From c2e6335a319d61b641fb6fcbb0a4a5dc88a58014 Mon Sep 17 00:00:00 2001 From: James Procter Date: Mon, 27 Feb 2023 17:27:44 +0000 Subject: [PATCH] JAL-4134 display tree for columns - selecting an internal node selects column in alignment --- src/jalview/gui/AlignFrame.java | 37 +++++++++ src/jalview/gui/AnnotationLabels.java | 31 +++++++ src/jalview/gui/TreeCanvas.java | 142 ++++++++++++++++++++++----------- src/jalview/gui/TreePanel.java | 25 ++++++ 4 files changed, 187 insertions(+), 48 deletions(-) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 7b310b1..82ec1d2 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -155,6 +155,7 @@ import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -4131,6 +4132,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return showNewickTree(nf, treeTitle, null, w, h, x, y); } + /** * Add a treeviewer for the tree extracted from a Newick file object to the * current alignment view @@ -4181,6 +4183,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } + + public void showContactMapTree(AlignmentAnnotation aa, + PAEContactMatrix cm) + { + int x = 4, y = 5; + int w = 400, h = 500; + try + { + NewickFile fin = new NewickFile( + new FileParse(cm.getNewickString(), DataSourceType.PASTE)); + fin.parse(); + if (fin.getTree() == null) + { + return; + } + String title = "PAE Matrix Tree for " + + cm.getReferenceSeq().getDisplayId(false); + TreePanel tp = new TreePanel(alignPanel, fin, aa, title); + + tp.setSize(w, h); + + if (x > 0 && y > 0) + { + tp.setLocation(x, y); + } + + Desktop.addInternalFrame(tp, title, w, h); + } catch (Throwable xx) + { + Console.error("Unexpected exception showing tree for contact matrix", + xx); + } + + } private boolean buildingMenu = false; /** @@ -5930,6 +5966,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return lastFeatureSettingsBounds; } + } class PrintThread extends Thread diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 804ab7b..c01a6f3 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -36,6 +36,7 @@ import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.AffineTransform; +import java.io.IOException; import java.util.Arrays; import java.util.Collections; import java.util.Iterator; @@ -50,18 +51,23 @@ import javax.swing.ToolTipManager; import jalview.analysis.AlignSeq; import jalview.analysis.AlignmentUtils; +import jalview.bin.Console; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FormatAdapter; +import jalview.io.NewickFile; import jalview.util.Comparison; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; /** * The panel that holds the labels for alignment annotations, providing @@ -416,6 +422,31 @@ public class AnnotationLabels extends JPanel consclipbrd.addActionListener(this); pop.add(consclipbrd); } + if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP + && PAEContactMatrix.PAEMATRIX + .equals(aa[selectedRow].getCalcId())) + { + final PAEContactMatrix cm = (PAEContactMatrix) av + .getContactMatrix(aa[selectedRow]); + if (cm.getNewickString()!=null && cm.getNewickString().length()>0) + { + item = new JMenuItem("Show Matrix"); + item.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + + ap.alignFrame.showContactMapTree(aa[selectedRow],cm); + + } + }); + pop.addSeparator(); + pop.add(item); + } + + } } pop.show(this, evt.getX(), evt.getY()); } diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index a1bcebd..b8bcc74 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -36,6 +36,7 @@ import java.awt.print.PageFormat; import java.awt.print.Printable; import java.awt.print.PrinterException; import java.awt.print.PrinterJob; +import java.util.BitSet; import java.util.Hashtable; import java.util.List; import java.util.Map; @@ -51,6 +52,8 @@ 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; @@ -806,12 +809,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, else { Vector leaves = tree.findLeaves(highlightNode); - + if (tp.getColumnWise()) { + markColumnsFor(getAssociatedPanels(), leaves, Color.red); + } else { for (int i = 0; i < leaves.size(); i++) { SequenceI seq = (SequenceI) leaves.elementAt(i).element(); treeSelectionChanged(seq); } + } av.sendSelection(); } @@ -981,69 +987,109 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, setColor(groups.get(i), col.brighter()); Vector l = tree.findLeaves(groups.get(i)); + if (!tp.getColumnWise()) { + createSeqGroupFor(aps, l, col); + } else { + markColumnsFor(aps,l,col); + } + } - Vector sequences = new Vector<>(); - - 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) l.elementAt(j).element(); + ((AlignViewport) codingComplement).getAlignPanel() + .updateAnnotation(); + } + } + } - if (!sequences.contains(s1)) - { - sequences.addElement(s1); + private void markColumnsFor(AlignmentPanel[] aps, Vector 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; + } + ColumnSelection cs = av.getColumnSelection(); + HiddenColumns hc = av.getAlignment().getHiddenColumns(); + { + int offp = (rseq!=null) ? rseq.findIndex(rseq.getStart()-1+colm) : colm; + + if (!av.hasHiddenColumns() || hc.isVisible(offp)) + { + if (cs.contains(offp)) + { + cs.removeElement(offp); + } else { + cs.addElement(offp); + } } } + } + } - ColourSchemeI cs = null; - SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true, - false, 0, av.getAlignment().getWidth() - 1); + public void createSeqGroupFor(AlignmentPanel[] aps, Vector l, + Color col) + { - _sg.setName("JTreeGroup:" + _sg.hashCode()); - _sg.setIdColour(col); + Vector sequences = new Vector<>(); - for (int a = 0; a < aps.length; a++) - { - SequenceGroup sg = new SequenceGroup(_sg); - AlignViewport viewport = aps[a].av; - - // Propagate group colours in each view - if (viewport.getGlobalColourScheme() != null) - { - cs = viewport.getGlobalColourScheme().getInstance(viewport, sg); - sg.setColourScheme(cs); - sg.getGroupColourScheme().setThreshold( - viewport.getResidueShading().getThreshold(), - viewport.isIgnoreGapsConsensus()); + for (int j = 0; j < l.size(); j++) + { + SequenceI s1 = (SequenceI) l.elementAt(j).element(); - 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); + if (!sequences.contains(s1)) + { + sequences.addElement(s1); } } - // notify the panel(s) to redo any group specific stuff - // also updates structure views if necessary + 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(); - 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); } } diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 9a4f2c4..6a07a4e 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -53,6 +53,7 @@ import jalview.bin.Console; import jalview.commands.CommandI; import jalview.commands.OrderCommand; import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.BinaryNode; @@ -123,6 +124,30 @@ public class TreePanel extends GTreePanel initTreePanel(alignPanel, null, null, newtree, inputData); } + /** + * columnwise tree associated with positions in aa + * + * @param alignPanel + * @param fin + * @param title + * @param aa + */ + public TreePanel(AlignmentPanel alignPanel, NewickFile fin, + AlignmentAnnotation aa, String title) + { + this(alignPanel, fin, title, null); + columnWise=true; + assocAnnotation = aa; + + + } + boolean columnWise=false; + AlignmentAnnotation assocAnnotation=null; + public boolean getColumnWise() + { + return columnWise; + } + public AlignmentI getAlignment() { return getTreeCanvas().getViewport().getAlignment(); -- 1.7.10.2