From 65d6d09cd08743d481d39521bb0298ea683888f8 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 5 May 2016 14:21:55 +0100 Subject: [PATCH] JAL-2094 first pass with jalview.api.ColorI interface --- examples/exampleFeatures.txt | 8 +- src/MCview/AppletPDBCanvas.java | 23 +- src/MCview/Atom.java | 6 +- src/MCview/Bond.java | 7 +- src/MCview/PDBCanvas.java | 29 +- src/MCview/PDBChain.java | 30 +- src/jalview/api/AlignViewportI.java | 5 +- src/jalview/api/FeatureColourI.java | 73 ++- src/jalview/api/FeatureRenderer.java | 17 +- src/jalview/api/SequenceRenderer.java | 6 +- src/jalview/api/ViewStyleI.java | 10 +- src/jalview/appletgui/AlignFrame.java | 5 +- src/jalview/appletgui/AnnotationColourChooser.java | 8 + src/jalview/appletgui/FeatureColourChooser.java | 71 +- src/jalview/appletgui/FeatureRenderer.java | 87 ++- src/jalview/appletgui/FeatureSettings.java | 122 ++-- src/jalview/appletgui/IdCanvas.java | 5 +- src/jalview/appletgui/OverviewPanel.java | 6 +- src/jalview/appletgui/RotatableCanvas.java | 36 +- src/jalview/appletgui/SeqCanvas.java | 3 +- src/jalview/appletgui/SequenceRenderer.java | 11 +- src/jalview/appletgui/TreeCanvas.java | 9 +- src/jalview/appletgui/UserDefinedColours.java | 54 +- src/jalview/controller/AlignViewController.java | 6 +- src/jalview/datamodel/SequenceGroup.java | 21 +- src/jalview/ext/ensembl/EnsemblGene.java | 7 +- src/jalview/ext/jmol/JmolCommands.java | 4 +- src/jalview/ext/rbvi/chimera/ChimeraCommands.java | 20 +- src/jalview/ext/varna/VarnaCommands.java | 10 +- src/jalview/gui/AlignmentPanel.java | 3 +- src/jalview/gui/AnnotationExporter.java | 3 +- src/jalview/gui/AppVarna.java | 3 +- src/jalview/gui/FeatureColourChooser.java | 95 +-- src/jalview/gui/FeatureRenderer.java | 34 +- src/jalview/gui/FeatureSettings.java | 201 +++--- src/jalview/gui/IdCanvas.java | 6 +- src/jalview/gui/Jalview2XML.java | 116 ++-- src/jalview/gui/Jalview2XML_V1.java | 3 +- src/jalview/gui/RotatableCanvas.java | 36 +- src/jalview/gui/SeqCanvas.java | 3 +- src/jalview/gui/SequenceRenderer.java | 21 +- src/jalview/gui/TextColourChooser.java | 20 +- src/jalview/gui/TreeCanvas.java | 10 +- src/jalview/io/AnnotationFile.java | 7 +- src/jalview/io/FeaturesFile.java | 126 ++-- src/jalview/io/HTMLOutput.java | 9 +- src/jalview/io/HtmlSvgOutput.java | 3 +- src/jalview/io/JSONFile.java | 3 +- src/jalview/io/PDBFeatureSettings.java | 8 +- src/jalview/io/packed/JalviewDataset.java | 15 +- src/jalview/io/packed/ParsePackedSet.java | 3 +- .../renderer/seqfeatures/FeatureRenderer.java | 19 +- src/jalview/schemes/FeatureColour.java | 684 ++++++++++++++++++++ src/jalview/schemes/FeatureColourAdapter.java | 102 ++- src/jalview/schemes/UserColourScheme.java | 2 +- src/jalview/util/ColorUtils.java | 8 +- src/jalview/util/Format.java | 36 +- src/jalview/viewmodel/AlignmentViewport.java | 21 +- .../seqfeatures/FeatureRendererModel.java | 160 ++--- .../seqfeatures/FeatureRendererSettings.java | 48 +- src/jalview/viewmodel/styles/ViewStyle.java | 16 +- src/jalview/ws/jws1/SeqSearchWSThread.java | 5 +- src/jalview/ws/jws2/AADisorderClient.java | 17 +- test/MCview/PDBChainTest.java | 44 +- .../ext/rbvi/chimera/ChimeraCommandsTest.java | 60 +- test/jalview/gui/SequenceRendererTest.java | 11 +- test/jalview/io/FeaturesFileTest.java | 44 +- test/jalview/schemes/FeatureColourTest.java | 314 +++++++++ test/jalview/util/ColorUtilsTest.java | 12 +- test/jalview/viewmodel/styles/ViewStyleTest.java | 10 +- 70 files changed, 2113 insertions(+), 927 deletions(-) create mode 100644 src/jalview/schemes/FeatureColour.java create mode 100644 test/jalview/schemes/FeatureColourTest.java diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt index dfadb50..b7038f5 100755 --- a/examples/exampleFeatures.txt +++ b/examples/exampleFeatures.txt @@ -1,5 +1,5 @@ ST-TURN-IIL blue|255,0,255|absolute|20.0|95.0|below|66.0 -GAMMA-TURN-CLASSIC red|0,255,255|20.0|95.0|below|66.0 +GAMMA-TURN-CLASSIC red|0,255,255|20.0|95.0|below|66.0 BETA-TURN-IR 9a6a94 BETA-TURN-IL d6a6ca BETA-BULGE 1dc451 @@ -22,8 +22,10 @@ NEST-RL 3e16b2 ASX-TURN-IIL a67c98 BETA-TURN-IIR c79792 PHOSPHORYLATION (T) c88395 -BETA-TURN-IIL 8b5b50 -ST-MOTIF ac25a1 +BETA-TURN-IIL