X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=a43b89b321a5336ed04e91f322338330919ccf80;hb=31714b90648bba773f68736b8c1700ae53805eee;hp=0e93da907699df53f6411d00544ea186cfab5666;hpb=d5702bf3268c2688e90d645ec635ad5bb5d3a76e;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 0e93da9..a43b89b 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -20,6 +20,17 @@ */ package jalview.gui; +import java.awt.Container; +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.List; + +import javax.swing.JInternalFrame; + import jalview.analysis.AlignmentUtils; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.api.AlignViewportI; @@ -29,6 +40,7 @@ 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; @@ -47,21 +59,11 @@ 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; -import java.awt.Container; -import java.awt.Dimension; -import java.awt.Font; -import java.awt.FontMetrics; -import java.awt.Rectangle; -import java.util.Hashtable; -import java.util.Iterator; -import java.util.List; - -import javax.swing.JInternalFrame; - /** * DOCUMENT ME! * @@ -77,9 +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 @@ -122,14 +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(); @@ -184,14 +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) @@ -206,7 +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)); @@ -289,8 +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) @@ -304,6 +306,7 @@ public class AlignViewport extends AlignmentViewport { residueShading.setConsensus(hconsensus); } + setColourAppliesToAllGroups(true); } boolean validCharWidth; @@ -443,30 +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)); - } - - /** * get hash of undo and redo list for the alignment * * @return long[] { historyList.hashCode, redoList.hashCode }; @@ -616,7 +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); } } @@ -706,16 +685,20 @@ public class AlignViewport extends AlignmentViewport { if (AlignmentUtils.isMappable(toAdd, getAlignment())) { - if (openLinkedAlignment(toAdd, title)) - { - return; - } + openLinkedAlignment(toAdd, title); + return; } } + addDataToAlignment(toAdd); + } - /* - * No mappings, or offer declined - add sequences to this alignment - */ + /** + * adds sequences to this alignment + * + * @param toAdd + */ + void addDataToAlignment(AlignmentI toAdd) + { // TODO: JAL-407 regardless of above - identical sequences (based on ID and // provenance) should share the same dataset sequence @@ -737,7 +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()); } @@ -750,30 +733,58 @@ public class AlignViewport extends AlignmentViewport * @param al * @param title */ - protected boolean openLinkedAlignment(AlignmentI al, String title) + protected void openLinkedAlignment(AlignmentI al, String title) { String[] options = new String[] { MessageManager.getString("action.no"), MessageManager.getString("label.split_window"), MessageManager.getString("label.new_window"), }; final String question = JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.open_split_window?")); - int response = JvOptionPane.showOptionDialog(Desktop.desktop, question, + final AlignViewport us = this; + + /* + * 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() + { + addDataToAlignment(al); + } + }).setResponseHandler(1, new Runnable() + { + @Override + public void run() + { + us.openLinkedAlignmentAs(al, title, true); + } + }).setResponseHandler(2, new Runnable() + { + @Override + public void run() + { + us.openLinkedAlignmentAs(al, title, false); + } + }); + dialog.showDialog(question, MessageManager.getString("label.open_split_window"), JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, options[0]); + } - if (response != 1 && response != 2) - { - return false; - } - final boolean openSplitPane = (response == 1); - final boolean openInNewWindow = (response == 2); - + 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. */ - AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment()) + AlignmentI thisAlignment = newWindowOrSplitPane + ? new Alignment(getAlignment()) : getAlignment(); AlignmentI protein = al.isNucleotide() ? thisAlignment : al; final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; @@ -794,7 +805,7 @@ 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 })); @@ -805,7 +816,7 @@ public class AlignViewport extends AlignmentViewport // alignFrame.setFileName(file, format); // } - if (openInNewWindow) + if (!newWindowOrSplitPane) { Desktop.addInternalFrame(newAlignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -813,19 +824,16 @@ 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) { } - if (openSplitPane) + if (newWindowOrSplitPane) { al.alignAs(thisAlignment); protein = openSplitFrame(newAlignFrame, thisAlignment); } - - return true; } /** @@ -887,10 +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); } } @@ -979,6 +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; @@ -986,12 +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 @@ -1000,13 +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); + } } } @@ -1015,7 +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)); + } } /* @@ -1030,5 +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; } }