*/
package jalview.gui;
-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.ResidueProperties;
-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.print.Printable;
import java.awt.print.PrinterException;
import java.awt.print.PrinterJob;
-import java.util.Enumeration;
+import java.util.BitSet;
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.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+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!
*
/** 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;
int labelLength = -1;
- Hashtable nameHash = new Hashtable();
+ Map<Object, Rectangle> nameHash = new Hashtable<>();
- Hashtable nodeHash = new Hashtable();
+ Map<BinaryNode, Rectangle> nodeHash = new Hashtable<>();
- SequenceNode highlightNode;
+ BinaryNode highlightNode;
boolean applyToAllViews = false;
{
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<BinaryNode> leaves = tree.findLeaves(tree.getTopNode());
boolean has_placeholders = false;
longestName = "";
for (int i = 0; i < leaves.size(); i++)
{
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+ BinaryNode lf = leaves.elementAt(i);
- if (lf.isPlaceholder())
+ if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder())
{
has_placeholders = true;
}
* DOCUMENT ME!
* @param chunk
* DOCUMENT ME!
- * @param scale
+ * @param wscale
* DOCUMENT ME!
* @param width
* DOCUMENT ME!
* @param offy
* DOCUMENT ME!
*/
- public void drawNode(Graphics g, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
+ public void drawNode(Graphics g, BinaryNode node, float chunk,
+ 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;
if (showDistances && (node.dist > 0))
{
- nodeLabel = new Format("%-.2f").form(node.dist);
+ nodeLabel = new Format("%g").form(node.dist);
}
if (showBootstrap && node.bootstrap > -1)
g.drawString(nodeLabel, xstart + 2, ypos - 2);
}
- String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
- .getName()) : node.getName();
+ String name = (markPlaceholders && ((node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder())))
+ ? (PLACEHOLDER + node.getName())
+ : node.getName();
int charWidth = fm.stringWidth(name) + 3;
int charHeight = font.getSize();
nameHash.put(node.element(), rect);
// Colour selected leaves differently
- SequenceGroup selected = av.getSelectionGroup();
+ boolean isSelected = false;
+ if (tp.getColumnWise())
+ {
+ isSelected = isColumnForNodeSelected(node);
+ }
+ else
+ {
+ SequenceGroup selected = av.getSelectionGroup();
- if ((selected != null)
- && selected.getSequences(null).contains(node.element()))
+ if ((selected != null)
+ && selected.getSequences(null).contains(node.element()))
+ {
+ isSelected = true;
+ }
+ }
+ if (isSelected)
{
g.setColor(Color.gray);
}
else
{
- drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
+ drawNode(g, (BinaryNode) node.left(), chunk, wscale, width, offx,
offy);
- drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
+ drawNode(g, (BinaryNode) 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) (((BinaryNode) node.left()).ycount * chunk)) + offy;
+ int yend = (node.right() == null ? 0
+ : (int) (((BinaryNode) 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 = "";
if (showDistances && (node.dist > 0))
{
- nodeLabel = new Format("%-.2f").form(node.dist);
+ nodeLabel = new Format("%g").form(node.dist);
}
if (showBootstrap && node.bootstrap > -1)
*/
public Object findElement(int x, int y)
{
- Enumeration keys = nameHash.keys();
-
- while (keys.hasMoreElements())
+ for (Entry<Object, Rectangle> 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<BinaryNode, Rectangle> 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();
}
}
int width = getWidth();
int height = getHeight();
- SequenceNode top = tree.getTopNode();
+ BinaryNode top = tree.getTopNode();
- float wscale = (float) ((width * .8) - (offx * 2))
- / tree.getMaxHeight();
+ 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;
* DOCUMENT ME!
* @param chunk
* DOCUMENT ME!
- * @param scale
+ * @param wscale
* DOCUMENT ME!
* @param width
* DOCUMENT ME!
* @param offy
* DOCUMENT ME!
*/
- public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
+ public void pickNode(Rectangle pickBox, BinaryNode node, float chunk,
+ 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;
-
- int xstart = (int) ((height - dist) * scale) + offx;
- int xend = (int) (height * scale) + offx;
+ double height = node.height;
+ // double dist = node.dist;
+ // 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, (BinaryNode) node.left(), chunk, wscale, width,
offx, offy);
- pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
+ pickNode(pickBox, (BinaryNode) node.right(), chunk, wscale, width,
offx, offy);
}
}
* @param c
* DOCUMENT ME!
