X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=3adb323852803b0658526f327b331e55dc21f895;hb=3609d4b908fa64cab35f2348401baab3347188fc;hp=96fea6ebf2ac66256f1ad2e69c626a7032b3bbbf;hpb=4306800413a28da102c15fe7301bcac7816445fe;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 96fea6e..3adb323 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -35,11 +35,11 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; -import jalview.datamodel.PDBEntry; 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; @@ -48,6 +48,7 @@ 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; @@ -61,7 +62,6 @@ import java.util.ArrayList; import java.util.Hashtable; import java.util.Iterator; import java.util.List; -import java.util.Vector; import javax.swing.JInternalFrame; @@ -80,9 +80,9 @@ public class AlignViewport extends AlignmentViewport boolean antiAlias = false; - private Rectangle explodedGeometry; + private Rectangle explodedGeometry = null; - String viewName; + private String viewName = null; /* * Flag set true on the view that should 'gather' multiple views of the same @@ -95,12 +95,6 @@ public class AlignViewport extends AlignmentViewport private AnnotationColumnChooser annotationColumnSelectionState; - boolean validCharWidth; - - public boolean followSelection = true; - - private Hashtable calcIdParams = new Hashtable<>(); - /** * Creates a new AlignViewport object. * @@ -215,7 +209,7 @@ public class AlignViewport extends AlignmentViewport */ private void applyViewProperties() { - antiAlias = Cache.getDefault("ANTI_ALIAS", false); + antiAlias = Cache.getDefault("ANTI_ALIAS", true); viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true)); setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true)); @@ -263,14 +257,13 @@ public class AlignViewport extends AlignmentViewport setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true); - AlignmentI al = getAlignment(); - al.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 (consensusProfiles == null && !isDataset) + if (hconsensus == null && !isDataset) { - if (!al.isNucleotide()) + if (!alignment.isNucleotide()) { showConservation = Cache.getDefault("SHOW_CONSERVATION", true); showQuality = Cache.getDefault("SHOW_QUALITY", true); @@ -282,6 +275,10 @@ public class AlignViewport extends AlignmentViewport 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); @@ -290,7 +287,7 @@ public class AlignViewport extends AlignmentViewport initAutoAnnotation(); // initInformation(); - String colourProperty = al.isNucleotide() + String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC : Preferences.DEFAULT_COLOUR_PROT; String schemeName = Cache.getProperty(colourProperty); @@ -301,7 +298,7 @@ public class AlignViewport extends AlignmentViewport ResidueColourScheme.NONE); } ColourSchemeI colourScheme = ColourSchemeProperty - .getColourScheme(al, schemeName); + .getColourScheme(this, alignment, schemeName); residueShading = new ResidueShader(colourScheme); if (colourScheme instanceof UserColourScheme) @@ -313,9 +310,12 @@ public class AlignViewport extends AlignmentViewport if (residueShading != null) { - residueShading.setConsensus(consensusProfiles); + residueShading.setConsensus(hconsensus); } + setColourAppliesToAllGroups(true); } + + boolean validCharWidth; /** * {@inheritDoc} @@ -399,9 +399,9 @@ public class AlignViewport extends AlignmentViewport /* * replace mappings on our alignment */ - if (getAlignment() != null && align != null) + if (alignment != null && align != null) { - getAlignment().setCodonFrames(align.getCodonFrames()); + alignment.setCodonFrames(align.getCodonFrames()); } } @@ -470,11 +470,11 @@ public class AlignViewport extends AlignmentViewport } else { - end = getAlignment().getWidth(); + end = alignment.getWidth(); } - return getAlignment().getHiddenColumns().getVisContigsIterator(start, - end, false); + return (alignment.getHiddenColumns().getVisContigsIterator(start, + end, false)); } /** @@ -523,6 +523,8 @@ public class AlignViewport extends AlignmentViewport return false; } + public boolean followSelection = true; + /** * @return true if view selection should always follow the selections * broadcast by other selection sources @@ -587,23 +589,19 @@ public class AlignViewport extends AlignmentViewport return StructureSelectionManager .getStructureSelectionManager(Desktop.instance); } - + @Override public boolean isNormaliseSequenceLogo() { return normaliseSequenceLogo; } - - public void setNormaliseSequenceLogo(boolean state) + @Override +public void setNormaliseSequenceLogo(boolean state) { normaliseSequenceLogo = state; } - public void setNormaliseHMMSequenceLogo(boolean state) - { - normaliseHMMSequenceLogo = state; - } /** * @@ -614,6 +612,8 @@ public class AlignViewport extends AlignmentViewport { return validCharWidth; } + + private Hashtable calcIdParams = new Hashtable<>(); public AutoCalcSetting getCalcIdSettingsFor(String calcId) { @@ -807,7 +807,7 @@ public class AlignViewport extends AlignmentViewport AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); newAlignFrame.setTitle(title); - newAlignFrame.statusBar.setText(MessageManager + newAlignFrame.setStatus(MessageManager .formatMessage("label.successfully_loaded_file", new Object[] { title })); @@ -900,10 +900,9 @@ 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); } } @@ -992,19 +991,60 @@ 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; } - + 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(); - displayed.clear(); + if (!mergeOnly) + { + // only clear displayed features if we are mergeing + 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 @@ -1013,13 +1053,32 @@ public class AlignViewport extends AlignmentViewport { FeatureColourI preferredColour = featureSettings .getFeatureColour(type); - if (preferredColour != null) - { - fr.setColour(type, preferredColour); - } - if (featureSettings.isFeatureDisplayed(type)) + FeatureMatcherSetI preferredFilters = featureSettings + .getFeatureFilters(type); + + FeatureColourI origColour = fr.getFeatureStyle(type); + if (!mergeOnly || (!origRenderOrder.contains(type) + || origColour == null + || (!origColour.isGraduatedColour() + && origColour.getColour() != null + && origColour.getColour().equals( + ColorUtils.createColourFromName(type))))) { - displayed.setVisible(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); + } + if (preferredFilters != null + && (!mergeOnly || fr.getFeatureFilter(type) != null)) + { + fr.setFeatureFilter(type, preferredFilters); + } + if (featureSettings.isFeatureDisplayed(type)) + { + displayed.setVisible(type); + } } } @@ -1028,7 +1087,12 @@ public class AlignViewport extends AlignmentViewport */ 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)); + } } /* @@ -1045,10 +1109,13 @@ public class AlignViewport extends AlignmentViewport fr.setTransparency(featureSettings.getTransparency()); } - @Override - public boolean isNormaliseHMMSequenceLogo() + public String getViewName() { - return normaliseHMMSequenceLogo; + return viewName; } + public void setViewName(String viewName) + { + this.viewName = viewName; + } }