X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=445e967ea5e1e16a5ac809a6f73e8bcee041473f;hb=c437fc72420baf7b045d417fb6cabcebe87987c5;hp=40ab6bbe5693623afdc133f60a2d07c2c6463a8e;hpb=06ce849ffedc7ab10a3c54cda96b9a7dec58c136;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 40ab6bb..445e967 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -86,6 +86,7 @@ import jalview.schemes.ResidueProperties; import jalview.schemes.TCoffeeColourScheme; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.jws1.Discoverer; @@ -160,6 +161,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; + ViewportRanges vpRanges; + public AlignViewControllerI avc; List alignPanels = new ArrayList(); @@ -331,6 +334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBar = new ProgressBar(this.statusPanel, this.statusBar); } + vpRanges = viewport.getRanges(); avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) @@ -640,8 +644,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; - alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq; + alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges + .getStartRes(); + alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges + .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); break; @@ -679,8 +685,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - - viewport.endSeq + viewport.startSeq); + alignPanel.setScrollValues(vpRanges.getStartRes(), + 2 * vpRanges.getStartSeq() - vpRanges.getEndSeq()); } break; case KeyEvent.VK_PAGE_DOWN: @@ -690,8 +696,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - + viewport.endSeq - viewport.startSeq); + alignPanel.setScrollValues(vpRanges.getStartRes(), + vpRanges.getEndSeq()); } break; } @@ -1254,8 +1260,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { FileFormatI format = fileFormat; cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) - .formatSequences(format, - exportData.getAlignment(), + .formatSequences(format, exportData.getAlignment(), exportData.getOmitHidden(), exportData.getStartEndPostions(), viewport.getColumnSelection())); @@ -1846,8 +1851,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } String output = new FormatAdapter().formatSequences(FileFormat.Fasta, - seqs, - omitHidden, null); + seqs, omitHidden, null); StringSelection ss = new StringSelection(output); @@ -2143,7 +2147,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - viewport.setEndSeq(alignment.getHeight()); + vpRanges.setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2547,7 +2551,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); - viewport.setStartRes(0); + vpRanges.setStartRes(0); } else { @@ -2614,13 +2618,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + int startRes = seq.findPosition(vpRanges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - viewport.setStartRes(seq.findIndex(startRes) - 1); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2653,12 +2657,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + int startRes = seq.findPosition(vpRanges.getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); - viewport.setStartRes(seq.findIndex(startRes) - 1); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -3300,11 +3304,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * colour scheme to all groups. If unchecked, groups may have their own * independent colour schemes. * + * @param selected */ @Override - protected void applyToAllGroups_actionPerformed() + public void applyToAllGroups_actionPerformed(boolean selected) { - viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); + viewport.setColourAppliesToAllGroups(selected); } /** @@ -3346,19 +3351,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (cs != null) { ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName()); - // Make sure viewport is up to date w.r.t. any sliders - if (viewport.getAbovePIDThreshold()) - { - int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, - "Background"); - viewport.setThreshold(threshold); - } - - if (viewport.getConservationSelected()) - { - cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, - cs, "Background")); - } } viewport.setGlobalColourScheme(cs); @@ -3367,50 +3359,36 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Show the PID threshold slider panel */ @Override protected void modifyPID_actionPerformed() { - if (viewport.getAbovePIDThreshold() - && viewport.getGlobalColourScheme() != null) - { - SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), "Background"); - SliderPanel.showPIDSlider(); - } + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.showPIDSlider(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Show the Conservation slider panel */ @Override protected void modifyConservation_actionPerformed() { - if (viewport.getConservationSelected() - && viewport.getGlobalColourScheme() != null) - { - SliderPanel.setConservationSlider(alignPanel, - viewport.getGlobalColourScheme(), "Background"); - SliderPanel.showConservationSlider(); - } + SliderPanel.setConservationSlider(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.showConservationSlider(); } /** * Action on selecting or deselecting (Colour) By Conservation */ @Override - protected void conservationMenuItem_actionPerformed() + public void conservationMenuItem_actionPerformed(boolean selected) { - boolean selected = conservationMenuItem.isSelected(); modifyConservation.setEnabled(selected); viewport.setConservationSelected(selected); + viewport.getResidueShading().setConservationApplied(selected); changeColour(viewport.getGlobalColourScheme()); if (selected) @@ -3427,11 +3405,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Action on selecting or deselecting (Colour) Above PID Threshold */ @Override - public void abovePIDThreshold_actionPerformed() + public void abovePIDThreshold_actionPerformed(boolean selected) { - boolean selected = abovePIDThreshold.isSelected(); modifyPID.setEnabled(selected); viewport.setAbovePIDThreshold(selected); + if (!selected) + { + viewport.getResidueShading().setThreshold(0, + viewport.isIgnoreGapsConsensus()); + } changeColour(viewport.getGlobalColourScheme()); if (selected) @@ -4787,8 +4769,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (FileFormat.Jnet.equals(format)) { - JPredFile predictions = new JPredFile( - file, sourceType); + JPredFile predictions = new JPredFile(file, sourceType); new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); @@ -4858,6 +4839,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /* + * 'focus' any colour slider that is open to the selected viewport + */ + if (viewport.getConservationSelected()) + { + SliderPanel.setConservationSlider(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + } + else + { + SliderPanel.hideConservationSlider(); + } + if (viewport.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + } + else + { + SliderPanel.hidePIDSlider(); + } + + /* * If there is a frame linked to this one in a SplitPane, switch it to the * same view tab index. No infinite recursion of calls should happen, since * tabSelectionChanged() should not get invoked on setting the selected @@ -5696,17 +5699,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, colourMenu.add(modifyPID); colourMenu.add(annotationColour); - /* - * select the default colour for the alignment (this may be - * overridden later) - */ - boolean nucleotide = viewport.getAlignment().isNucleotide(); - String defaultColourScheme = Cache.getDefault( - nucleotide ? Preferences.DEFAULT_COLOUR_NUC - : Preferences.DEFAULT_COLOUR_PROT, - ResidueColourScheme.NONE); + ColourSchemeI colourScheme = viewport.getGlobalColourScheme(); + String schemeName = colourScheme == null ? null : colourScheme + .getSchemeName(); - ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme); + ColourMenuHelper.setColourSelected(colourMenu, schemeName); + } + + /** + * Disable inapplicable items in the Select menu when it is clicked + */ + @Override + protected void configureSelectMenu() + { + createGroup.setEnabled(false); + unGroup.setEnabled(false); + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg != null) + { + List groups = viewport.getAlignment().getGroups(); + createGroup.setEnabled(groups == null || !groups.contains(sg)); + unGroup.setEnabled(groups != null && groups.contains(sg)); + } } }