*/
- public void setColor(SequenceNode node, Color c)
+ public void setColor(BinaryNode node, Color c)
{
if (node == null)
{
return;
}
- if ((node.left() == null) && (node.right() == null)) // TODO: internal node
+ node.color = c;
+ if (node.element() instanceof SequenceI)
{
- node.color = c;
-
- if (node.element() instanceof SequenceI)
+ final SequenceI seq = (SequenceI) node.element();
+ AlignmentPanel[] aps = getAssociatedPanels();
+ if (aps != null)
{
- AlignmentPanel[] aps = getAssociatedPanels();
- if (aps != null)
+ for (int a = 0; a < aps.length; a++)
{
- for (int a = 0; a < aps.length; a++)
- {
- final SequenceI seq = (SequenceI) node.element();
- aps[a].av.setSequenceColour(seq, c);
- }
+ aps[a].av.setSequenceColour(seq, c);
}
}
}
- else
- {
- node.color = c;
- setColor((SequenceNode) node.left(), c);
- setColor((SequenceNode) node.right(), c);
- }
+ setColor((BinaryNode) node.left(), c);
+ setColor((BinaryNode) node.right(), c);
}
/**
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);
if (tree == null)
{
- g.drawString(MessageManager.getString("label.calculating_tree")
- + "....", 20, getHeight() / 2);
+ g.drawString(
+ MessageManager.getString("label.calculating_tree") + "....",
+ 20, getHeight() / 2);
}
else
{
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))))
+ if (fitToWindow || (!fitToWindow && (scrollPane
+ .getHeight() > ((fm.getHeight() * nameCount) + offy))))
{
draw(g, scrollPane.getWidth(), scrollPane.getHeight());
setPreferredSize(null);
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();
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();
+ 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;
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 (evt.isPopupTrigger())
+ return;
+ }
+
+ if (evt.getClickCount() > 1)
+ {
+ tree.swapNodes(highlightNode);
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ }
+ else
+ {
+ Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
+ if (tp.getColumnWise()) {
+ markColumnsFor(getAssociatedPanels(), leaves, Color.red);
+ } else {
+ for (int i = 0; i < leaves.size(); i++)
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_subtree_colour"),
- highlightNode.color);
- if (col != null)
- {
- setColor(highlightNode, col);
- }
+ SequenceI seq = (SequenceI) leaves.elementAt(i).element();
+ treeSelectionChanged(seq);
}
- else if (evt.getClickCount() > 1)
- {
- tree.swapNodes(highlightNode);
- tree.reCount(tree.getTopNode());
- tree.findHeight(tree.getTopNode());
}
- 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());
- repaint();
- }
+ /**
+ * 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()
+ {
+ String ttl = MessageManager.getString("label.select_subtree_colour");
+ ColourChooserListener listener = new ColourChooserListener()
+ {
+ @Override
+ public void colourSelected(Color c)
+ {
+ setColor(highlightNode, c);
+ PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ repaint();
+ }
+ };
+ JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color,
+ listener);
}
@Override
Object ob = findElement(evt.getX(), evt.getY());
- if (ob instanceof SequenceNode)
+ if (ob instanceof BinaryNode)
{
- highlightNode = (SequenceNode) ob;
- this.setToolTipText("<html>"
- + MessageManager.getString("label.highlightnode"));
+ highlightNode = (BinaryNode) ob;
+ this.setToolTipText(
+ "<html>" + MessageManager.getString("label.highlightnode"));
repaint();
}
}
/**
- * 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;
}
- else if (!(ob instanceof SequenceNode))
+ else if (!(ob instanceof BinaryNode))
{
// Find threshold
if (tree.getMaxHeight() != 0)
threshold = (float) (x - offx)
/ (float) (getWidth() - labelLength - (2 * offx));
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
+ List<BinaryNode> groups = tree.groupNodes(threshold);
setColor(tree.getTopNode(), Color.black);
AlignmentPanel[] aps = getAssociatedPanels();
.deleteAllGroups();
aps[a].av.getCodingComplement().clearSequenceColours();
}
+ aps[a].av.setUpdateStructures(true);
+ }
+ colourGroups(groups);
+
+ /*
+ * clear partition (don't show vertical line) if
+ * it is to the right of all nodes
+ */
+ if (groups.isEmpty())
+ {
+ threshold = 0f;
}
- colourGroups();
}
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+ PaintRefresher.Refresh(tp,
+ getAssociatedPanel().av.getSequenceSetId());
repaint();
}
}
- void colourGroups()
+ void colourGroups(List<BinaryNode> 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());
-
- Vector l = tree.findLeaves(
- (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+ setColor(groups.get(i), col.brighter());
- Vector sequences = new Vector();
+ Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
+ if (!tp.getColumnWise()) {
+ createSeqGroupFor(aps, l, col);
+ } else {
