package jalview.gui;
import jalview.analysis.Conservation;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
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;
import java.awt.print.PrinterJob;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
import javax.swing.JColorChooser;
/** DOCUMENT ME!! */
public static final String PLACEHOLDER = " * ";
- NJTree tree;
+ TreeModel tree;
JScrollPane scrollPane;
TreePanel tp;
- AlignViewport av;
+ private AlignViewport av;
- AlignmentPanel ap;
+ private AlignmentPanel ap;
Font font;
int offy;
- float threshold;
+ private float threshold;
String longestName;
{
this.tp = tp;
this.av = ap.av;
- this.ap = ap;
+ this.setAssociatedPanel(ap);
font = av.getFont();
scrollPane = scroller;
addMouseListener(this);
* @param tree
* DOCUMENT ME!
*/
- public void setTree(NJTree tree)
+ public void setTree(TreeModel tree)
{
this.tree = tree;
tree.findHeight(tree.getTopNode());
// Now have to calculate longest name based on the leaves
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+ Vector<SequenceNode> 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())
{
* DOCUMENT ME!
* @param chunk
* DOCUMENT ME!
- * @param scale
+ * @param wscale
* DOCUMENT ME!
* @param width
* DOCUMENT ME!
* DOCUMENT ME!
*/
public void drawNode(Graphics g, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
+ double wscale, int width, int offx, int offy)
{
if (node == null)
{
if ((node.left() == null) && (node.right() == null))
{
// Drawing leaf node
- float height = node.height;
- float dist = node.dist;
+ double height = node.height;
+ double dist = node.dist;
- int xstart = (int) ((height - dist) * scale) + offx;
- int xend = (int) (height * scale) + offx;
+ int xstart = (int) ((height - dist) * wscale) + offx;
+ int xend = (int) (height * wscale) + offx;
int ypos = (int) (node.ycount * chunk) + offy;
g.drawString(nodeLabel, xstart + 2, ypos - 2);
}
- String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
- .getName()) : node.getName();
+ String name = (markPlaceholders && node.isPlaceholder())
+ ? (PLACEHOLDER + node.getName())
+ : node.getName();
int charWidth = fm.stringWidth(name) + 3;
int charHeight = font.getSize();
}
else
{
- drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
+ drawNode(g, (SequenceNode) node.left(), chunk, wscale, width, offx,
offy);
- drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
+ drawNode(g, (SequenceNode) node.right(), chunk, wscale, width, offx,
offy);
- float height = node.height;
- float dist = node.dist;
+ double height = node.height;
+ double dist = node.dist;
- int xstart = (int) ((height - dist) * scale) + offx;
- int xend = (int) (height * scale) + offx;
+ int xstart = (int) ((height - dist) * wscale) + offx;
+ int xend = (int) (height * wscale) + offx;
int ypos = (int) (node.ycount * chunk) + offy;
g.setColor(node.color.darker());
g.fillRect(xend - 2, ypos - 2, 4, 4);
}
- int ystart = (int) (((SequenceNode) node.left()).ycount * chunk)
- + offy;
- int yend = (int) (((SequenceNode) node.right()).ycount * chunk)
+ int ystart = (node.left() == null ? 0
+ : (int) (((SequenceNode) node.left()).ycount * chunk)) + offy;
+ int yend = (node.right() == null ? 0
+ : (int) (((SequenceNode) node.right()).ycount * chunk))
+ offy;
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
nodeHash.put(node, pos);
- g.drawLine((int) (height * scale) + offx, ystart,
- (int) (height * scale) + offx, yend);
+ g.drawLine((int) (height * wscale) + offx, ystart,
+ (int) (height * wscale) + offx, yend);
String nodeLabel = "";
SequenceNode top = tree.getTopNode();
- float wscale = (float) ((width * .8) - (offx * 2))
- / tree.getMaxHeight();
+ double wscale = ((width * .8) - (offx * 2)) / tree.getMaxHeight();
if (top.count == 0)
{
* DOCUMENT ME!
* @param chunk
* DOCUMENT ME!
- * @param scale
+ * @param wscale
* DOCUMENT ME!
* @param width
* DOCUMENT ME!
* DOCUMENT ME!
