X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=9fa98ee3e8bdd66651e6e6754e4bd221da4bf210;hb=400b50efffaa43ae2c3b4d3f653bf8215c5d1edc;hp=9cb3d18c08cf6ef85238d082cad7c2b792b59cfb;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 9cb3d18..9fa98ee 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -29,7 +29,6 @@ import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceNode; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; import jalview.structure.SelectionSource; import jalview.util.Format; @@ -175,13 +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()) { @@ -546,6 +545,7 @@ 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(); @@ -580,6 +580,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @throws PrinterException * DOCUMENT ME! */ + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -634,6 +635,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param g * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { super.paintComponent(g); @@ -677,6 +679,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param fontSize * DOCUMENT ME! */ + @Override public void setFont(Font font) { this.font = font; @@ -744,80 +747,99 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } /** - * 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); @@ -843,20 +865,48 @@ 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(); @@ -891,12 +941,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, aps[a].av.setSelectionGroup(null); aps[a].av.getAlignment().deleteAllGroups(); aps[a].av.clearSequenceColours(); - } - if (av.getCodingComplement() != null) - { - av.getCodingComplement().setSelectionGroup(null); - av.getCodingComplement().getAlignment().deleteAllGroups(); - av.getCodingComplement().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(); } @@ -914,17 +965,16 @@ 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)) { @@ -947,17 +997,21 @@ 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.isIgnoreGapsConsensus()); - } + // if (cs != null) + // { + // cs.setThreshold(av.getViewportColourScheme().getThreshold(), + // av.isIgnoreGapsConsensus()); + // } } - sg.cs = cs; + sg.setColourScheme(cs); + sg.getGroupColourScheme().setThreshold( + av.getViewportColourScheme().getThreshold(), + av.isIgnoreGapsConsensus()); // sg.recalcConservation(); sg.setName("JTreeGroup:" + sg.hashCode()); sg.setIdColour(col); @@ -965,53 +1019,49 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, for (int a = 0; a < aps.length; a++) { if (aps[a].av.getGlobalColourScheme() != null - && aps[a].av.getGlobalColourScheme().conservationApplied()) + && aps[a].av.getViewportColourScheme() + .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? - av.getAlignment().addGroup(sg); - final AlignViewportI codingComplement = av.getCodingComplement(); - if (codingComplement != null) - { - SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av, - codingComplement); - if (mappedGroup.getSequences().size() > 0) + // TODO can we push all of the below into AlignViewportI? + final AlignViewportI codingComplement = aps[a].av + .getCodingComplement(); + if (codingComplement != null) { - codingComplement.getAlignment().addGroup(mappedGroup); - for (SequenceI seq : mappedGroup.getSequences()) + SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av, + codingComplement); + if (mappedGroup.getSequences().size() > 0) { - codingComplement.setSequenceColour(seq, col.brighter()); + 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 - } - - if (av.getCodingComplement() != null) - { - ((AlignViewport) av.getCodingComplement()).getAlignPanel() - .updateAnnotation(); - /* - * idPanel. repaint () - */ + final AlignViewportI codingComplement = aps[a].av + .getCodingComplement(); + if (codingComplement != null) + { + ((AlignViewport) codingComplement).getAlignPanel() + .updateAnnotation(); + } } }