X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=9a38d4caa25ad9345d038430b99ced076c2555bb;hb=844c332f108aba635608f13dedf2b08777b3a477;hp=b3a0a758e2bfd829f837a83eac4deaccdd495b40;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index b3a0a75..9a38d4c 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -20,17 +20,46 @@ */ package jalview.gui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.print.*; -import javax.swing.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.util.*; +import jalview.analysis.Conservation; +import jalview.analysis.NJTree; +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.schemes.ColourSchemeProperty; +import jalview.schemes.UserColourScheme; +import jalview.structure.SelectionSource; +import jalview.util.Format; +import jalview.util.MappingUtils; +import jalview.util.MessageManager; + +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.Point; +import java.awt.Rectangle; +import java.awt.RenderingHints; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +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.Vector; + +import javax.swing.JColorChooser; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; /** * DOCUMENT ME! @@ -39,7 +68,7 @@ import jalview.util.*; * @version $Revision$ */ public class TreeCanvas extends JPanel implements MouseListener, Runnable, - Printable, MouseMotionListener + Printable, MouseMotionListener, SelectionSource { /** DOCUMENT ME!! */ public static final String PLACEHOLDER = " * "; @@ -145,13 +174,13 @@ 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(), new Vector()); + Vector leaves = tree.findLeaves(tree.getTopNode()); boolean has_placeholders = false; longestName = ""; for (int i = 0; i < leaves.size(); i++) { - SequenceNode lf = (SequenceNode) leaves.elementAt(i); + SequenceNode lf = leaves.elementAt(i); if (lf.isPlaceholder()) { @@ -208,7 +237,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (node.element() instanceof SequenceI) { - SequenceI seq = (SequenceI) ((SequenceNode) node).element(); + SequenceI seq = (SequenceI) node.element(); if (av.getSequenceColour(seq) == Color.white) { @@ -258,14 +287,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2, charWidth, charHeight); - nameHash.put((SequenceI) node.element(), rect); + nameHash.put(node.element(), rect); // Colour selected leaves differently SequenceGroup selected = av.getSelectionGroup(); if ((selected != null) - && selected.getSequences(null).contains( - (SequenceI) node.element())) + && selected.getSequences(null).contains(node.element())) { g.setColor(Color.gray); @@ -290,7 +318,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, int xend = (int) (height * scale) + offx; int ypos = (int) (node.ycount * chunk) + offy; - g.setColor(((SequenceNode) node).color.darker()); + g.setColor(node.color.darker()); // Draw horizontal line g.drawLine(xstart, ypos, xend, ypos); @@ -493,7 +521,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { for (int a = 0; a < aps.length; a++) { - aps[a].av.setSequenceColour((SequenceI) node.element(), c); + final SequenceI seq = (SequenceI) node.element(); + aps[a].av.setSequenceColour(seq, c); } } } @@ -516,10 +545,20 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } // put printing in a thread to avoid painting problems + @Override public void run() { PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); + PageFormat defaultPage = printJob.defaultPage(); + PageFormat pf = printJob.pageDialog(defaultPage); + + if (defaultPage == pf) + { + /* + * user cancelled + */ + return; + } printJob.setPrintable(this, pf); @@ -550,6 +589,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @throws PrinterException * DOCUMENT ME! */ + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -604,6 +644,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param g * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { super.paintComponent(g); @@ -647,6 +688,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param fontSize * DOCUMENT ME! */ + @Override public void setFont(Font font) { this.font = font; @@ -682,8 +724,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar - float wscale = (float) (width - labelLength - (offx * 2)) - / tree.getMaxHeight(); + float wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight(); SequenceNode top = tree.getTopNode(); @@ -708,86 +749,106 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g2.setColor(Color.gray); } - int x = (int) ((threshold * (float) (getWidth() - labelLength - (2 * offx))) + offx); + int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx); g2.drawLine(x, 0, x, getHeight()); } } /** - * DOCUMENT ME! + * Empty method to satisfy the MouseListener interface * * @param e - * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent e) { + /* + * isPopupTrigger is set on mouseReleased on Windows + */ + if (e.isPopupTrigger()) + { + chooseSubtreeColour(); + e.consume(); // prevent mouseClicked happening + } } /** - * DOCUMENT ME! + * Empty method to satisfy the MouseListener interface * * @param e - * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent e) { } /** - * DOCUMENT ME! + * Empty method to satisfy the MouseListener interface * * @param e - * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent e) { } /** - * DOCUMENT ME! + * Handles a mouse click on a tree node (clicks elsewhere are handled in + * mousePressed). Click selects the sub-tree, double-click swaps leaf nodes + * order, right-click opens a dialogue to choose colour for the sub-tree. * * @param e - * DOCUMENT ME! */ + @Override public void mouseClicked(MouseEvent evt) { - if (highlightNode != null) + if (highlightNode == null) { - if (SwingUtilities.isRightMouseButton(evt)) - { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_subtree_colour"), highlightNode.color); - if (col != null) - { - setColor(highlightNode, col); - } - } - else if (evt.getClickCount() > 1) + return; + } + + if (evt.getClickCount() > 1) + { + tree.swapNodes(highlightNode); + tree.reCount(tree.getTopNode()); + tree.findHeight(tree.getTopNode()); + } + else + { + Vector leaves = tree.findLeaves(highlightNode); + + for (int i = 0; i < leaves.size(); i++) { - tree.swapNodes(highlightNode); - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); + SequenceI seq = (SequenceI) leaves.elementAt(i).element(); + treeSelectionChanged(seq); } - else - { - Vector leaves = new Vector(); - tree.findLeaves(highlightNode, leaves); + av.sendSelection(); + } - for (int i = 0; i < leaves.size(); i++) - { - SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i)) - .element(); - treeSelectionChanged(seq); - } - av.sendSelection(); - } + PaintRefresher.Refresh(tp, av.getSequenceSetId()); + repaint(); + } - PaintRefresher.Refresh(tp, av.getSequenceSetId()); + /** + * Offer the user the option to choose a colour for the highlighted node and + * its children; this colour is also applied to the corresponding sequence ids + * in the alignment + */ + void chooseSubtreeColour() + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_subtree_colour"), + highlightNode.color); + if (col != null) + { + setColor(highlightNode, col); + PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); repaint(); } } + @Override public void mouseMoved(MouseEvent evt) { av.setCurrentTree(tree); @@ -813,20 +874,48 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } } + @Override public void mouseDragged(MouseEvent ect) { } /** - * DOCUMENT ME! + * Handles a mouse press on a sequence name or the tree background canvas + * (click on a node is handled in mouseClicked). The action is to create + * groups by partitioning the tree at the mouse position. Colours for the + * groups (and sequence names) are generated randomly. * * @param e - * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent e) { av.setCurrentTree(tree); + /* + * isPopupTrigger is set for mousePressed (Mac) + * or mouseReleased (Windows) + */ + if (e.isPopupTrigger()) + { + if (highlightNode != null) + { + chooseSubtreeColour(); + } + return; + } + + /* + * defer right-click handling on Windows to + * mouseClicked; note isRightMouseButton + * also matches Cmd-click on Mac which should do + * nothing here + */ + if (SwingUtilities.isRightMouseButton(e)) + { + return; + } + int x = e.getX(); int y = e.getY(); @@ -854,11 +943,20 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, AlignmentPanel[] aps = getAssociatedPanels(); + // TODO push calls below into a single AlignViewportI method? + // see also AlignViewController.deleteGroups for (int a = 0; a < aps.length; a++) { aps[a].av.setSelectionGroup(null); aps[a].av.getAlignment().deleteAllGroups(); aps[a].av.clearSequenceColours(); + if (aps[a].av.getCodingComplement() != null) + { + aps[a].av.getCodingComplement().setSelectionGroup(null); + aps[a].av.getCodingComplement().getAlignment() + .deleteAllGroups(); + aps[a].av.getCodingComplement().clearSequenceColours(); + } } colourGroups(); } @@ -876,17 +974,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { Color col = new Color((int) (Math.random() * 255), (int) (Math.random() * 255), (int) (Math.random() * 255)); - setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter()); + setColor(tree.getGroups().elementAt(i), col.brighter()); - Vector l = tree.findLeaves( - (SequenceNode) tree.getGroups().elementAt(i), new Vector()); + Vector l = tree.findLeaves(tree.getGroups() + .elementAt(i)); - Vector sequences = new Vector(); + Vector sequences = new Vector(); for (int j = 0; j < l.size(); j++) { - SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j)) - .element(); + SequenceI s1 = (SequenceI) l.elementAt(j).element(); if (!sequences.contains(s1)) { @@ -909,45 +1006,72 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty - .getColourName(av.getGlobalColourScheme())); + cs = ColourSchemeProperty.getColourScheme(sg, + ColourSchemeProperty.getColourName(av + .getGlobalColourScheme())); } // cs is null if shading is an annotationColourGradient - if (cs != null) - { - cs.setThreshold(av.getGlobalColourScheme().getThreshold(), - av.getIgnoreGapsConsensus()); - } + // if (cs != null) + // { + // cs.setThreshold(av.getViewportColourScheme().getThreshold(), + // av.isIgnoreGapsConsensus()); + // } } - sg.cs = cs; + sg.setColourScheme(cs); + sg.getGroupColourScheme().setThreshold( + av.getResidueShading().getThreshold(), + av.isIgnoreGapsConsensus()); // sg.recalcConservation(); sg.setName("JTreeGroup:" + sg.hashCode()); sg.setIdColour(col); + for (int a = 0; a < aps.length; a++) { if (aps[a].av.getGlobalColourScheme() != null - && aps[a].av.getGlobalColourScheme().conservationApplied()) + && aps[a].av.getResidueShading() + .conservationApplied()) { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(null), + Conservation c = new Conservation("Group", sg.getSequences(null), sg.getStartRes(), sg.getEndRes()); - c.calculate(); c.verdict(false, aps[a].av.getConsPercGaps()); sg.cs.setConservation(c); } aps[a].av.getAlignment().addGroup(new SequenceGroup(sg)); + // TODO can we push all of the below into AlignViewportI? + final AlignViewportI codingComplement = aps[a].av + .getCodingComplement(); + if (codingComplement != null) + { + SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av, + codingComplement); + if (mappedGroup.getSequences().size() > 0) + { + codingComplement.getAlignment().addGroup(mappedGroup); + for (SequenceI seq : mappedGroup.getSequences()) + { + codingComplement.setSequenceColour(seq, col.brighter()); + } + } + } } } - // notify the panel to redo any group specific stuff. + + // notify the panel(s) to redo any group specific stuff. for (int a = 0; a < aps.length; a++) { aps[a].updateAnnotation(); // TODO: JAL-868 - need to ensure view colour change message is broadcast // to any Jmols listening in + final AlignViewportI codingComplement = aps[a].av + .getCodingComplement(); + if (codingComplement != null) + { + ((AlignViewport) codingComplement).getAlignPanel() + .updateAnnotation(); + } } - } /** @@ -994,8 +1118,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - return new AlignmentPanel[] - { ap }; + return new AlignmentPanel[] { ap }; } } }