X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=2d82579c2873f3e218c89a3dcbb40c7e048c684c;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=184944775754cbf8d3cdf53d0de187c00ec02c1e;hpb=564c47bdd60cf84046269e45d2f85f39408e4441;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 1849447..2d82579 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -29,6 +29,7 @@ import jalview.api.FeatureSettingsModelI; import jalview.api.FeaturesDisplayedI; import jalview.api.ViewStyleI; import jalview.bin.Cache; +import jalview.bin.Console; import jalview.commands.CommandI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; @@ -39,6 +40,7 @@ import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.FeatureMatcherSetI; import jalview.renderer.ResidueShader; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; @@ -73,14 +75,11 @@ import javax.swing.JInternalFrame; public class AlignViewport extends AlignmentViewport implements SelectionSource { - public final static int NO_SPLIT = 0; public final static int SPLIT_FRAME = 1; public final static int NEW_WINDOW = 2; - - Font font; boolean cursorMode = false; @@ -132,14 +131,14 @@ public class AlignViewport extends AlignmentViewport sequenceSetID = seqsetid; viewId = viewid; // TODO remove these once 2.4.VAMSAS release finished - if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + if (seqsetid != null) { - Cache.log.debug( + Console.debug( "Setting viewport's sequence set id : " + sequenceSetID); } - if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + if (viewId != null) { - Cache.log.debug("Setting viewport's view id : " + viewId); + Console.debug("Setting viewport's view id : " + viewId); } init(); @@ -170,7 +169,7 @@ public class AlignViewport extends AlignmentViewport * @param hiddenColumns * @param seqsetid * (may be null) -f */ + */ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns, String seqsetid) { @@ -194,14 +193,14 @@ f */ sequenceSetID = seqsetid; viewId = viewid; // TODO remove these once 2.4.VAMSAS release finished - if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + if (seqsetid != null) { - Cache.log.debug( + Console.debug( "Setting viewport's sequence set id : " + sequenceSetID); } - if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + if (viewId != null) { - Cache.log.debug("Setting viewport's view id : " + viewId); + Console.debug("Setting viewport's view id : " + viewId); } if (hiddenColumns != null) @@ -223,7 +222,7 @@ f */ setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false)); setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false)); - autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); + autoCalculateConsensusAndConservation = Cache.getDefault("AUTO_CALC_CONSENSUS", true); setPadGaps(Cache.getDefault("PAD_GAPS", true)); setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); @@ -264,14 +263,13 @@ f */ setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true); - alignment - .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); + alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); // We must set conservation and consensus before setting colour, // as Blosum and Clustal require this to be done - if (hconsensus == null && !isDataset) + if (hconsensus == null && !isDataset) { - if (!alignment.isNucleotide()) + if (!alignment.isNucleotide()) { showConservation = Cache.getDefault("SHOW_CONSERVATION", true); showQuality = Cache.getDefault("SHOW_QUALITY", true); @@ -283,13 +281,19 @@ f */ showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false); + // for now, use consensus options for Information till it gets its own + setShowHMMSequenceLogo(showSequenceLogo); + setNormaliseHMMSequenceLogo(normaliseSequenceLogo); + setShowInformationHistogram(showConsensusHistogram); showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); showConsensus = Cache.getDefault("SHOW_IDENTITY", true); showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true); } initAutoAnnotation(); - String colourProperty = alignment.isNucleotide() + // initInformation(); + + String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC : Preferences.DEFAULT_COLOUR_PROT; String schemeName = Cache.getProperty(colourProperty); @@ -299,8 +303,8 @@ f */ schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR, ResidueColourScheme.NONE); } - ColourSchemeI colourScheme = ColourSchemeProperty - .getColourScheme(this, alignment, schemeName); + ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this, + alignment, schemeName); residueShading = new ResidueShader(colourScheme); if (colourScheme instanceof UserColourScheme) @@ -312,11 +316,12 @@ f */ if (residueShading != null) { - residueShading.setConsensus(hconsensus); + residueShading.setConsensus(hconsensus); } setColourAppliesToAllGroups(true); } + boolean validCharWidth; /** @@ -394,14 +399,14 @@ f */ if (align != null) { StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); ssm.registerMappings(align.getCodonFrames()); } /* * replace mappings on our alignment */ - if (alignment != null && align != null) + if (alignment != null && align != null) { alignment.setCodonFrames(align.getCodonFrames()); } @@ -416,7 +421,7 @@ f */ if (mappings != null) { StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); for (AlignedCodonFrame acf : mappings) { if (noReferencesTo(acf)) @@ -454,31 +459,6 @@ f */ } /** - * returns the visible column regions of the alignment - * - * @param selectedRegionOnly - * true to just return the contigs intersecting with the selected - * area - * @return - */ - public Iterator getViewAsVisibleContigs(boolean selectedRegionOnly) - { - int start = 0; - int end = 0; - if (selectedRegionOnly && selectionGroup != null) - { - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes() + 1; - } - else - { - end = alignment.getWidth(); - } - return (alignment.getHiddenColumns().getVisContigsIterator(start, end, - false)); - } - - /** * get hash of undo and redo list for the alignment * * @return long[] { historyList.hashCode, redoList.hashCode }; @@ -542,7 +522,7 @@ f */ public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + .getStructureSelectionManager(Desktop.getInstance()) .sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), new HiddenColumns(getAlignment().getHiddenColumns()), @@ -588,16 +568,18 @@ f */ public StructureSelectionManager getStructureSelectionManager() { return StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); } + @Override public boolean isNormaliseSequenceLogo() { return normaliseSequenceLogo; } - public void setNormaliseSequenceLogo(boolean state) + @Override +public void setNormaliseSequenceLogo(boolean state) { normaliseSequenceLogo = state; } @@ -612,6 +594,7 @@ f */ return validCharWidth; } + private Hashtable calcIdParams = new Hashtable<>(); public AutoCalcSetting getCalcIdSettingsFor(String calcId) @@ -628,7 +611,7 @@ f */ // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass()) if (needsUpdate) { - Cache.log.debug("trigger update for " + calcId); + Console.debug("trigger update for " + calcId); } } @@ -754,7 +737,7 @@ f */ } ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18 - firePropertyChange("alignment", null, getAlignment().getSequences()); + notifyAlignment(); } /** @@ -780,23 +763,23 @@ f */ * dialog responses 0, 1, 2 (even though JOptionPane shows them * in reverse order) */ - JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop) + JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane()) .setResponseHandler(NO_SPLIT, new Runnable() { @Override public void run() { - addDataToAlignment(al); + addDataToAlignment(al); } }).setResponseHandler(SPLIT_FRAME, new Runnable() { @Override public void run() { + // Make a copy of this one to open it in a splitframe openLinkedAlignmentAs(getAlignPanel().alignFrame, new Alignment(getAlignment()), al, title, SPLIT_FRAME); -// us.openLinkedAlignmentAs(al, title, true); } }).setResponseHandler(NEW_WINDOW, new Runnable() { @@ -812,6 +795,7 @@ f */ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, options[0]); } + /** * Open a split frame or a new window * @@ -824,11 +808,11 @@ f */ AlignmentI thisAlignment, AlignmentI al, String title, int mode) { /* - * Identify protein and dna alignments. Make a copy of this one if opening - * in a new split pane. + * Identify protein and dna alignments. */ AlignmentI protein = al.isNucleotide() ? thisAlignment : al; AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; + /* * Map sequences. At least one should get mapped as we have already passed * the test for 'mappability'. Any mappings made will be added to the @@ -864,8 +848,7 @@ f */ try { - newAlignFrame.setMaximum( - jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); + newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -899,7 +882,6 @@ f */ AlignFrame.DEFAULT_HEIGHT); copyMe.setTitle(thisFrame.getTitle()); - AlignmentI al = newAlignFrame.viewport.getAlignment(); final AlignFrame proteinFrame = al.isNucleotide() ? copyMe : newAlignFrame; @@ -1032,10 +1014,10 @@ f */ } /** - * Applies the supplied feature settings descriptor to currently known features. - * This supports an 'initial configuration' of feature colouring based on a - * preset or user favourite. This may then be modified in the usual way using - * the Feature Settings dialogue. + * Applies the supplied feature settings descriptor to currently known + * features. This supports an 'initial configuration' of feature colouring + * based on a preset or user favourite. This may then be modified in the usual + * way using the Feature Settings dialogue. * * @param featureSettings */ @@ -1048,8 +1030,8 @@ f */ /** * when mergeOnly is set, then group and feature visibility or feature colours * are not modified for features and groups already known to the feature - * renderer. Feature ordering is always adjusted, and transparency is always set - * regardless. + * renderer. Feature ordering is always adjusted, and transparency is always + * set regardless. * * @param featureSettings * @param mergeOnly @@ -1061,12 +1043,12 @@ f */ { return; } - FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas .getFeatureRenderer(); List origRenderOrder = new ArrayList(), origGroups = new ArrayList(); - // preserve original render order - allows differentiation between user configured colours and autogenerated ones + // preserve original render order - allows differentiation between user + // configured colours and autogenerated ones origRenderOrder.addAll(fr.getRenderOrder()); origGroups.addAll(fr.getFeatureGroups()); @@ -1090,6 +1072,8 @@ f */ { FeatureColourI preferredColour = featureSettings .getFeatureColour(type); + FeatureMatcherSetI preferredFilters = featureSettings + .getFeatureFilters(type); FeatureColourI origColour = fr.getFeatureStyle(type); if (!mergeOnly || (!origRenderOrder.contains(type) || origColour == null @@ -1098,16 +1082,26 @@ f */ && origColour.getColour().equals( ColorUtils.createColourFromName(type))))) { - // if we are merging, only update if there wasn't already a colour defined for + // if we are merging, only update if there wasn't already a colour + // defined for // this type if (preferredColour != null) { fr.setColour(type, preferredColour); } + if (preferredFilters != null + && (!mergeOnly || fr.getFeatureFilter(type) != null)) + { + fr.setFeatureFilter(type, preferredFilters); + } if (featureSettings.isFeatureDisplayed(type)) { displayed.setVisible(type); } + else if (featureSettings.isFeatureHidden(type)) + { + displayed.setHidden(type); + } } } @@ -1118,7 +1112,8 @@ f */ { if (!mergeOnly || !origGroups.contains(group)) { - // when merging, display groups only if the aren't already marked as not visible + // when merging, display groups only if the aren't already marked as not + // visible fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group)); } @@ -1136,6 +1131,8 @@ f */ fr.orderFeatures(featureSettings); } fr.setTransparency(featureSettings.getTransparency()); + + fr.notifyFeaturesChanged(); } public String getViewName()