From d8fcaf315395d614059f4345c20ff2f86a4476f1 Mon Sep 17 00:00:00 2001 From: James Procter Date: Fri, 26 May 2023 12:52:58 +0100 Subject: [PATCH] =?utf8?q?JAL-1556=20initial=20implementation=20-=20no=20tes?= =?utf8?q?ts=20as=20yet=20but=20=E2=80=98works=E2=80=99?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/gui/AnnotationColourChooser.java | 79 +++++++++--- src/jalview/gui/AnnotationColumnChooser.java | 23 +++- src/jalview/gui/AnnotationLabels.java | 166 +++++++++++++++++--------- 3 files changed, 195 insertions(+), 73 deletions(-) diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index a0ab709..e582072 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -41,12 +41,14 @@ import javax.swing.JPanel; import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; import jalview.datamodel.GraphLine; import jalview.datamodel.SequenceGroup; import jalview.gui.JalviewColourChooser.ColourChooserListener; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; +import net.bytebuddy.dynamic.DynamicType.Builder.MethodDefinition.ParameterDefinition.Initial; import net.miginfocom.swing.MigLayout; @SuppressWarnings("serial") @@ -72,6 +74,10 @@ public class AnnotationColourChooser extends AnnotationRowFilter public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap) { + this(av,ap,null); + } + public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,AnnotationColourGradient initSettings) + { super(av, ap); oldcs = av.getGlobalColourScheme(); if (av.getAlignment().getGroups() != null) @@ -105,11 +111,28 @@ public class AnnotationColourChooser extends AnnotationRowFilter setDefaultMinMax(); adjusting = true; - if (oldcs instanceof AnnotationColourGradient) + if (oldcs instanceof AnnotationColourGradient && initSettings==null) + { + // init from oldcs + initialiseFrom((AnnotationColourGradient) oldcs); + } else { + // use initial colour gradient - if any.. + initialiseFrom(initSettings); + } + + jbInit(); + adjusting = false; + + updateView(); + frame.invalidate(); + frame.pack(); + } + private void initialiseFrom(AnnotationColourGradient acg) + { + if (acg!=null) { - AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; useOriginalColours.setSelected( - acg.isPredefinedColours() || acg.getBaseColour() != null); + acg.isPredefinedColours() || acg.getBaseColour() != null); if (!acg.isPredefinedColours() && acg.getBaseColour() == null) { minColour.setBackground(acg.getMinColour()); @@ -124,10 +147,14 @@ public class AnnotationColourChooser extends AnnotationRowFilter populateThresholdComboBox(threshold); - if (oldcs instanceof AnnotationColourGradient) + if (acg!=null) { - AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; String label = getAnnotationMenuLabel(acg.getAnnotation()); + // TODO: workaround below shouldn't be necessary - there's a bug in getAnnotationMenuLabel! + if (acg.isSeqAssociated()) + { + label = acg.getAnnotation().label; + } annotations.setSelectedItem(label); switch (acg.getAboveThreshold()) { @@ -147,13 +174,6 @@ public class AnnotationColourChooser extends AnnotationRowFilter thresholdIsMin.setSelected(acg.isThresholdIsMinMax()); thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold())); } - - jbInit(); - adjusting = false; - - updateView(); - frame.invalidate(); - frame.pack(); } @Override @@ -356,9 +376,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter return; } + int selIndex = annotations + .getSelectedIndex(); + int annIndex = annmap[selIndex]; setCurrentAnnotation( - av.getAlignment().getAlignmentAnnotation()[annmap[annotations - .getSelectedIndex()]]); + av.getAlignment().getAlignmentAnnotation()[annIndex]); int selectedThresholdItem = getSelectedThresholdItem( getThreshold().getSelectedIndex()); @@ -447,4 +469,33 @@ public class AnnotationColourChooser extends AnnotationRowFilter super.sliderDragReleased(); ap.paintAlignment(true, true); } + + /** + * construct and display a colourchooser for a given annotation row + * + * @param av + * @param ap + * @param alignmentAnnotation + * @param perseq - when true, enable per-sequence if alignment annotation is per sequence + */ + public static void displayFor(AlignViewport av, AlignmentPanel ap, + AlignmentAnnotation alignmentAnnotation, boolean perSeq) + { + ColourSchemeI global = av.getGlobalColourScheme(); + AnnotationColourGradient newCS = new AnnotationColourGradient(alignmentAnnotation, global, alignmentAnnotation.threshold!=null ? AnnotationColourGradient.ABOVE_THRESHOLD:AnnotationColourGradient.NO_THRESHOLD); + if (alignmentAnnotation.sequenceRef!=null) + { + newCS.setSeqAssociated(perSeq); + } + for (int i=0;i(getAnnotationItems(false))); populateThresholdComboBox(threshold); AnnotationColumnChooser lastChooser = av @@ -134,6 +139,16 @@ public class AnnotationColumnChooser extends AnnotationRowFilter percentThreshold .setSelected(lastChooser.percentThreshold.isSelected()); } + if (selectedAnnotation!