X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;fp=src%2Fjalview%2Fgui%2FAlignViewport.java;h=7d01222db89aa2ca1ba1ef796bff46116f4dd4a2;hb=4f77328104498504339216829abf5ea87e2791ec;hp=eb9c1805d3bf5b61038d780740c7ac8c9838406d;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index eb9c180..7d01222 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -206,26 +206,24 @@ public class AlignViewport extends AlignmentViewport */ private void applyViewProperties() { - antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, false); - - viewStyle.setShowJVSuffix( - Cache.getDefault(Preferences.SHOW_JVSUFFIX, true)); - setShowAnnotation(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true)); - - setRightAlignIds(Cache.getDefault(Preferences.RIGHT_ALIGN_IDS, false)); - setCentreColumnLabels(Cache.getDefault(Preferences.CENTRE_COLUMN_LABELS, false)); - autoCalculateConsensusAndConservation = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true); - - setPadGaps(Cache.getDefault(Preferences.PAD_GAPS, true)); - setShowNPFeats(Cache.getDefault(Preferences.SHOW_NPFEATS_TOOLTIP, true)); - setShowDBRefs(Cache.getDefault(Preferences.SHOW_DBREFS_TOOLTIP, true)); - viewStyle.setSeqNameItalics(Cache.getDefault(Preferences.ID_ITALICS, true)); - viewStyle.setWrapAlignment( - Cache.getDefault(Preferences.WRAP_ALIGNMENT, false)); + antiAlias = Cache.getDefault("ANTI_ALIAS", false); + + 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); + + setPadGaps(Cache.getDefault("PAD_GAPS", true)); + setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); + setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); + viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true)); + viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false)); viewStyle.setShowUnconserved( - Cache.getDefault(Preferences.SHOW_UNCONSERVED, false)); - sortByTree = Cache.getDefault(Preferences.SORT_BY_TREE, false); - followSelection = Cache.getDefault(Preferences.FOLLOW_SELECTIONS, true); + Cache.getDefault("SHOW_UNCONSERVED", false)); + sortByTree = Cache.getDefault("SORT_BY_TREE", false); + followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true); sortAnnotationsBy = SequenceAnnotationOrder .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, SequenceAnnotationOrder.NONE.name())); @@ -239,10 +237,9 @@ public class AlignViewport extends AlignmentViewport { applyViewProperties(); - String fontName = Cache.getDefault(Preferences.FONT_NAME, "SansSerif"); - String fontStyle = Cache.getDefault(Preferences.FONT_STYLE, - Font.PLAIN + ""); - String fontSize = Cache.getDefault(Preferences.FONT_SIZE, "10"); + String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); + String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); + String fontSize = Cache.getDefault("FONT_SIZE", "10"); int style = 0; @@ -258,8 +255,7 @@ public class AlignViewport extends AlignmentViewport setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true); alignment - .setGapCharacter(Cache.getDefault(Preferences.GAP_SYMBOL, "-") - .charAt(0)); + .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 @@ -267,22 +263,18 @@ public class AlignViewport extends AlignmentViewport { if (!alignment.isNucleotide()) { - showConservation = Cache.getDefault(Preferences.SHOW_CONSERVATION, - true); - showQuality = Cache.getDefault(Preferences.SHOW_QUALITY, true); - showGroupConservation = Cache - .getDefault(Preferences.SHOW_GROUP_CONSERVATION, false); + showConservation = Cache.getDefault("SHOW_CONSERVATION", true); + showQuality = Cache.getDefault("SHOW_QUALITY", true); + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", + false); } - showConsensusHistogram = Cache - .getDefault(Preferences.SHOW_CONSENSUS_HISTOGRAM, true); - showSequenceLogo = Cache.getDefault(Preferences.SHOW_CONSENSUS_LOGO, + showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", + true); + showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); + normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false); - - normaliseSequenceLogo = Cache - .getDefault(Preferences.NORMALISE_CONSENSUS_LOGO, false); - showGroupConsensus = Cache - .getDefault(Preferences.SHOW_GROUP_CONSENSUS, false); - showConsensus = Cache.getDefault(Preferences.SHOW_IDENTITY, true); + showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); + showConsensus = Cache.getDefault("SHOW_IDENTITY", true); showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true); } @@ -297,8 +289,8 @@ 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) @@ -391,8 +383,9 @@ public class AlignViewport extends AlignmentViewport */ if (align != null) { - Desktop.getInstance().getStructureSelectionManager() - .registerMappings(align.getCodonFrames()); + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.registerMappings(align.getCodonFrames()); } /* @@ -412,8 +405,8 @@ public class AlignViewport extends AlignmentViewport List mappings = al.getCodonFrames(); if (mappings != null) { - StructureSelectionManager ssm = Desktop.getInstance() - .getStructureSelectionManager(); + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); for (AlignedCodonFrame acf : mappings) { if (noReferencesTo(acf)) @@ -538,10 +531,12 @@ public class AlignViewport extends AlignmentViewport @Override public void sendSelection() { - Desktop.getInstance().getStructureSelectionManager().sendSelection( - new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), - new HiddenColumns(getAlignment().getHiddenColumns()), this); + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(Desktop.instance) + .sendSelection(new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), + this); } /** @@ -582,7 +577,8 @@ public class AlignViewport extends AlignmentViewport @Override public StructureSelectionManager getStructureSelectionManager() { - return Desktop.getInstance().getStructureSelectionManager(); + return StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); } @Override @@ -751,12 +747,6 @@ public class AlignViewport extends AlignmentViewport firePropertyChange("alignment", null, getAlignment().getSequences()); } - public final static int NO_SPLIT = 0; - - public final static int SPLIT_FRAME = 1; - - public final static int NEW_WINDOW = 2; - /** * Show a dialog with the option to open and link (cDNA <-> protein) as a new * alignment, either as a standalone alignment or in a split frame. Returns @@ -773,62 +763,54 @@ public class AlignViewport extends AlignmentViewport MessageManager.getString("label.new_window"), }; 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.getDesktopPane()) - .setResponseHandler(NO_SPLIT, new Runnable() + JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop) + .setResponseHandler(0, new Runnable() { @Override public void run() { - addDataToAlignment(al); + addDataToAlignment(al); } - }).setResponseHandler(SPLIT_FRAME, new Runnable() + }).setResponseHandler(1, new Runnable() { @Override public void run() { - openLinkedAlignmentAs(getAlignPanel().alignFrame, - new Alignment(getAlignment()), al, title, - SPLIT_FRAME); + us.openLinkedAlignmentAs(al, title, true); } - }).setResponseHandler(NEW_WINDOW, new Runnable() + }).setResponseHandler(2, new Runnable() { @Override public void run() { - openLinkedAlignmentAs(null, getAlignment(), al, title, - NEW_WINDOW); + us.openLinkedAlignmentAs(al, title, false); } }); - dialog.showDialog(question, + dialog.showDialog(question, MessageManager.getString("label.open_split_window"), JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, options[0]); } - /** - * 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) - { + 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 = newWindowOrSplitPane + ? new Alignment(getAlignment()) + : getAlignment(); AlignmentI protein = al.isNucleotide() ? thisAlignment : al; - AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; + final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; /* * Map sequences. At least one should get mapped as we have already passed @@ -857,7 +839,7 @@ public class AlignViewport extends AlignmentViewport // alignFrame.setFileName(file, format); // } - if (mode == NEW_WINDOW) + if (!newWindowOrSplitPane) { Desktop.addInternalFrame(newAlignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -865,16 +847,16 @@ public class AlignViewport extends AlignmentViewport try { - newAlignFrame.setMaximum(jalview.bin.Cache - .getDefault(Preferences.SHOW_FULLSCREEN, false)); + newAlignFrame.setMaximum( + jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } - if (mode == SPLIT_FRAME) + if (newWindowOrSplitPane) { al.alignAs(thisAlignment); - openSplitFrame(thisFrame, newAlignFrame, thisAlignment); + protein = openSplitFrame(newAlignFrame, thisAlignment); } } @@ -888,8 +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 */ - static protected AlignmentI openSplitFrame(AlignFrame thisFrame, - AlignFrame newAlignFrame, AlignmentI complement) + protected AlignmentI openSplitFrame(AlignFrame newAlignFrame, + AlignmentI complement) { /* * Make a new frame with a copy of the alignment we are adding to. If this @@ -898,7 +880,7 @@ public class AlignViewport extends AlignmentViewport */ AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - copyMe.setTitle(thisFrame.getTitle()); + copyMe.setTitle(getAlignPanel().alignFrame.getTitle()); AlignmentI al = newAlignFrame.viewport.getAlignment(); final AlignFrame proteinFrame = al.isNucleotide() ? copyMe