X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=954cfcc64f880da7b1e412956c8f5fc3d8a29668;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=4edb580ce8efd36c428db206c5c51549d781f6f7;hpb=d82d17a7ba88f90e6b8b1b591245a7ee70b3975c;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 4edb580..954cfcc 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -47,6 +47,7 @@ import jalview.schemes.UserColourScheme; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.AutoCalcSetting; @@ -56,6 +57,7 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Rectangle; +import java.util.ArrayList; import java.util.Hashtable; import java.util.Iterator; import java.util.List; @@ -77,9 +79,9 @@ public class AlignViewport extends AlignmentViewport boolean antiAlias = false; - private Rectangle explodedGeometry; + private Rectangle explodedGeometry = null; - private String viewName; + private String viewName = null; /* * Flag set true on the view that should 'gather' multiple views of the same @@ -206,25 +208,29 @@ public class AlignViewport extends AlignmentViewport */ private void applyViewProperties() { - antiAlias = Cache.getDefault("ANTI_ALIAS", false); + // BH! using final static strings here because we also use these in + // JS version startup api + // BH was false + antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, true); - viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true)); + viewStyle.setShowJVSuffix( + Cache.getDefault(Preferences.SHOW_JVSUFFIX, true)); setShowAnnotation(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true)); - setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false)); - setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false)); - autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); + setRightAlignIds(Cache.getDefault(Preferences.RIGHT_ALIGN_IDS, false)); + setCentreColumnLabels(Cache.getDefault(Preferences.CENTRE_COLUMN_LABELS, false)); + autoCalculateConsensusAndConservation = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true); - setPadGaps(Cache.getDefault("PAD_GAPS", true)); - setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); - setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); - viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true)); + setPadGaps(Cache.getDefault(Preferences.PAD_GAPS, true)); + setShowNPFeats(Cache.getDefault(Preferences.SHOW_NPFEATS_TOOLTIP, true)); + setShowDBRefs(Cache.getDefault(Preferences.SHOW_DBREFS_TOOLTIP, true)); + viewStyle.setSeqNameItalics(Cache.getDefault(Preferences.ID_ITALICS, true)); viewStyle.setWrapAlignment( Cache.getDefault(Preferences.WRAP_ALIGNMENT, false)); viewStyle.setShowUnconserved( Cache.getDefault(Preferences.SHOW_UNCONSERVED, false)); sortByTree = Cache.getDefault(Preferences.SORT_BY_TREE, false); - followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true); + followSelection = Cache.getDefault(Preferences.FOLLOW_SELECTIONS, true); sortAnnotationsBy = SequenceAnnotationOrder .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, SequenceAnnotationOrder.NONE.name())); @@ -238,9 +244,10 @@ public class AlignViewport extends AlignmentViewport { applyViewProperties(); - String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); - String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); - String fontSize = Cache.getDefault("FONT_SIZE", "10"); + String fontName = Cache.getDefault(Preferences.FONT_NAME, "SansSerif"); + String fontStyle = Cache.getDefault(Preferences.FONT_STYLE, + Font.PLAIN + ""); + String fontSize = Cache.getDefault(Preferences.FONT_SIZE, "10"); int style = 0; @@ -256,7 +263,8 @@ public class AlignViewport extends AlignmentViewport setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true); alignment - .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); + .setGapCharacter(Cache.getDefault(Preferences.GAP_SYMBOL, "-") + .charAt(0)); // We must set conservation and consensus before setting colour, // as Blosum and Clustal require this to be done @@ -264,21 +272,22 @@ public class AlignViewport extends AlignmentViewport { if (!alignment.isNucleotide()) { - showConservation = Cache.getDefault(Preferences.SHOW_CONSERVATION, true); + showConservation = Cache.getDefault(Preferences.SHOW_CONSERVATION, + true); showQuality = Cache.getDefault(Preferences.SHOW_QUALITY, true); - showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", - false); + showGroupConservation = Cache + .getDefault(Preferences.SHOW_GROUP_CONSERVATION, false); } - showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", - true); - showSequenceLogo = Cache.getDefault(Preferences.SHOW_CONSENSUS_LOGO, false); - - normaliseSequenceLogo = Cache.getDefault( - Preferences.NORMALISE_CONSENSUS_LOGO, + showConsensusHistogram = Cache + .getDefault(Preferences.SHOW_CONSENSUS_HISTOGRAM, true); + showSequenceLogo = Cache.getDefault(Preferences.SHOW_CONSENSUS_LOGO, false); + + normaliseSequenceLogo = Cache + .getDefault(Preferences.NORMALISE_CONSENSUS_LOGO, false); showGroupConsensus = Cache .getDefault(Preferences.SHOW_GROUP_CONSENSUS, false); - showConsensus = Cache.getDefault("SHOW_IDENTITY", true); + showConsensus = Cache.getDefault(Preferences.SHOW_IDENTITY, true); showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true); } @@ -387,7 +396,7 @@ public class AlignViewport extends AlignmentViewport */ if (align != null) { - Desktop.getInstance().getStructureSelectionManager() + Desktop.getStructureSelectionManager() .registerMappings(align.getCodonFrames()); } @@ -408,7 +417,7 @@ public class AlignViewport extends AlignmentViewport List mappings = al.getCodonFrames(); if (mappings != null) { - StructureSelectionManager ssm = Desktop.getInstance() + StructureSelectionManager ssm = Desktop .getStructureSelectionManager(); for (AlignedCodonFrame acf : mappings) { @@ -534,7 +543,7 @@ public class AlignViewport extends