From 7e04981d43b16398bd5bd2fad98a5216035d90bb Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 10 Dec 2020 13:04:48 +0000 Subject: [PATCH] JAL-1713 refactorings to allow save/restore Overview to/from project --- src/jalview/gui/AlignFrame.java | 14 ++- src/jalview/gui/OverviewCanvas.java | 70 ++++++++++--- src/jalview/gui/OverviewPanel.java | 33 ++++--- src/jalview/gui/Preferences.java | 53 +++++----- src/jalview/renderer/OverviewRenderer.java | 2 +- src/jalview/renderer/OverviewResColourFinder.java | 104 +++++++++++--------- test/jalview/renderer/OverviewRendererTest.java | 13 +-- .../renderer/OverviewResColourFinderTest.java | 85 +++++++--------- 8 files changed, 212 insertions(+), 162 deletions(-) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 1f3f409..5fe7c59 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -3368,10 +3368,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Opens an Overview panel for the alignment, unless one is open already * * @param e - * DOCUMENT ME! */ @Override public void overviewMenuItem_actionPerformed(ActionEvent e) @@ -3381,8 +3380,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } + boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, + false); + openOverviewPanel(showHiddenRegions); + } + + public OverviewPanel openOverviewPanel(boolean showHidden) + { JInternalFrame frame = new JInternalFrame(); - final OverviewPanel overview = new OverviewPanel(alignPanel); + final OverviewPanel overview = new OverviewPanel(alignPanel, showHidden); frame.setContentPane(overview); Desktop.addInternalFrame(frame, MessageManager .formatMessage("label.overview_params", new Object[] @@ -3407,6 +3413,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } alignPanel.setOverviewPanel(overview); + + return overview; } @Override diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java index 8e67992..586ac2c 100644 --- a/src/jalview/gui/OverviewCanvas.java +++ b/src/jalview/gui/OverviewCanvas.java @@ -20,13 +20,6 @@ */ package jalview.gui; -import jalview.api.AlignViewportI; -import jalview.bin.Cache; -import jalview.renderer.OverviewRenderer; -import jalview.renderer.OverviewResColourFinder; -import jalview.viewmodel.OverviewDimensions; -import jalview.viewmodel.seqfeatures.FeatureRendererModel; - import java.awt.Color; import java.awt.Dimension; import java.awt.Graphics; @@ -34,8 +27,26 @@ import java.awt.image.BufferedImage; import javax.swing.JPanel; +import jalview.api.AlignViewportI; +import jalview.bin.Cache; +import jalview.renderer.OverviewRenderer; +import jalview.renderer.OverviewResColourFinder; +import jalview.viewmodel.OverviewDimensions; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; + public class OverviewCanvas extends JPanel { + public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray; + + public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white; + + public static final Color OVERVIEW_DEFAULT_RESIDUE = Color.white; + + public static final Color OVERVIEW_DEFAULT_LEGACY_RESIDUE = Color.lightGray; + + public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray + .darker(); + private static final Color TRANS_GREY = new Color(100, 100, 100, 25); // This is set true if the alignment view changes whilst @@ -79,10 +90,12 @@ public class OverviewCanvas extends JPanel boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false); Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR, - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + OVERVIEW_DEFAULT_GAP); Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR, - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); - cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol); + OVERVIEW_DEFAULT_HIDDEN); + Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE : OVERVIEW_DEFAULT_RESIDUE; + + cf = new OverviewResColourFinder(gapCol, residueCol, hiddenCol); setSize(od.getWidth(), od.getHeight()); } @@ -182,7 +195,7 @@ public class OverviewCanvas extends JPanel @Override public void paintComponent(Graphics g) { - //super.paintComponent(g); + // super.paintComponent(g); if (restart) { @@ -207,9 +220,8 @@ public class OverviewCanvas extends JPanel { // if there is annotation, scale the alignment and annotation // separately - if (od.getGraphHeight() > 0 - && od.getSequencesHeight() > 0 // BH 2019 - ) + if (od.getGraphHeight() > 0 && od.getSequencesHeight() > 0 // BH 2019 + ) { BufferedImage topImage = lastMiniMe.getSubimage(0, 0, od.getWidth(), od.getSequencesHeight()); @@ -250,13 +262,12 @@ public class OverviewCanvas extends JPanel { g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); } - + // draw the box g.setColor(Color.red); od.drawBox(g); } - public void dispose() { dispose = true; @@ -270,4 +281,31 @@ public class OverviewCanvas extends JPanel } } } + + public Color getGapColour() + { + return cf.getGapColour(); + } + + public Color getHiddenColour() + { + return cf.getHiddenColour(); + } + + public Color getResidueColour() + { + return cf.getResidueColour(); + } + + /** + * Sets the colours to use for gaps, residues and hidden regions + * + * @param gaps + * @param residues + * @param hidden + */ + public void setColours(Color gaps, Color residues, Color hidden) + { + cf = new OverviewResColourFinder(gaps, residues, hidden); + } } diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index a5aaf7c..6cb4b96 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -20,15 +20,6 @@ */ package jalview.gui; -import jalview.bin.Cache; -import jalview.renderer.OverviewRenderer; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.viewmodel.OverviewDimensions; -import jalview.viewmodel.OverviewDimensionsHideHidden; -import jalview.viewmodel.OverviewDimensionsShowHidden; -import jalview.viewmodel.ViewportListenerI; - import java.awt.BorderLayout; import java.awt.Cursor; import java.awt.Dimension; @@ -48,6 +39,14 @@ import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; +import jalview.renderer.OverviewRenderer; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.OverviewDimensions; +import jalview.viewmodel.OverviewDimensionsHideHidden; +import jalview.viewmodel.OverviewDimensionsShowHidden; +import jalview.viewmodel.ViewportListenerI; + /** * Panel displaying an overview of the full alignment, with an interactive box * representing the viewport onto the alignment. @@ -80,14 +79,14 @@ public class OverviewPanel extends JPanel * * @param alPanel * The alignment panel which is shown in the overview panel + * @param isShowHidden TODO */ - public OverviewPanel(AlignmentPanel alPanel) + public OverviewPanel(AlignmentPanel alPanel, boolean isShowHidden) { this.av = alPanel.av; this.ap = alPanel; - showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, - false); + showHidden = isShowHidden; if (showHidden) { od = new OverviewDimensionsShowHidden(av.getRanges(), @@ -420,4 +419,14 @@ public class OverviewPanel extends JPanel od = null; } } + + public boolean isShowHiddenRegions() + { + return showHidden; + } + + public OverviewCanvas getCanvas() + { + return oviewCanvas; + } } diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index c61c70e..404e294 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -328,12 +328,10 @@ public class Preferences extends GPreferences /* * Set overview panel defaults */ - gapColour.setBackground( - Cache.getDefaultColour(GAP_COLOUR, - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP)); - hiddenColour.setBackground( - Cache.getDefaultColour(HIDDEN_COLOUR, - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN)); + gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR, + OverviewCanvas.OVERVIEW_DEFAULT_GAP)); + hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR, + OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN)); useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false)); gapLabel.setEnabled(!useLegacyGap.isSelected()); gapColour.setEnabled(!useLegacyGap.isSelected()); @@ -356,7 +354,8 @@ public class Preferences extends GPreferences * set choice of structure viewer, and path if saved as a preference; * default to Jmol (first choice) if an unexpected value is found */ - String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()); + String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, + ViewerType.JMOL.name()); structViewer.setSelectedItem(viewerType); String viewerPath = ""; ViewerType type = null; @@ -392,10 +391,11 @@ public class Preferences extends GPreferences { if (validateViewerPath()) { - Cache.setProperty(structViewer.getSelectedItem() - .equals(ViewerType.CHIMERAX.name()) - ? CHIMERAX_PATH - : CHIMERA_PATH, structureViewerPath.getText()); + Cache.setProperty( + structViewer.getSelectedItem().equals( + ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH + : CHIMERA_PATH, + structureViewerPath.getText()); } } }); @@ -583,8 +583,7 @@ public class Preferences extends GPreferences annotations_actionPerformed(null); // update the display of the annotation // settings - - + /* * Set Backups tab defaults */ @@ -604,7 +603,7 @@ public class Preferences extends GPreferences comboBox.addItem(promptEachTimeOpt); comboBox.addItem(lineArtOpt); comboBox.addItem(textOpt); - + /* * JalviewJS doesn't support Lineart so force it to Text */ @@ -750,8 +749,7 @@ public class Preferences extends GPreferences Boolean.toString(structFromPdb.isSelected())); String viewer = structViewer.getSelectedItem().toString(); String viewerPath = structureViewerPath.getText(); - Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, - viewer); + Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer); if (viewer.equals(ViewerType.CHIMERA.name())) { Cache.setOrRemove(CHIMERA_PATH, viewerPath); @@ -897,16 +895,16 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty(BackupFiles.ENABLED, Boolean.toString(enableBackupFiles.isSelected())); int preset = getComboIntStringKey(backupfilesPresetsCombo); - Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset)); + Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", + Integer.toString(preset)); if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM) { BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry(); BackupFilesPresetEntry.backupfilesPresetEntriesValues.put( BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE); - Cache.applicationProperties - .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG, - customBFPE.toString()); + Cache.applicationProperties.setProperty( + BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString()); } BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues @@ -1192,8 +1190,7 @@ public class Preferences extends GPreferences if (!useLegacyGap.isSelected()) { JalviewColourChooser.showColourChooser(this, - MessageManager.getString("label.select_gap_colour"), - gap); + MessageManager.getString("label.select_gap_colour"), gap); } } @@ -1201,8 +1198,7 @@ public class Preferences extends GPreferences public void hiddenColour_actionPerformed(JPanel hidden) { JalviewColourChooser.showColourChooser(this, - MessageManager.getString("label.select_hidden_colour"), - hidden); + MessageManager.getString("label.select_hidden_colour"), hidden); } @Override @@ -1211,13 +1207,11 @@ public class Preferences extends GPreferences boolean enabled = useLegacyGap.isSelected(); if (enabled) { - gapColour.setBackground( - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP); + gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_LEGACY_GAP); } else { - gapColour.setBackground( - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_GAP); } gapColour.setEnabled(!enabled); gapLabel.setEnabled(!enabled); @@ -1229,8 +1223,7 @@ public class Preferences extends GPreferences useLegacyGap.setSelected(false); useLegacyGaps_actionPerformed(null); showHiddenAtStart.setSelected(false); - hiddenColour.setBackground( - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); + hiddenColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN); } @Override diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java index c9096e2..b126465 100644 --- a/src/jalview/renderer/OverviewRenderer.java +++ b/src/jalview/renderer/OverviewRenderer.java @@ -225,7 +225,7 @@ public class OverviewRenderer int getColumnColourFromSequence(SequenceGroup[] allGroups, SequenceI seq, int lastcol) { - Color color = resColFinder.GAP_COLOUR; + Color color = resColFinder.gapColour; if ((seq != null) && (seq.getLength() > lastcol)) { diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java index a497d92..89dc9e7 100644 --- a/src/jalview/renderer/OverviewResColourFinder.java +++ b/src/jalview/renderer/OverviewResColourFinder.java @@ -20,68 +20,60 @@ */ package jalview.renderer; +import java.awt.Color; + import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.util.Comparison; -import java.awt.Color; - public class OverviewResColourFinder extends ResidueColourFinder { - final Color GAP_COLOUR; // default colour to use at gaps - - final Color RESIDUE_COLOUR; // default colour to use at residues - - final Color HIDDEN_COLOUR; // colour for hidden regions - - boolean useLegacy = false; - - public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray; + /* + * colour for gaps (unless overridden by colour scheme) + * - as set in Preferences, _or_ read from a project file + */ + Color gapColour; - public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white; + /* + * colour for residues if no colour scheme set (before feature colouring) + * - as set in Preferences, _or_ read from a project file + */ + Color residueColour; - public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray - .darker(); + /* + * colour for hidden regions + * - as set in Preferences, _or_ read from a project file + */ + Color hiddenColour; /** * Constructor without colour settings (used by applet) + * @deprecated */ + @Deprecated public OverviewResColourFinder() { - this(false, OVERVIEW_DEFAULT_GAP, OVERVIEW_DEFAULT_HIDDEN); + this(Color.lightGray, Color.white, Color.darkGray.darker()); } /** - * Constructor with colour settings + * Constructor given default colours for gaps, residues and hidden regions * - * @param useLegacyColouring - * whether to use legacy gap colouring (white gaps, grey residues) - * @param gapCol - * gap colour if not legacy - * @param hiddenCol - * hidden region colour (transparency applied by rendering code) + * @param gaps + * @param residues + * @param hidden */ - public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol, - Color hiddenCol) + public OverviewResColourFinder(Color gaps, Color residues, Color hidden) { - if (useLegacyColouring) - { - GAP_COLOUR = Color.white; - RESIDUE_COLOUR = Color.lightGray; - HIDDEN_COLOUR = hiddenCol; - } - else - { - GAP_COLOUR = gapCol; - RESIDUE_COLOUR = Color.white; - HIDDEN_COLOUR = hiddenCol; - } + gapColour = gaps; + residueColour = residues; + hiddenColour = hidden; } @Override public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i) { - Color resBoxColour = RESIDUE_COLOUR; + Color resBoxColour = residueColour; char currentChar = seq.getCharAt(i); // In the overview window, gaps are coloured grey, unless the colour scheme @@ -92,7 +84,7 @@ public class OverviewResColourFinder extends ResidueColourFinder if (Comparison.isGap(currentChar) && (!shader.getColourScheme().hasGapColour())) { - resBoxColour = GAP_COLOUR; + resBoxColour = gapColour; } else { @@ -101,7 +93,7 @@ public class OverviewResColourFinder extends ResidueColourFinder } else if (Comparison.isGap(currentChar)) { - resBoxColour = GAP_COLOUR; + resBoxColour = gapColour; } return resBoxColour; @@ -113,8 +105,8 @@ public class OverviewResColourFinder extends ResidueColourFinder */ @Override protected Color getResidueBoxColour(boolean showBoxes, - ResidueShaderI shader, - SequenceGroup[] allGroups, SequenceI seq, int i) + ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq, + int i) { ResidueShaderI currentShader; SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups, @@ -132,12 +124,34 @@ public class OverviewResColourFinder extends ResidueColourFinder } /** - * Supply hidden colour + * Returns the colour used for hidden regions + * + * @return + */ + public Color getHiddenColour() + { + return hiddenColour; + } + + /** + * Returns the colour used for gaps, if not overridden by the alignment colour + * scheme + * + * @return + */ + public Color getGapColour() + { + return gapColour; + } + + /** + * Returns