=null) + { + try { + setCurrentAnnotation(selectedAnnotation); + annotations.setSelectedItem(getAnnotationMenuLabel(selectedAnnotation)); + } catch (Exception x) + { + Console.error("Couldn't select annotation in column chooser",x); + } + } try { @@ -850,4 +865,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter gSearchPanel.searchBox.updateCache(); ngSearchPanel.searchBox.updateCache(); } + + public static void displayFor(AlignViewport av, AlignmentPanel ap, + AlignmentAnnotation alignmentAnnotation) + { + AnnotationColumnChooser colchooser = new AnnotationColumnChooser(av, ap, alignmentAnnotation); + } } diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index f4c37fd..8930629 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -66,6 +66,7 @@ import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FormatAdapter; import jalview.io.NewickFile; +import jalview.schemes.AnnotationColourGradient; import jalview.util.Comparison; import jalview.util.MessageManager; import jalview.util.Platform; @@ -424,82 +425,131 @@ public class AnnotationLabels extends JPanel consclipbrd.addActionListener(this); pop.add(consclipbrd); } + + addColourOrFilterByOptions(ap,aa[selectedRow],pop); + if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP) { - - final ContactMatrixI cm = av.getContactMatrix(aa[selectedRow]); - if (cm != null) + addContactMatrixOptions(ap,aa[selectedRow],pop); + // Set/adjust threshold for grouping ? + // colour alignment by this [type] + // select/hide columns by this row + + } + } + + pop.show(this, evt.getX(), evt.getY()); + } + + static void addColourOrFilterByOptions(final AlignmentPanel ap, + final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop) + { + JMenuItem item; + item = new JMenuItem(MessageManager.getString("label.colour_by_annotation")); + item.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,false); + }; + }); + pop.add(item); + if (alignmentAnnotation.sequenceRef!=null) + { + item = new JMenuItem(MessageManager.getString("label.colour_by_annotation")+" ("+MessageManager.getString("label.per_seq")+")"); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - pop.addSeparator(); + AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,true); + }; + }); + pop.add(item); + } + item = new JMenuItem(MessageManager.getString("action.select_by_annotation")); + item.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + AnnotationColumnChooser.displayFor(ap.av,ap,alignmentAnnotation); + }; + }); + pop.add(item); + } + static void addContactMatrixOptions(final AlignmentPanel ap, + final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop) + { + + final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation); + JMenuItem item; + if (cm != null) + { + pop.addSeparator(); - if (cm.hasGroups()) - { - JCheckBoxMenuItem chitem = new JCheckBoxMenuItem("Show Groups on Matrix"); - boolean showGroups = aa[selectedRow].isShowGroupsForContactMatrix(); - final AlignmentAnnotation sel_row=aa[selectedRow]; - chitem.setState(showGroups); - chitem.addActionListener(new ActionListener() - { + if (cm.hasGroups()) + { + JCheckBoxMenuItem chitem = new JCheckBoxMenuItem("Show Groups on Matrix"); + boolean showGroups = alignmentAnnotation.isShowGroupsForContactMatrix(); + final AlignmentAnnotation sel_row=alignmentAnnotation; + chitem.setState(showGroups); + chitem.addActionListener(new ActionListener() + { - @Override - public void actionPerformed(ActionEvent e) - { - sel_row.setShowGroupsForContactMatrix(chitem.getState()); - ap.getAnnotationPanel() - .paint(ap.getAnnotationPanel().getGraphics()); - } - }); - pop.add(chitem); - } - if (cm.hasTree()) + @Override + public void actionPerformed(ActionEvent e) { - item = new JMenuItem("Show Tree for Matrix"); - item.addActionListener(new ActionListener() - { + sel_row.setShowGroupsForContactMatrix(chitem.getState()); + ap.getAnnotationPanel() + .paint(ap.getAnnotationPanel().getGraphics()); + } + }); + pop.add(chitem); + } + if (cm.hasTree()) + { + item = new JMenuItem("Show Tree for Matrix"); + item.addActionListener(new ActionListener() + { - @Override - public void actionPerformed(ActionEvent e) - { + @Override + public void actionPerformed(ActionEvent e) + { - ap.alignFrame.showContactMapTree(aa[selectedRow], cm); + ap.alignFrame.showContactMapTree(alignmentAnnotation, cm); - } - }); - pop.add(item); } - else + }); + pop.add(item); + } + else + { + item = new JMenuItem("Calculate Tree for Matrix"); + item.addActionListener(new ActionListener() + { + // TODO - refactor to analysis background thread + @Override + public void actionPerformed(ActionEvent e) { - item = new JMenuItem("Calculate Tree for Matrix"); - item.addActionListener(new ActionListener() + new Thread(new Runnable() { - // TODO - refactor to analysis background thread @Override - public void actionPerformed(ActionEvent e) + public void run() { - new Thread(new Runnable() - { - @Override - public void run() - { - AlignmentAnnotation alan = aa[selectedRow]; - cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true)); - ap.alignFrame.showContactMapTree(alan, cm); - } - }).start(); + AlignmentAnnotation alan = alignmentAnnotation; + cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true)); + ap.alignFrame.showContactMapTree(alan, cm); } - }); - pop.add(item); - + }).start(); } - // Show/Hide group shading on matrix view - // Set/adjust threshold for grouping ? - // colour alignment by this [type] - // select/hide columns by this row - - } + }); + pop.add(item); } } - pop.show(this, evt.getX(), evt.getY()); } /** -- 1.7.10.2