X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=7ab84ad1002eb0b5539502807409cf44d71cc7d4;hb=b071bd09ddaa39085176a8bc5baf29c4b2887d5f;hp=5ef256870ebb29804bfbcac19efb46e0d5949db8;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 5ef2568..7ab84ad 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; @@ -71,15 +73,23 @@ 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; 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 @@ -160,7 +170,7 @@ public class AlignViewport extends AlignmentViewport * @param hiddenColumns * @param seqsetid * (may be null) - */ +f */ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns, String seqsetid) { @@ -206,14 +216,14 @@ 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)); 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)); @@ -384,7 +394,7 @@ public class AlignViewport extends AlignmentViewport if (align != null) { StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); ssm.registerMappings(align.getCodonFrames()); } @@ -406,7 +416,7 @@ public class AlignViewport extends AlignmentViewport if (mappings != null) { StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); for (AlignedCodonFrame acf : mappings) { if (noReferencesTo(acf)) @@ -532,7 +542,7 @@ public class AlignViewport extends AlignmentViewport public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + .getStructureSelectionManager(Desktop.getInstance()) .sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), new HiddenColumns(getAlignment().getHiddenColumns()), @@ -578,7 +588,7 @@ public class AlignViewport extends AlignmentViewport public StructureSelectionManager getStructureSelectionManager() { return StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); } @Override @@ -743,8 +753,9 @@ public class AlignViewport extends AlignmentViewport } } - ranges.setEndSeq(getAlignment().getHeight()); - firePropertyChange("alignment", null, getAlignment().getSequences()); + ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18 + notifyAlignment(); + } /** @@ -770,48 +781,55 @@ public class AlignViewport extends AlignmentViewport * dialog responses 0, 1, 2 (even though JOptionPane shows them * in reverse order) */ - JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop) - .setResponseHandler(0, new Runnable() + JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane()) + .setResponseHandler(NO_SPLIT, new Runnable() { @Override public void run() { addDataToAlignment(al); } - }).setResponseHandler(1, new Runnable() + }).setResponseHandler(SPLIT_FRAME, new Runnable() { @Override public void run() { - us.openLinkedAlignmentAs(al, title, true); + openLinkedAlignmentAs(getAlignPanel().alignFrame, + new Alignment(getAlignment()), al, title, + SPLIT_FRAME); +// us.openLinkedAlignmentAs(al, title, true); } - }).setResponseHandler(2, new Runnable() + }).setResponseHandler(NEW_WINDOW, new Runnable() { @Override public void run() { - us.openLinkedAlignmentAs(al, title, false); + openLinkedAlignmentAs(null, getAlignment(), al, title, + NEW_WINDOW); } }); - dialog.showDialog(question, + dialog.showDialog(question, MessageManager.getString("label.open_split_window"), JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, options[0]); } - - protected void openLinkedAlignmentAs(AlignmentI al, String title, - boolean newWindowOrSplitPane) - { + /** + * Open a split frame or a new window + * + * @param al + * @param title + * @param mode + * SPLIT_FRAME or NEW_WINDOW + */ + 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. */ - AlignmentI thisAlignment = newWindowOrSplitPane - ? new Alignment(getAlignment()) - : getAlignment(); AlignmentI protein = al.isNucleotide() ? thisAlignment : al; - final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; - + 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 @@ -839,7 +857,7 @@ public class AlignViewport extends AlignmentViewport // alignFrame.setFileName(file, format); // } - if (!newWindowOrSplitPane) + if (mode == NEW_WINDOW) { Desktop.addInternalFrame(newAlignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -853,10 +871,10 @@ public class AlignViewport extends AlignmentViewport { } - if (newWindowOrSplitPane) + if (mode == SPLIT_FRAME) { al.alignAs(thisAlignment); - protein = openSplitFrame(newAlignFrame, thisAlignment); + openSplitFrame(thisFrame, newAlignFrame, thisAlignment); } } @@ -870,8 +888,8 @@ public class AlignViewport extends AlignmentViewport * cdna/protein complement alignment to show in the other split half * @return the protein alignment in the split frame */ - protected AlignmentI openSplitFrame(AlignFrame newAlignFrame, - AlignmentI complement) + static protected AlignmentI openSplitFrame(AlignFrame thisFrame, + AlignFrame newAlignFrame, AlignmentI complement) { /* * Make a new frame with a copy of the alignment we are adding to. If this @@ -880,7 +898,8 @@ public class AlignViewport extends AlignmentViewport */ AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - copyMe.setTitle(getAlignPanel().alignFrame.getTitle()); + copyMe.setTitle(thisFrame.getTitle()); + AlignmentI al = newAlignFrame.viewport.getAlignment(); final AlignFrame proteinFrame = al.isNucleotide() ? copyMe @@ -919,10 +938,9 @@ 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); } } @@ -1011,19 +1029,60 @@ 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 @@ -1032,13 +1091,24 @@ public class AlignViewport extends AlignmentViewport { FeatureColourI preferredColour = featureSettings .getFeatureColour(type); - if (preferredColour != null) - { - fr.setColour(type, preferredColour); - } - if (featureSettings.isFeatureDisplayed(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 (featureSettings.isFeatureDisplayed(type)) + { + displayed.setVisible(type); + } } } @@ -1047,7 +1117,12 @@ 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)); + } } /* @@ -1073,4 +1148,5 @@ public class AlignViewport extends AlignmentViewport { this.viewName = viewName; } + }