X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=2d82579c2873f3e218c89a3dcbb40c7e048c684c;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=30ccdbee7e9bd89a2d9d9d812ef018d59c4de5d1;hpb=04c8f7bff663aa469127e9eed4164e02933782f1;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 30ccdbe..2d82579 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -40,6 +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; @@ -60,6 +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; @@ -73,6 +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; @@ -215,7 +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)); @@ -256,14 +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); @@ -275,13 +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); @@ -304,11 +316,12 @@ public class AlignViewport extends AlignmentViewport if (residueShading != null) { - residueShading.setConsensus(hconsensus); + residueShading.setConsensus(hconsensus); } setColourAppliesToAllGroups(true); } + boolean validCharWidth; /** @@ -386,14 +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()); } @@ -408,7 +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)) @@ -509,7 +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()), @@ -555,16 +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; } @@ -579,6 +594,7 @@ public class AlignViewport extends AlignmentViewport return validCharWidth; } + private Hashtable calcIdParams = new Hashtable<>(); public AutoCalcSetting getCalcIdSettingsFor(String calcId) @@ -721,7 +737,7 @@ public class AlignViewport extends AlignmentViewport } ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18 - firePropertyChange("alignment", null, getAlignment().getSequences()); + notifyAlignment(); } /** @@ -741,53 +757,61 @@ public class AlignViewport extends AlignmentViewport final String question = JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.open_split_window?")); 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() + 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); + // Make a copy of this one to open it in a splitframe + openLinkedAlignmentAs(getAlignPanel().alignFrame, + new Alignment(getAlignment()), al, title, + SPLIT_FRAME); } - }).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. + * Identify protein and dna alignments. */ - 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 @@ -816,7 +840,7 @@ 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); @@ -829,10 +853,10 @@ public class AlignViewport extends AlignmentViewport { } - if (newWindowOrSplitPane) + if (mode == SPLIT_FRAME) { al.alignAs(thisAlignment); - protein = openSplitFrame(newAlignFrame, thisAlignment); + openSplitFrame(thisFrame, newAlignFrame, thisAlignment); } } @@ -846,8 +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 @@ -856,7 +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 @@ -1019,11 +1043,10 @@ public class AlignViewport extends AlignmentViewport { return; } - FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas .getFeatureRenderer(); - List origRenderOrder = new ArrayList<>(); - List origGroups = new ArrayList<>(); + List origRenderOrder = new ArrayList(), + origGroups = new ArrayList(); // preserve original render order - allows differentiation between user // configured colours and autogenerated ones origRenderOrder.addAll(fr.getRenderOrder()); @@ -1035,7 +1058,7 @@ public class AlignViewport extends AlignmentViewport if (!mergeOnly) { // only clear displayed features if we are mergeing - // displayed.clear(); + displayed.clear(); } // TODO this clears displayed.featuresRegistered - do we care? // @@ -1049,6 +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 @@ -1064,6 +1089,11 @@ public class AlignViewport extends AlignmentViewport { fr.setColour(type, preferredColour); } + if (preferredFilters != null + && (!mergeOnly || fr.getFeatureFilter(type) != null)) + { + fr.setFeatureFilter(type, preferredFilters); + } if (featureSettings.isFeatureDisplayed(type)) { displayed.setVisible(type);