+ markColumnsFor(aps,l,col);
+ }
+ }
- for (int j = 0; j < l.size(); j++)
+ // notify the panel(s) to redo any group specific stuff
+ // also updates structure views if necessary
+ for (int a = 0; a < aps.length; a++)
+ {
+ aps[a].updateAnnotation();
+ final AlignViewportI codingComplement = aps[a].av
+ .getCodingComplement();
+ if (codingComplement != null)
{
- SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
- .element();
-
- if (!sequences.contains(s1))
- {
- sequences.addElement(s1);
- }
+ ((AlignViewport) codingComplement).getAlignPanel()
+ .updateAnnotation();
}
+ }
+ }
- ColourSchemeI cs = null;
- SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
- false, 0, av.getAlignment().getWidth() - 1);
+ private boolean isColumnForNodeSelected(BinaryNode bn)
+ {
+ SequenceI rseq = tp.assocAnnotation.sequenceRef;
+ int colm = -1;
+ try
+ {
+ colm = Integer.parseInt(
+ bn.getName().substring(bn.getName().indexOf("c") + 1));
+ } catch (Exception e)
+ {
+ return false;
+ }
+ ColumnSelection cs = av.getColumnSelection();
+ HiddenColumns hc = av.getAlignment().getHiddenColumns();
+ int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() - 1 + colm)
+ : colm;
- if (av.getGlobalColourScheme() != null)
- {
- if (av.getGlobalColourScheme() instanceof UserColourScheme)
- {
- cs = new UserColourScheme(
- ((UserColourScheme) av.getGlobalColourScheme())
- .getColours());
+ if (!av.hasHiddenColumns() || hc.isVisible(offp))
+ {
+ return cs.contains(offp);
+ }
+ return false;
+ }
- }
- else
- {
- cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
- .getColourName(av.getGlobalColourScheme()));
- }
- // cs is null if shading is an annotationColourGradient
- if (cs != null)
- {
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
- av.isIgnoreGapsConsensus());
- }
+ private void markColumnsFor(AlignmentPanel[] aps, Vector<BinaryNode> l,
+ Color col)
+ {
+ SequenceI rseq = tp.assocAnnotation.sequenceRef;
+ for (BinaryNode bn:l)
+ {
+ int colm=-1;
+ try {
+ colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1));
+ } catch (Exception e)
+ {
+ continue;
}
- sg.cs = cs;
- // sg.recalcConservation();
- sg.setName("JTreeGroup:" + sg.hashCode());
- sg.setIdColour(col);
-
- for (int a = 0; a < aps.length; a++)
+ ColumnSelection cs = av.getColumnSelection();
+ HiddenColumns hc = av.getAlignment().getHiddenColumns();
{
- if (aps[a].av.getGlobalColourScheme() != null
- && aps[a].av.getGlobalColourScheme().conservationApplied())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, 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)
- {
- if (codingComplement != null)
+ int offp = (rseq!=null) ? rseq.findIndex(rseq.getStart()-1+colm) : colm;
+
+ if (!av.hasHiddenColumns() || hc.isVisible(offp))
+ {
+ if (cs.contains(offp))
{
- 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());
- }
- }
+ cs.removeElement(offp);
+ } else {
+ cs.addElement(offp);
}
}
}
+ }
+ }
+
+ public void createSeqGroupFor(AlignmentPanel[] aps, Vector<BinaryNode> l,
+ Color col)
+ {
+
+ Vector<SequenceI> sequences = new Vector<>();
+
+ for (int j = 0; j < l.size(); j++)
+ {
+ SequenceI s1 = (SequenceI) l.elementAt(j).element();
+
+ if (!sequences.contains(s1))
+ {
+ sequences.addElement(s1);
+ }
}
- // notify the panel(s) to redo any group specific stuff.
+ ColourSchemeI cs = null;
+ SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true,
+ false, 0, av.getAlignment().getWidth() - 1);
+
+ _sg.setName("JTreeGroup:" + _sg.hashCode());
+ _sg.setIdColour(col);
+
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)
+ SequenceGroup sg = new SequenceGroup(_sg);
+ AlignViewport viewport = aps[a].av;
+
+ // Propagate group colours in each view
+ if (viewport.getGlobalColourScheme() != null)
{
- ((AlignViewport) codingComplement).getAlignPanel()
- .updateAnnotation();
+ cs = viewport.getGlobalColourScheme().getInstance(viewport, sg);
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setThreshold(
+ viewport.getResidueShading().getThreshold(),
+ viewport.isIgnoreGapsConsensus());
+ if (viewport.getResidueShading().conservationApplied())
+ {
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
+ c.calculate();
+ c.verdict(false, viewport.getConsPercGaps());
+ sg.cs.setConservation(c);
+ }
}
-
+ // indicate that associated structure views will need an update
+ viewport.setUpdateStructures(true);
+ // propagate structure view update and sequence group to complement view
+ viewport.addSequenceGroup(sg);
}
-
}
/**
}
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;
+ }
+
+ public boolean isApplyToAllViews()
+ {
+ return this.applyToAllViews;
+ }
+
+ public void setApplyToAllViews(boolean applyToAllViews)
+ {
+ this.applyToAllViews = applyToAllViews;
+ }
}
git://source.jalview.org / jalview.git / blobdiff