*/
public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
+ double wscale, int width, int offx, int offy)
{
if (node == null)
{
if ((node.left() == null) && (node.right() == null))
{
- float height = node.height;
- float dist = node.dist;
+ double height = node.height;
+ double dist = node.dist;
- int xstart = (int) ((height - dist) * scale) + offx;
- int xend = (int) (height * scale) + offx;
+ int xstart = (int) ((height - dist) * wscale) + offx;
+ int xend = (int) (height * wscale) + offx;
int ypos = (int) (node.ycount * chunk) + offy;
}
else
{
- pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
+ pickNode(pickBox, (SequenceNode) node.left(), chunk, wscale, width,
offx, offy);
- pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
+ pickNode(pickBox, (SequenceNode) node.right(), chunk, wscale, width,
offx, offy);
}
}
}
// 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);
* @throws PrinterException
* DOCUMENT ME!
*/
+ @Override
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
{
* @param g
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
super.paintComponent(g);
if (tree == null)
{
- g.drawString(MessageManager.getString("label.calculating_tree")
- + "....", 20, getHeight() / 2);
+ g.drawString(
+ MessageManager.getString("label.calculating_tree") + "....",
+ 20, getHeight() / 2);
}
else
{
repaint();
}
- if (fitToWindow
- || (!fitToWindow && (scrollPane.getHeight() > ((fm
- .getHeight() * nameHash.size()) + offy))))
+ if (fitToWindow || (!fitToWindow && (scrollPane
+ .getHeight() > ((fm.getHeight() * nameHash.size()) + offy))))
{
draw(g, scrollPane.getWidth(), scrollPane.getHeight());
setPreferredSize(null);
* @param fontSize
* DOCUMENT ME!
*/
+ @Override
public void setFont(Font font)
{
this.font = font;
labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar
- float wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight();
+ double wscale = (width - labelLength - (offx * 2))
+ / tree.getMaxHeight();
SequenceNode top = tree.getTopNode();
g2.setColor(Color.gray);
}
- int x = (int) ((threshold * (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<SequenceNode> 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, getAssociatedPanel().av.getSequenceSetId());
repaint();
}
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
av.setCurrentTree(tree);
if (ob instanceof SequenceNode)
{
highlightNode = (SequenceNode) ob;
- this.setToolTipText("<html>"
- + MessageManager.getString("label.highlightnode"));
+ this.setToolTipText(
+ "<html>" + MessageManager.getString("label.highlightnode"));
repaint();
}
}
}
+ @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();
if (ob instanceof SequenceI)
{
treeSelectionChanged((Sequence) ob);
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
repaint();
av.sendSelection();
return;
threshold = (float) (x - offx)
/ (float) (getWidth() - labelLength - (2 * offx));
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
+ List<SequenceNode> groups = tree.groupNodes(threshold);
setColor(tree.getTopNode(), Color.black);
AlignmentPanel[] aps = getAssociatedPanels();
aps[a].av.getCodingComplement().clearSequenceColours();
}
}
- colourGroups();
+ colourGroups(groups);
+
+ /*
+ * clear partition (don't show vertical line) if
+ * it is to the right of all nodes
+ */
+ if (groups.isEmpty())
+ {
+ threshold = 0f;
+ }
}
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
repaint();
}
}
- void colourGroups()
+ void colourGroups(List<SequenceNode> groups)
{
AlignmentPanel[] aps = getAssociatedPanels();
- for (int i = 0; i < tree.getGroups().size(); i++)
+ for (int i = 0; i < groups.size(); i++)
{
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(groups.get(i), col.brighter());
- Vector l = tree.findLeaves(
- (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+ Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
- Vector sequences = new Vector();
+ Vector<SequenceI> 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))
{
}
else
{
- cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
+ 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);
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);
.getCodingComplement();
if (codingComplement != null)
{
- if (codingComplement != null)
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
+ codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
{
- SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
- av, codingComplement);
- if (mappedGroup.getSequences().size() > 0)
+ codingComplement.getAlignment().addGroup(mappedGroup);
+ for (SequenceI seq : mappedGroup.getSequences())
{
- codingComplement.getAlignment().addGroup(mappedGroup);
- for (SequenceI seq : mappedGroup.getSequences())
- {
- codingComplement.setSequenceColour(seq, col.brighter());
- }
+ codingComplement.setSequenceColour(seq, col.brighter());
}
}
}
{
((AlignViewport) codingComplement).getAlignPanel()
.updateAnnotation();
-
}
-
}
-
}
/**
}
else
{
- return new AlignmentPanel[] { ap };
+ return new AlignmentPanel[] { getAssociatedPanel() };
}
}
+
+ public AlignmentPanel getAssociatedPanel()
+ {
+ return ap;
+ }
+
+ public void setAssociatedPanel(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public float getThreshold()
+ {
+ return threshold;
+ }
+
+ public void setThreshold(float threshold)
+ {
+ this.threshold = threshold;
+ }
}
git://source.jalview.org / jalview.git / blobdiff