label +#8b5b50 +ST-MOTIF label|||0|0 +#ac25a1 STARTGROUP uniprot Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java index df98833..89318d5 100644 --- a/src/MCview/AppletPDBCanvas.java +++ b/src/MCview/AppletPDBCanvas.java @@ -27,10 +27,12 @@ import jalview.appletgui.SequenceRenderer; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.io.StructureFile; +import jalview.schemes.Colour; import jalview.structure.AtomSpec; import jalview.structure.StructureListener; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import java.awt.Color; @@ -584,8 +586,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, for (int i = 0; i < chain.bonds.size(); i++) { Bond tmp = chain.bonds.elementAt(i); - tmp.startCol = Color.lightGray; - tmp.endCol = Color.lightGray; + tmp.startCol = Colour.lightGray; + tmp.endCol = Colour.lightGray; if (chain != mainchain) { continue; @@ -660,26 +662,27 @@ public class AppletPDBCanvas extends Panel implements MouseListener, { if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) { - g.setColor(tmpBond.startCol.darker().darker()); + g.setColor(ColorUtils.getColor(tmpBond.startCol).darker() + .darker()); drawLine(g, xstart, ystart, xmid, ymid); - g.setColor(tmpBond.endCol.darker().darker()); + g.setColor(ColorUtils.getColor(tmpBond.endCol).darker().darker()); drawLine(g, xmid, ymid, xend, yend); } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) { - g.setColor(tmpBond.startCol.darker()); + g.setColor(ColorUtils.getColor(tmpBond.startCol).darker()); drawLine(g, xstart, ystart, xmid, ymid); - g.setColor(tmpBond.endCol.darker()); + g.setColor(ColorUtils.getColor(tmpBond.endCol).darker()); drawLine(g, xmid, ymid, xend, yend); } else { - g.setColor(tmpBond.startCol); + g.setColor(ColorUtils.getColor(tmpBond.startCol)); drawLine(g, xstart, ystart, xmid, ymid); - g.setColor(tmpBond.endCol); + g.setColor(ColorUtils.getColor(tmpBond.endCol)); drawLine(g, xmid, ymid, xend, yend); } @@ -704,9 +707,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener, } else if (!depthcue && !bymolecule) { - g.setColor(tmpBond.startCol); + g.setColor(ColorUtils.getColor(tmpBond.startCol)); drawLine(g, xstart, ystart, xmid, ymid); - g.setColor(tmpBond.endCol); + g.setColor(ColorUtils.getColor(tmpBond.endCol)); drawLine(g, xmid, ymid, xend, yend); } else diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java index 68a7c21..7db845b 100755 --- a/src/MCview/Atom.java +++ b/src/MCview/Atom.java @@ -20,10 +20,10 @@ */ package MCview; +import jalview.api.ColorI; +import jalview.schemes.Colour; import jalview.schemes.ResidueProperties; -import java.awt.Color; - public class Atom { public float x; @@ -46,7 +46,7 @@ public class Atom public int type; - Color color = Color.lightGray; + ColorI color = Colour.lightGray; public String chain; diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java index 371ccd5..57d77bd 100755 --- a/src/MCview/Bond.java +++ b/src/MCview/Bond.java @@ -20,7 +20,8 @@ */ package MCview; -import java.awt.Color; +import jalview.api.ColorI; +import jalview.schemes.Colour; public class Bond { @@ -28,9 +29,9 @@ public class Bond float[] end; - Color startCol = Color.lightGray; + ColorI startCol = Colour.lightGray; - Color endCol = Color.lightGray; + ColorI endCol = Colour.lightGray; public Atom at1; diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java index 1c7a1f7..d8e0366 100644 --- a/src/MCview/PDBCanvas.java +++ b/src/MCview/PDBCanvas.java @@ -27,10 +27,12 @@ import jalview.gui.AlignmentPanel; import jalview.gui.FeatureRenderer; import jalview.gui.SequenceRenderer; import jalview.io.StructureFile; +import jalview.schemes.Colour; import jalview.structure.AtomSpec; import jalview.structure.StructureListener; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; +import jalview.util.ColorUtils; import java.awt.Color; import java.awt.Dimension; @@ -553,8 +555,8 @@ public class PDBCanvas extends JPanel implements MouseListener, for (int i = 0; i < chain.bonds.size(); i++) { Bond tmp = chain.bonds.elementAt(i); - tmp.startCol = Color.lightGray; - tmp.endCol = Color.lightGray; + tmp.startCol = Colour.lightGray; + tmp.endCol = Colour.lightGray; if (chain != mainchain) { continue; @@ -629,26 +631,27 @@ public class PDBCanvas extends JPanel implements MouseListener, if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) { - g.setColor(tmpBond.startCol.darker().darker()); + g.setColor(ColorUtils.getColor(tmpBond.startCol).darker() + .darker()); drawLine(g, xstart, ystart, xmid, ymid); - g.setColor(tmpBond.endCol.darker().darker()); + g.setColor(ColorUtils.getColor(tmpBond.endCol).darker().darker()); drawLine(g, xmid, ymid, xend, yend); } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) { - g.setColor(tmpBond.startCol.darker()); + g.setColor(ColorUtils.getColor(tmpBond.startCol).darker()); drawLine(g, xstart, ystart, xmid, ymid); - g.setColor(tmpBond.endCol.darker()); + g.setColor(ColorUtils.getColor(tmpBond.endCol).darker()); drawLine(g, xmid, ymid, xend, yend); } else { - g.setColor(tmpBond.startCol); + g.setColor(ColorUtils.getColor(tmpBond.startCol)); drawLine(g, xstart, ystart, xmid, ymid); - g.setColor(tmpBond.endCol); + g.setColor(ColorUtils.getColor(tmpBond.endCol)); drawLine(g, xmid, ymid, xend, yend); } } @@ -672,9 +675,9 @@ public class PDBCanvas extends JPanel implements MouseListener, } else if (!depthcue && !bymolecule) { - g.setColor(tmpBond.startCol); + g.setColor(ColorUtils.getColor(tmpBond.startCol)); drawLine(g, xstart, ystart, xmid, ymid); - g.setColor(tmpBond.endCol); + g.setColor(ColorUtils.getColor(tmpBond.endCol)); drawLine(g, xmid, ymid, xend, yend); } else @@ -684,14 +687,16 @@ public class PDBCanvas extends JPanel implements MouseListener, if (highlightBond1 != null && highlightBond1 == tmpBond) { - g.setColor(tmpBond.endCol.brighter().brighter().brighter() + g.setColor(ColorUtils.getColor(tmpBond.endCol).brighter() + .brighter().brighter() .brighter()); drawLine(g, xmid, ymid, xend, yend); } if (highlightBond2 != null && highlightBond2 == tmpBond) { - g.setColor(tmpBond.startCol.brighter().brighter().brighter() + g.setColor(ColorUtils.getColor(tmpBond.startCol).brighter() + .brighter().brighter() .brighter()); drawLine(g, xstart, ystart, xmid, ymid); } diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 3b84ee3..e048cd6 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -21,12 +21,14 @@ package MCview; import jalview.analysis.AlignSeq; +import jalview.api.ColorI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.Mapping; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.StructureMapping; @@ -486,26 +488,26 @@ public class PDBChain } else { - b.startCol = Color.gray; - b.endCol = Color.gray; + b.startCol = Colour.gray; + b.endCol = Colour.gray; } } } - public static Color getChargeColour(String resName) + public static ColorI getChargeColour(String resName) { - Color result = Color.lightGray; + ColorI result = Colour.lightGray; if ("ASP".equals(resName) || "GLU".equals(resName)) { - result = Color.red; + result = Colour.red; } else if ("LYS".equals(resName) || "ARG".equals(resName)) { - result = Color.blue; + result = Colour.blue; } else if ("CYS".equals(resName)) { - result = Color.yellow; + result = Colour.yellow; } return result; } @@ -525,15 +527,17 @@ public class PDBChain try { index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue(); - b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); + b.startCol = new Colour(cs.findColour(ResidueProperties.aa[index] + .charAt(0))); index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue(); - b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); + b.endCol = new Colour(cs.findColour(ResidueProperties.aa[index] + .charAt(0))); } catch (Exception e) { - b.startCol = Color.gray; - b.endCol = Color.gray; + b.startCol = Colour.gray; + b.endCol = Colour.gray; } } } @@ -542,8 +546,8 @@ public class PDBChain { for (Bond b : bonds) { - b.startCol = col; - b.endCol = col; + b.startCol = new Colour(col); + b.endCol = new Colour(col); } } diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index 45e77ba..c7d7a37 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -31,7 +31,6 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeI; -import java.awt.Color; import java.util.Hashtable; import java.util.List; import java.util.Map; @@ -179,9 +178,9 @@ public interface