X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=2d82579c2873f3e218c89a3dcbb40c7e048c684c;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=ba7aad4fe443b6f54d06e907f7779213ca998438;hpb=4f9cb2ca5ee0d5556c44b223b0cc87334c7df74a;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index ba7aad4..2d82579 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; @@ -39,6 +40,7 @@ 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; @@ -59,6 +61,7 @@ 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; @@ -72,6 +75,11 @@ 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; @@ -123,14 +131,14 @@ 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 +193,14 @@ 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) @@ -214,7 +222,7 @@ public class AlignViewport extends AlignmentViewport 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)); @@ -255,14 +263,13 @@ public class AlignViewport extends AlignmentViewport setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true); - alignment - .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 (hconsensus == null && !isDataset) + if (hconsensus == null && !isDataset) { - if (!alignment.isNucleotide()) + if (!alignment.isNucleotide()) { showConservation = Cache.getDefault("SHOW_CONSERVATION", true); showQuality = Cache.getDefault("SHOW_QUALITY", true); @@ -274,13 +281,19 @@ 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); showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true); } initAutoAnnotation(); - String colourProperty = alignment.isNucleotide() + // initInformation(); + + String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC : Preferences.DEFAULT_COLOUR_PROT; String schemeName = Cache.getProperty(colourProperty); @@ -290,8 +303,8 @@ public class AlignViewport extends AlignmentViewport schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR, ResidueColourScheme.NONE); } - ColourSchemeI colourScheme = ColourSchemeProperty - .getColourScheme(this, alignment, schemeName); + ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this, + alignment, schemeName); residueShading = new ResidueShader(colourScheme); if (colourScheme instanceof UserColourScheme) @@ -303,11 +316,12 @@ public class AlignViewport extends AlignmentViewport if (residueShading != null) { - residueShading.setConsensus(hconsensus); + residueShading.setConsensus(hconsensus); } setColourAppliesToAllGroups(true); } + boolean validCharWidth; /** @@ -385,14 +399,14 @@ public class AlignViewport extends AlignmentViewport if (align != null) { StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); ssm.registerMappings(align.getCodonFrames()); } /* * replace mappings on our alignment */ - if (alignment != null && align != null) + if (alignment != null && align != null) { alignment.setCodonFrames(align.getCodonFrames()); } @@ -407,7 +421,7 @@ public class AlignViewport extends AlignmentViewport if (mappings != null) { StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); for (AlignedCodonFrame acf : mappings) { if (noReferencesTo(acf)) @@ -508,7 +522,7 @@ 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()), @@ -554,16 +568,18 @@ public class AlignViewport extends AlignmentViewport public StructureSelectionManager getStructureSelectionManager() { return StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); } + @Override public boolean isNormaliseSequenceLogo() { return normaliseSequenceLogo; } - public void setNormaliseSequenceLogo(boolean state) + @Override +public void setNormaliseSequenceLogo(boolean state) { normaliseSequenceLogo = state; } @@ -578,6 +594,7 @@ public class AlignViewport extends AlignmentViewport return validCharWidth; } + private Hashtable calcIdParams = new Hashtable<>(); public AutoCalcSetting getCalcIdSettingsFor(String calcId) @@ -594,7 +611,7 @@ public class AlignViewport extends AlignmentViewport // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass()) if (needsUpdate) { - Cache.log.debug("trigger update for " + calcId); + Console.debug("trigger update for " + calcId); } } @@ -684,16 +701,20 @@ 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 @@ -715,8 +736,8 @@ public class AlignViewport extends AlignmentViewport } } - ranges.setEndSeq(getAlignment().getHeight()); - firePropertyChange("alignment", null, getAlignment().getSequences()); + ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18 + notifyAlignment(); } /** @@ -728,33 +749,69 @@ 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.getDesktopPane()) + .setResponseHandler(NO_SPLIT, new Runnable() + { + @Override + public void run() + { + addDataToAlignment(al); + } + }).setResponseHandler(SPLIT_FRAME, new Runnable() + { + @Override + public void run() + { + // Make a copy of this one to open it in a splitframe + openLinkedAlignmentAs(getAlignPanel().alignFrame, + new Alignment(getAlignment()), al, title, + SPLIT_FRAME); + } + }).setResponseHandler(NEW_WINDOW, new Runnable() + { + @Override + public void run() + { + openLinkedAlignmentAs(null, getAlignment(), al, title, + NEW_WINDOW); + } + }); + 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); - + /** + * 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. + * Identify protein and dna alignments. */ - AlignmentI thisAlignment = openSplitPane ? 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 @@ -783,7 +840,7 @@ public class AlignViewport extends AlignmentViewport // alignFrame.setFileName(file, format); // } - if (openInNewWindow) + if (mode == NEW_WINDOW) { Desktop.addInternalFrame(newAlignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -791,19 +848,16 @@ 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 (mode == SPLIT_FRAME) { al.alignAs(thisAlignment); - protein = openSplitFrame(newAlignFrame, thisAlignment); + openSplitFrame(thisFrame, newAlignFrame, thisAlignment); } - - return true; } /** @@ -816,8 +870,8 @@ 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 @@ -826,7 +880,7 @@ 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 @@ -960,10 +1014,10 @@ public class AlignViewport extends AlignmentViewport } /** - * 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. + * 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 */ @@ -976,8 +1030,8 @@ public class AlignViewport extends AlignmentViewport /** * 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. + * renderer. Feature ordering is always adjusted, and transparency is always + * set regardless. * * @param featureSettings * @param mergeOnly @@ -989,12 +1043,12 @@ public class AlignViewport extends AlignmentViewport { 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 + // preserve original render order - allows differentiation between user + // configured colours and autogenerated ones origRenderOrder.addAll(fr.getRenderOrder()); origGroups.addAll(fr.getFeatureGroups()); @@ -1018,6 +1072,8 @@ public class AlignViewport extends AlignmentViewport { FeatureColourI preferredColour = featureSettings .getFeatureColour(type); + FeatureMatcherSetI preferredFilters = featureSettings + .getFeatureFilters(type); FeatureColourI origColour = fr.getFeatureStyle(type); if (!mergeOnly || (!origRenderOrder.contains(type) || origColour == null @@ -1026,16 +1082,26 @@ public class AlignViewport extends AlignmentViewport && origColour.getColour().equals( ColorUtils.createColourFromName(type))))) { - // if we are merging, only update if there wasn't already a colour defined for + // 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); } + else if (featureSettings.isFeatureHidden(type)) + { + displayed.setHidden(type); + } } } @@ -1046,7 +1112,8 @@ public class AlignViewport extends AlignmentViewport { if (!mergeOnly || !origGroups.contains(group)) { - // when merging, display groups only if the aren't already marked as not visible + // when merging, display groups only if the aren't already marked as not + // visible fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group)); } @@ -1064,6 +1131,8 @@ public class AlignViewport extends AlignmentViewport fr.orderFeatures(featureSettings); } fr.setTransparency(featureSettings.getTransparency()); + + fr.notifyFeaturesChanged(); } public String getViewName()