X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=a1bcebd25a43917bf7d0561cc58889ee4219638b;hb=948828a5fed141e2ed319586687b80b6d0298268;hp=180467a1ab4f0d1178ec62bb3d758ddee9c9823a;hpb=16d109024847af92482237e43f99b82fd997451a;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 180467a..a1bcebd 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -20,18 +20,6 @@ */ package jalview.gui; -import jalview.analysis.Conservation; -import jalview.analysis.TreeModel; -import jalview.api.AlignViewportI; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.datamodel.SequenceNode; -import jalview.schemes.ColourSchemeI; -import jalview.structure.SelectionSource; -import jalview.util.Format; -import jalview.util.MessageManager; - import java.awt.Color; import java.awt.Dimension; import java.awt.Font; @@ -48,17 +36,31 @@ import java.awt.print.PageFormat; import java.awt.print.Printable; import java.awt.print.PrinterException; import java.awt.print.PrinterJob; -import java.util.Enumeration; import java.util.Hashtable; import java.util.List; +import java.util.Map; +import java.util.Map.Entry; import java.util.Vector; -import javax.swing.JColorChooser; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; 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; +import jalview.datamodel.SequenceNode; +import jalview.gui.JalviewColourChooser.ColourChooserListener; +import jalview.schemes.ColourSchemeI; +import jalview.structure.SelectionSource; +import jalview.util.Format; +import jalview.util.MessageManager; + /** * DOCUMENT ME! * @@ -103,11 +105,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, int labelLength = -1; - Hashtable nameHash = new Hashtable(); + Map nameHash = new Hashtable<>(); - Hashtable nodeHash = new Hashtable(); + Map nodeHash = new Hashtable<>(); - SequenceNode highlightNode; + BinaryNode highlightNode; boolean applyToAllViews = false; @@ -172,15 +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; } @@ -214,7 +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) @@ -258,7 +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) @@ -276,7 +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(); @@ -305,9 +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; @@ -331,9 +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); @@ -346,7 +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) @@ -378,31 +380,25 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, */ public Object findElement(int x, int y) { - Enumeration keys = nameHash.keys(); - - while (keys.hasMoreElements()) + for (Entry entry : nameHash.entrySet()) { - Object ob = keys.nextElement(); - Rectangle rect = (Rectangle) nameHash.get(ob); + Rectangle rect = entry.getValue(); if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) && (y <= (rect.y + rect.height))) { - return ob; + return entry.getKey(); } } - keys = nodeHash.keys(); - - while (keys.hasMoreElements()) + for (Entry entry : nodeHash.entrySet()) { - Object ob = keys.nextElement(); - Rectangle rect = (Rectangle) nodeHash.get(ob); + Rectangle rect = entry.getValue(); if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) && (y <= (rect.y + rect.height))) { - return ob; + return entry.getKey(); } } @@ -420,14 +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; @@ -453,7 +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) @@ -464,9 +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; @@ -487,9 +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); } } @@ -502,7 +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) { @@ -522,8 +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); } /** @@ -651,13 +646,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { fm = g.getFontMetrics(font); - if (nameHash.size() == 0) + int nameCount = nameHash.size(); + if (nameCount == 0) { repaint(); } if (fitToWindow || (!fitToWindow && (scrollPane - .getHeight() > ((fm.getHeight() * nameHash.size()) + offy)))) + .getHeight() > ((fm.getHeight() * nameCount) + offy)))) { draw(g, scrollPane.getWidth(), scrollPane.getHeight()); setPreferredSize(null); @@ -665,8 +661,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, else { setPreferredSize(new Dimension(scrollPane.getWidth(), - fm.getHeight() * nameHash.size())); - draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size()); + fm.getHeight() * nameCount)); + draw(g, scrollPane.getWidth(), fm.getHeight() * nameCount); } scrollPane.revalidate(); @@ -718,12 +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; @@ -809,7 +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++) { @@ -830,15 +826,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, */ void chooseSubtreeColour() { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_subtree_colour"), - highlightNode.color); - if (col != null) + String ttl = MessageManager.getString("label.select_subtree_colour"); + ColourChooserListener listener = new ColourChooserListener() { - setColor(highlightNode, col); - PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId()); - repaint(); - } + @Override + public void colourSelected(Color c) + { + setColor(highlightNode, c); + PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + repaint(); + } + }; + JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color, + listener); } @Override @@ -848,9 +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(); @@ -917,12 +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) @@ -930,7 +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(); @@ -963,13 +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++) @@ -978,7 +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<>();