X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=9a38d4caa25ad9345d038430b99ced076c2555bb;hb=484abc22be60686d5188c8ff1b90613e821ea946;hp=254d032605980b6c627fee32fc73823d85e41792;hpb=0d74306f282be2d15eeb5d8de53a949c0124a0a5;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 254d032..9a38d4c 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()) { @@ -550,7 +549,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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); @@ -748,21 +756,27 @@ 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) @@ -770,10 +784,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } /** - * DOCUMENT ME! + * Empty method to satisfy the MouseListener interface * * @param e - * DOCUMENT ME! */ @Override public void mouseExited(MouseEvent e) @@ -781,10 +794,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } /** - * 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) @@ -794,15 +808,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, return; } - /* - * isPopupTrigger is set on mouseReleased / - * mouseClicked on Windows - */ - if (evt.isPopupTrigger()) - { - chooseSubtreeColour(); - } - else if (evt.getClickCount() > 1) + if (evt.getClickCount() > 1) { tree.swapNodes(highlightNode); tree.reCount(tree.getTopNode()); @@ -810,13 +816,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - Vector leaves = new Vector(); - tree.findLeaves(highlightNode, leaves); + Vector leaves = tree.findLeaves(highlightNode); for (int i = 0; i < leaves.size(); i++) { - SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i)) - .element(); + SequenceI seq = (SequenceI) leaves.elementAt(i).element(); treeSelectionChanged(seq); } av.sendSelection(); @@ -876,10 +880,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } /** - * 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) @@ -888,7 +894,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, /* * isPopupTrigger is set for mousePressed (Mac) - * or mouseReleased / mouseClicked (Windows) + * or mouseReleased (Windows) */ if (e.isPopupTrigger()) { @@ -901,8 +907,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, /* * defer right-click handling on Windows to - * mouseClicked; this also matches Cmd-click on Mac - * which should do nothing here + * mouseClicked; note isRightMouseButton + * also matches Cmd-click on Mac which should do + * nothing here */ if (SwingUtilities.isRightMouseButton(e)) { @@ -967,17 +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)) { @@ -1000,17 +1006,21 @@ 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.getResidueShading().getThreshold(), + av.isIgnoreGapsConsensus()); // sg.recalcConservation(); sg.setName("JTreeGroup:" + sg.hashCode()); sg.setIdColour(col); @@ -1018,12 +1028,11 @@ 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.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);