AlignmentViewport @Override public void sendSelection() { - Desktop.getInstance().getStructureSelectionManager().sendSelection( + Desktop.getStructureSelectionManager().sendSelection( new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), new HiddenColumns(getAlignment().getHiddenColumns()), this); @@ -578,7 +587,7 @@ public class AlignViewport extends AlignmentViewport @Override public StructureSelectionManager getStructureSelectionManager() { - return Desktop.getInstance().getStructureSelectionManager(); + return Desktop.getStructureSelectionManager(); } @Override @@ -769,20 +778,20 @@ public class AlignViewport extends AlignmentViewport MessageManager.getString("label.new_window"), }; final String question = JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.open_split_window?")); - /* * options No, Split Window, New Window correspond to * dialog responses 0, 1, 2 (even though JOptionPane shows them * in reverse order) */ - JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane()) + JvOptionPane dialog = JvOptionPane + .newOptionDialog(Desktop.getDesktopPane()) .setResponseHandler(NO_SPLIT, new Runnable() { @Override public void run() { - addDataToAlignment(al); + addDataToAlignment(al); } }).setResponseHandler(SPLIT_FRAME, new Runnable() { @@ -790,8 +799,8 @@ public class AlignViewport extends AlignmentViewport public void run() { openLinkedAlignmentAs(getAlignPanel().alignFrame, - new Alignment(getAlignment()), al, - title, SPLIT_FRAME); + new Alignment(getAlignment()), al, title, + SPLIT_FRAME); } }).setResponseHandler(NEW_WINDOW, new Runnable() { @@ -816,14 +825,13 @@ public class AlignViewport extends AlignmentViewport * @param mode * SPLIT_FRAME or NEW_WINDOW */ - public static void openLinkedAlignmentAs(AlignFrame thisFrame, AlignmentI thisAlignment, - AlignmentI al, String title, - int mode) + public static void openLinkedAlignmentAs(AlignFrame thisFrame, + 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. - */ + // BH: thisAlignment is already a copy if mode == SPLIT_FRAME + // Identify protein and dna alignments. Make a copy of this one if opening + // in a new split pane. + AlignmentI protein = al.isNucleotide() ? thisAlignment : al; AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; @@ -862,8 +870,7 @@ public class AlignViewport extends AlignmentViewport try { - newAlignFrame.setMaximum( - jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); + newAlignFrame.setMaximum(Cache.getDefault(Preferences.SHOW_FULLSCREEN, false)); } catch (java.beans.PropertyVetoException ex) { } @@ -886,8 +893,7 @@ public class AlignViewport extends AlignmentViewport * @return the protein alignment in the split frame */ static protected AlignmentI openSplitFrame(AlignFrame thisFrame, - AlignFrame newAlignFrame, - AlignmentI complement) + AlignFrame newAlignFrame, AlignmentI complement) { /* * Make a new frame with a copy of the alignment we are adding to. If this @@ -935,10 +941,9 @@ public class AlignViewport extends AlignmentViewport if (ap != null) { // modify GUI elements to reflect geometry change - Dimension idw = getAlignPanel().getIdPanel().getIdCanvas() - .getPreferredSize(); + Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize(); idw.width = i; - getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw); + ap.getIdPanel().getIdCanvas().setPreferredSize(idw); } } @@ -1027,6 +1032,35 @@ public class AlignViewport extends AlignmentViewport @Override public void applyFeaturesStyle(FeatureSettingsModelI featureSettings) { + transferFeaturesStyles(featureSettings, false); + } + + /** + * 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 + */ + @Override + public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings) + { + transferFeaturesStyles(featureSettings, true); + } + + /** + * 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. + * + * @param featureSettings + * @param mergeOnly + */ + private void transferFeaturesStyles(FeatureSettingsModelI featureSettings, + boolean mergeOnly) + { if (featureSettings == null) { return; @@ -1034,12 +1068,24 @@ public class AlignViewport extends AlignmentViewport 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 + origRenderOrder.addAll(fr.getRenderOrder()); + origGroups.addAll(fr.getFeatureGroups()); + fr.findAllFeatures(true); List renderOrder = fr.getRenderOrder(); FeaturesDisplayedI displayed = fr.getFeaturesDisplayed(); + if (!mergeOnly) + { + // only clear displayed features if we are merging displayed.clear(); + } // TODO this clears displayed.featuresRegistered - do we care? - + // + // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where + // feature visibility has already been configured is not very friendly /* * set feature colour if specified by feature settings * set visibility of all features @@ -1048,6 +1094,16 @@ public class AlignViewport extends AlignmentViewport { FeatureColourI preferredColour = featureSettings .getFeatureColour(type); + FeatureColourI origColour = fr.getFeatureStyle(type); + if (!mergeOnly || (!origRenderOrder.contains(type) + || origColour == null + || (!origColour.isGraduatedColour() + && origColour.getColour() != null + && origColour.getColour().equals( + ColorUtils.createColourFromName(type))))) + { + // if we are merging, only update if there wasn't already a colour defined for + // this type if (preferredColour != null) { fr.setColour(type, preferredColour); @@ -1057,13 +1113,19 @@ public class AlignViewport extends AlignmentViewport displayed.setVisible(type); } } + } /* * set visibility of feature groups */ for (String group : fr.getFeatureGroups()) { - fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group)); + if (!mergeOnly || !origGroups.contains(group)) + { + // when merging, display groups only if the aren't already marked as not visible + fr.setGroupVisibility(group, + featureSettings.isGroupDisplayed(group)); + } } /*