the colour used for residues (before applying any feature + * colouring) if there is no alignment colour scheme * - * @return colour of hidden regions + * @return */ - protected Color getHiddenColour() + public Color getResidueColour() { - return HIDDEN_COLOUR; + return gapColour; } } diff --git a/test/jalview/renderer/OverviewRendererTest.java b/test/jalview/renderer/OverviewRendererTest.java index 1d532f7..b77ae26 100644 --- a/test/jalview/renderer/OverviewRendererTest.java +++ b/test/jalview/renderer/OverviewRendererTest.java @@ -22,6 +22,10 @@ package jalview.renderer; import static org.testng.Assert.assertEquals; +import java.awt.Color; + +import org.testng.annotations.Test; + import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.Sequence; @@ -35,18 +39,15 @@ import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.OverviewDimensions; import jalview.viewmodel.OverviewDimensionsShowHidden; import jalview.viewmodel.ViewportRanges; - -import java.awt.Color; - -import org.testng.annotations.Test; public class OverviewRendererTest { @Test public void testGetColumnColourFromSequence() { - OverviewResColourFinder cf = new OverviewResColourFinder(false, - Color.PINK, Color.green); // gapColour, hiddenColour + // gapColour, residueColour, hiddenColour + OverviewResColourFinder cf = new OverviewResColourFinder( + Color.PINK, Color.white, Color.green); Sequence seq1 = new Sequence("seq1", "PQ-RL-"); Sequence seq2 = new Sequence("seq2", "FVE"); AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java index 1687516..028777e 100644 --- a/test/jalview/renderer/OverviewResColourFinderTest.java +++ b/test/jalview/renderer/OverviewResColourFinderTest.java @@ -22,6 +22,12 @@ package jalview.renderer; import static org.testng.AssertJUnit.assertEquals; +import java.awt.Color; +import java.util.ArrayList; + +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; @@ -30,16 +36,11 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.AlignViewport; import jalview.gui.JvOptionPane; +import jalview.gui.OverviewCanvas; import jalview.schemes.ColourSchemeI; import jalview.schemes.UserColourScheme; import jalview.schemes.ZappoColourScheme; -import java.awt.Color; -import java.util.ArrayList; - -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - public class OverviewResColourFinderTest { @@ -61,11 +62,9 @@ public class OverviewResColourFinderTest // gaps are grey, residues white assertEquals(Color.white, rcf.getResidueColour(true, - av.getResidueShading(), - null, seq, 0, null)); - assertEquals(Color.lightGray, rcf - .getResidueColour(true, av.getResidueShading(), null, seq, 2, - null)); + av.getResidueShading(), null, seq, 0, null)); + assertEquals(Color.lightGray, rcf.getResidueColour(true, + av.getResidueShading(), null, seq, 2, null)); // unaffected by showBoxes setting assertEquals(Color.white, rcf.getResidueColour(false, @@ -85,23 +84,18 @@ public class OverviewResColourFinderTest av.setGlobalColourScheme(new ZappoColourScheme()); // @see ResidueProperties.zappo - assertEquals(Color.pink, - rcf.getResidueColour(true, av.getResidueShading(), - null, seq, 0, null)); // M - assertEquals(Color.green, - rcf.getResidueColour(true, av.getResidueShading(), - null, seq, 2, null)); // T - assertEquals(Color.magenta, - rcf.getResidueColour(true, av.getResidueShading(), - null, seq, 5, null)); // G - assertEquals(Color.orange, - rcf.getResidueColour(true, av.getResidueShading(), - null, seq, 12, null)); // F + assertEquals(Color.pink, rcf.getResidueColour(true, + av.getResidueShading(), null, seq, 0, null)); // M + assertEquals(Color.green, rcf.getResidueColour(true, + av.getResidueShading(), null, seq, 2, null)); // T + assertEquals(Color.magenta, rcf.getResidueColour(true, + av.getResidueShading(), null, seq, 5, null)); // G + assertEquals(Color.orange, rcf.getResidueColour(true, + av.getResidueShading(), null, seq, 12, null)); // F // gap colour not specified so gaps are lightGray - assertEquals(Color.lightGray, rcf - .getResidueColour(true, av.getResidueShading(), null, seq, 