X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=30ccdbee7e9bd89a2d9d9d812ef018d59c4de5d1;hb=eca4795050a0f7eca3d5dece68eaa54987cebd15;hp=b357734fa932dd41a6f4cdfeac9c6b2c568089af;hpb=3516fc4a1037ffc86d51f900850ed7a04a0174cb;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index b357734f..30ccdbe 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; @@ -47,8 +48,8 @@ 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.util.dialogrunner.RunResponse; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.AutoCalcSetting; @@ -57,8 +58,8 @@ 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; import javax.swing.JInternalFrame; @@ -78,9 +79,9 @@ 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 @@ -123,14 +124,14 @@ 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(); @@ -185,14 +186,14 @@ 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); } if (hiddenColumns != null) @@ -207,7 +208,7 @@ 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)); @@ -290,8 +291,8 @@ public class AlignViewport extends AlignmentViewport schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR, ResidueColourScheme.NONE); } - ColourSchemeI colourScheme = ColourSchemeProperty - .getColourScheme(alignment, schemeName); + ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this, + alignment, schemeName); residueShading = new ResidueShader(colourScheme); if (colourScheme instanceof UserColourScheme) @@ -305,6 +306,7 @@ public class AlignViewport extends AlignmentViewport { residueShading.setConsensus(hconsensus); } + setColourAppliesToAllGroups(true); } boolean validCharWidth; @@ -444,31 +446,6 @@ public class AlignViewport extends AlignmentViewport } /** - * 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 }; @@ -618,7 +595,7 @@ public class AlignViewport extends AlignmentViewport // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass()) if (needsUpdate) { - Cache.log.debug("trigger update for " + calcId); + Console.debug("trigger update for " + calcId); } } @@ -712,14 +689,16 @@ public class AlignViewport extends AlignmentViewport return; } } - alignmentDataAdded(toAdd); + addDataToAlignment(toAdd); } - private void alignmentDataAdded(AlignmentI toAdd) + /** + * adds sequences to this alignment + * + * @param toAdd + */ + void addDataToAlignment(AlignmentI toAdd) { - /* - * No mappings, or offer declined - add sequences to this alignment - */ // TODO: JAL-407 regardless of above - identical sequences (based on ID and // provenance) should share the same dataset sequence @@ -741,7 +720,7 @@ public class AlignViewport extends AlignmentViewport } } - ranges.setEndSeq(getAlignment().getHeight()); + ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18 firePropertyChange("alignment", null, getAlignment().getSequences()); } @@ -762,29 +741,36 @@ public class AlignViewport extends AlignmentViewport final String question = JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.open_split_window?")); final AlignViewport us = this; - JvOptionPane.newOptionDialog(Desktop.desktop) - .response(new RunResponse(1) + + /* + * 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.desktop) + .setResponseHandler(0, new Runnable() { @Override public void run() { - us.openLinkedAlignmentAs(al, title, true); + addDataToAlignment(al); } - }).response(new RunResponse(2) + }).setResponseHandler(1, new Runnable() { @Override public void run() { - us.openLinkedAlignmentAs(al, title, false); + us.openLinkedAlignmentAs(al, title, true); } - }).defaultResponse(new Runnable() + }).setResponseHandler(2, new Runnable() { @Override public void run() { - alignmentDataAdded(al); + us.openLinkedAlignmentAs(al, title, false); } - }).showDialog(question, + }); + dialog.showDialog(question, MessageManager.getString("label.open_split_window"), JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, options[0]); @@ -792,7 +778,7 @@ public class AlignViewport extends AlignmentViewport protected void openLinkedAlignmentAs(AlignmentI al, String title, boolean newWindowOrSplitPane) - { + { /* * Identify protein and dna alignments. Make a copy of this one if opening * in a new split pane. @@ -838,8 +824,7 @@ public class AlignViewport extends AlignmentViewport try { - newAlignFrame.setMaximum( - jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); + newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -910,10 +895,9 @@ 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); } } @@ -1002,6 +986,35 @@ 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; @@ -1009,12 +1022,25 @@ public class AlignViewport extends AlignmentViewport FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas .getFeatureRenderer(); + List origRenderOrder = new ArrayList<>(); + List 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 @@ -1023,13 +1049,29 @@ public class AlignViewport extends AlignmentViewport { FeatureColourI preferredColour = featureSettings .getFeatureColour(type); - if (preferredColour != null) + FeatureColourI origColour = fr.getFeatureStyle(type); + if (!mergeOnly || (!origRenderOrder.contains(type) + || origColour == null + || (!origColour.isGraduatedColour() + && origColour.getColour() != null + && origColour.getColour().equals( + ColorUtils.createColourFromName(type))))) { - fr.setColour(type, preferredColour); - } - if (featureSettings.isFeatureDisplayed(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 (featureSettings.isFeatureDisplayed(type)) + { + displayed.setVisible(type); + } + else if (featureSettings.isFeatureHidden(type)) + { + displayed.setHidden(type); + } } } @@ -1038,7 +1080,13 @@ 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)); + } } /* @@ -1053,5 +1101,17 @@ public class AlignViewport extends AlignmentViewport fr.orderFeatures(featureSettings); } fr.setTransparency(featureSettings.getTransparency()); + + fr.notifyFeaturesChanged(); + } + + public String getViewName() + { + return viewName; + } + + public void setViewName(String viewName) + { + this.viewName = viewName; } }