X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=6f143dbb5b54f24342db1cc7c355d17558822b99;hp=fa30e131ec588e81015f96004caf68c98924ac07;hb=20b5e49eaffdbc56b9d0274200a12204e362d5b1;hpb=6f153aac5d457ab69f994d71df1cf30b69d07af5 diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index fa30e13..6f143db 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -20,21 +20,6 @@ */ package jalview.gui; -import jalview.analysis.Conservation; -import jalview.analysis.TreeModel; -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; @@ -51,17 +36,30 @@ 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.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.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! * @@ -80,9 +78,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, TreePanel tp; - AlignViewport av; + private AlignViewport av; - AlignmentPanel ap; + private AlignmentPanel ap; Font font; @@ -100,15 +98,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, int offy; - float threshold; + private float threshold; String longestName; int labelLength = -1; - Hashtable nameHash = new Hashtable(); + Map nameHash = new Hashtable<>(); - Hashtable nodeHash = new Hashtable(); + Map nodeHash = new Hashtable<>(); SequenceNode highlightNode; @@ -130,7 +128,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { this.tp = tp; this.av = ap.av; - this.ap = ap; + this.setAssociatedPanel(ap); font = av.getFont(); scrollPane = scroller; addMouseListener(this); @@ -261,7 +259,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (showDistances && (node.dist > 0)) { - nodeLabel = new Format("%-.2f").form(node.dist); + nodeLabel = new Format("%g").form(node.dist); } if (showBootstrap && node.bootstrap > -1) @@ -349,7 +347,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (showDistances && (node.dist > 0)) { - nodeLabel = new Format("%-.2f").form(node.dist); + nodeLabel = new Format("%g").form(node.dist); } if (showBootstrap && node.bootstrap > -1) @@ -381,31 +379,25 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, */ public Object findElement(int x, int y) { - Enumeration keys = nameHash.keys(); - - while (keys.hasMoreElements()) + for (Entry 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 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(); } } @@ -467,9 +459,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if ((node.left() == null) && (node.right() == null)) { double height = node.height; - double dist = node.dist; - - int xstart = (int) ((height - dist) * wscale) + offx; + // double dist = node.dist; + // int xstart = (int) ((height - dist) * wscale) + offx; int xend = (int) (height * wscale) + offx; int ypos = (int) (node.ycount * chunk) + offy; @@ -512,29 +503,21 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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((SequenceNode) node.left(), c); + setColor((SequenceNode) node.right(), c); } /** @@ -662,13 +645,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { 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)))) + .getHeight() > ((fm.getHeight() * nameCount) + offy)))) { draw(g, scrollPane.getWidth(), scrollPane.getHeight()); setPreferredSize(null); @@ -676,8 +660,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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(); @@ -841,15 +825,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, */ void chooseSubtreeColour() { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_subtree_colour"), - highlightNode.color); - if (col != null) + String ttl = MessageManager.getString("label.select_subtree_colour"); + ColourChooserListener listener = new ColourChooserListener() { - setColor(highlightNode, col); - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); - repaint(); - } + @Override + public void colourSelected(Color c) + { + setColor(highlightNode, c); + PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + repaint(); + } + }; + JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color, + listener); } @Override @@ -928,7 +916,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (ob instanceof SequenceI) { treeSelectionChanged((Sequence) ob); - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + PaintRefresher.Refresh(tp, + getAssociatedPanel().av.getSequenceSetId()); repaint(); av.sendSelection(); return; @@ -960,6 +949,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, .deleteAllGroups(); aps[a].av.getCodingComplement().clearSequenceColours(); } + aps[a].av.setUpdateStructures(true); } colourGroups(groups); @@ -973,7 +963,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } } - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + PaintRefresher.Refresh(tp, + getAssociatedPanel().av.getSequenceSetId()); repaint(); } @@ -1003,76 +994,48 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } ColourSchemeI cs = null; - SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true, + SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true, false, 0, av.getAlignment().getWidth() - 1); - if (av.getGlobalColourScheme() != null) - { - if (av.getGlobalColourScheme() instanceof UserColourScheme) - { - cs = new UserColourScheme( - ((UserColourScheme) av.getGlobalColourScheme()) - .getColours()); - - } - else - { - cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty - .getColourName(av.getGlobalColourScheme())); - } - // cs is null if shading is an annotationColourGradient - // if (cs != null) - // { - // cs.setThreshold(av.getViewportColourScheme().getThreshold(), - // av.isIgnoreGapsConsensus()); - // } - } - sg.setColourScheme(cs); - sg.getGroupColourScheme().setThreshold( - av.getResidueShading().getThreshold(), - av.isIgnoreGapsConsensus()); - // sg.recalcConservation(); - sg.setName("JTreeGroup:" + sg.hashCode()); - sg.setIdColour(col); + _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.getResidueShading().conservationApplied()) - { - 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); - } + SequenceGroup sg = new SequenceGroup(_sg); + AlignViewport viewport = aps[a].av; - 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) + // Propagate group colours in each view + if (viewport.getGlobalColourScheme() != null) { - SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av, - codingComplement); - if (mappedGroup.getSequences().size() > 0) + cs = viewport.getGlobalColourScheme().getInstance(viewport, sg); + sg.setColourScheme(cs); + sg.getGroupColourScheme().setThreshold( + viewport.getResidueShading().getThreshold(), + viewport.isIgnoreGapsConsensus()); + + if (viewport.getResidueShading().conservationApplied()) { - codingComplement.getAlignment().addGroup(mappedGroup); - for (SequenceI seq : mappedGroup.getSequences()) - { - codingComplement.setSequenceColour(seq, col.brighter()); - } + 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); } } - // notify the panel(s) to redo any group specific stuff. + // 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(); - // 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) @@ -1127,7 +1090,47 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } 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; + } }