightNode = (SequenceNode) ob; + highlightNode = (BinaryNode) ob; this.setToolTipText( "" + MessageManager.getString("label.highlightnode")); repaint(); @@ -914,12 +917,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (ob instanceof SequenceI) { treeSelectionChanged((Sequence) ob); - PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId()); + PaintRefresher.Refresh(tp, + getAssociatedPanel().av.getSequenceSetId()); repaint(); av.sendSelection(); return; } - else if (!(ob instanceof SequenceNode)) + else if (!(ob instanceof BinaryNode)) { // Find threshold if (tree.getMaxHeight() != 0) @@ -927,7 +931,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, threshold = (float) (x - offx) / (float) (getWidth() - labelLength - (2 * offx)); - List groups = tree.groupNodes(threshold); + List groups = tree.groupNodes(threshold); setColor(tree.getTopNode(), Color.black); AlignmentPanel[] aps = getAssociatedPanels(); @@ -960,13 +964,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } } - PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId()); + PaintRefresher.Refresh(tp, + getAssociatedPanel().av.getSequenceSetId()); repaint(); } } - void colourGroups(List groups) + void colourGroups(List groups) { AlignmentPanel[] aps = getAssociatedPanels(); for (int i = 0; i < groups.size(); i++) @@ -975,7 +980,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, (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<>();