3, - null)); + assertEquals(Color.lightGray, rcf.getResidueColour(true, + av.getResidueShading(), null, seq, 3, null)); // unaffected by showBoxes setting assertEquals(Color.pink, rcf.getResidueColour(false, @@ -114,9 +108,8 @@ public class OverviewResColourFinderTest av.getResidueShading(), null, seq, 12, null)); // F // gap colour not specified so gaps are lightGray - assertEquals(Color.lightGray, rcf - .getResidueColour(false, av.getResidueShading(), null, seq, 3, - null)); + assertEquals(Color.lightGray, rcf.getResidueColour(false, + av.getResidueShading(), null, seq, 3, null)); } @@ -138,17 +131,15 @@ public class OverviewResColourFinderTest av.setGlobalColourScheme(new UserColourScheme(newColours)); // gap colour not specified so gaps are lightGray - assertEquals(Color.lightGray, rcf - .getResidueColour(true, av.getResidueShading(), null, seq, 3, - null)); + assertEquals(Color.lightGray, rcf.getResidueColour(true, + av.getResidueShading(), null, seq, 3, null)); newColours[23] = Color.pink; av.setGlobalColourScheme(new UserColourScheme(newColours)); // gap colour specified as pink assertEquals(Color.pink, rcf.getResidueColour(true, - av.getResidueShading(), - null, seq, 3, null)); + av.getResidueShading(), null, seq, 3, null)); // unaffected by showBoxes setting // gap colour not specified so gaps are lightGray @@ -169,7 +160,7 @@ public class OverviewResColourFinderTest { SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF"); AlignmentI al = new Alignment(new SequenceI[] { seq }); - + ColourSchemeI cs = new ZappoColourScheme(); ArrayList seqlist = new ArrayList<>(); seqlist.add(seq); @@ -178,10 +169,10 @@ public class OverviewResColourFinderTest al.addGroup(sg); SequenceGroup[] groups = new SequenceGroup[1]; groups[0] = sg; - + final AlignViewport av = new AlignViewport(al); ResidueColourFinder rcf = new OverviewResColourFinder(); - + // G in group specified as magenta in Zappo assertEquals(Color.magenta, rcf.getResidueColour(false, av.getResidueShading(), groups, seq, 7, null)); @@ -195,8 +186,8 @@ public class OverviewResColourFinderTest av.getResidueShading(), groups, seq, 2, null)); // use legacy colouring - rcf = new OverviewResColourFinder(true, Color.blue, Color.red); - + rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red); + // G in group specified as magenta in Zappo assertEquals(Color.magenta, rcf.getResidueColour(false, av.getResidueShading(), groups, seq, 7, null)); @@ -210,7 +201,7 @@ public class OverviewResColourFinderTest av.getResidueShading(), groups, seq, 2, null)); // use new colouring - rcf = new OverviewResColourFinder(false, Color.blue, Color.red); + rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red); // G in group specified as magenta in Zappo assertEquals(Color.magenta, rcf.getResidueColour(false, @@ -243,12 +234,10 @@ public class OverviewResColourFinderTest // gaps gap colour c = rcf.getBoxColour(shader, seq, 3); - assertEquals( - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP, - c); + assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c); // legacy colouring set explicitly via constructor - rcf = new OverviewResColourFinder(true, Color.blue, Color.red); + rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red); shader = new ResidueShader(); // residues light gray @@ -269,12 +258,10 @@ public class OverviewResColourFinderTest // gaps gap colour c = rcf.getBoxColour(shader, seq, 3); - assertEquals( - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP, - c); + assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c); // non legacy colouring with colour scheme - rcf = new OverviewResColourFinder(false, Color.blue, Color.red); + rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red); shader = new ResidueShader(new ZappoColourScheme()); // M residue pink @@ -286,7 +273,7 @@ public class OverviewResColourFinderTest assertEquals(Color.blue, c); // legacy colouring with colour scheme - rcf = new OverviewResColourFinder(true, Color.blue, Color.red); + rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red); // M residue pink c = rcf.getBoxColour(shader, seq, 0); -- 1.7.10.2