AlignViewportI extends ViewStyleI void updateGroupAnnotationSettings(boolean applyGlobalSettings, boolean preserveNewGroupSettings); - void setSequenceColour(SequenceI seq, Color col); + void setSequenceColour(SequenceI seq, ColorI col); - Color getSequenceColour(SequenceI seq); + ColorI getSequenceColour(SequenceI seq); void updateSequenceIdColours(); diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java index d8363f4..f68d7a7 100644 --- a/src/jalview/api/FeatureColourI.java +++ b/src/jalview/api/FeatureColourI.java @@ -1,6 +1,6 @@ package jalview.api; -import java.awt.Color; +import jalview.datamodel.SequenceFeature; public interface FeatureColourI { @@ -18,21 +18,21 @@ public interface FeatureColourI * * @return */ - Color getColour(); + ColorI getColour(); /** * Returns the minimum colour (when isGraduatedColour answers true) * * @return */ - Color getMinColour(); + ColorI getMinColour(); /** * Returns the maximum colour (when isGraduatedColour answers true) * * @return */ - Color getMaxColour(); + ColorI getMaxColour(); /** * Answers true if the feature is coloured by label (description); only @@ -73,10 +73,71 @@ public interface FeatureColourI */ float getThreshold(); + float getMax(); + + /** + * Returns the minimum score of the graduated colour range + * + * @return + */ + float getMin(); + + /** + * Answers true if either isAboveThreshold or isBelowThreshold answers true + * + * @return + */ + boolean hasThreshold(); + + /** + * Returns the computed colour for the given sequence feature + * + * @param feature + * @return + */ + ColorI getColor(SequenceFeature feature); + + /** + * Answers true if the feature has a simple colour, or is coloured by label, + * or has a graduated colour and the score of this feature instance is within + * the range to render (if any), i.e. does not lie below or above any + * threshold set. + * + * @param feature + * @return + */ + boolean isColored(SequenceFeature feature); + /** - * Answers true if ? + * Update the min-max range for a graduated colour scheme + * + * @param min + * @param max + */ + void updateBounds(float min, float max); + + /** + * Returns the colour in Jalview features file format * * @return */ - boolean isLowToHigh(); + String toJalviewFormat(String featureType); + + void setThreshold(float f); + + boolean isAutoScaled(); + + void setAutoScaled(boolean b); + + boolean isSimpleColour(); + + void setAboveThreshold(boolean b); + + void setThresholdMinMax(boolean b); + + void setBelowThreshold(boolean b); + + void setColourByLabel(boolean b); + + void setGraduatedColour(boolean b); } diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java index d9795a6..5477f57 100644 --- a/src/jalview/api/FeatureRenderer.java +++ b/src/jalview/api/FeatureRenderer.java @@ -23,7 +23,6 @@ package jalview.api; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; -import java.awt.Color; import java.util.List; import java.util.Map; @@ -48,7 +47,7 @@ public interface FeatureRenderer * - column position * @return */ - Color findFeatureColour(Color col, SequenceI sequenceI, int r); + ColorI findFeatureColour(ColorI col, SequenceI sequenceI, int r); /** * trigger the feature discovery process for a newly created feature renderer. @@ -60,17 +59,15 @@ public interface FeatureRenderer * @param ft * @return display style for a feature */ - Object getFeatureStyle(String ft); + FeatureColourI getFeatureStyle(String ft); /** * update the feature style for a particular feature * - * @param ft - * @param ggc - * - currently allows java.awt.Color and - * jalview.schemes.GraduatedColor + * @param featureType + * @param featureColour */ - void setColour(String ft, Object ggc); + void setColour(String featureType, FeatureColourI featureColour); AlignViewportI getViewport(); @@ -85,7 +82,7 @@ public interface FeatureRenderer * * @return */ - Map getFeatureColours(); + Map getFeatureColours(); /** * query the alignment view to find all features @@ -100,7 +97,7 @@ public interface FeatureRenderer * * @return */ - Map getDisplayedFeatureCols(); + Map getDisplayedFeatureCols(); /** * get all registered groups diff --git a/src/jalview/api/SequenceRenderer.java b/src/jalview/api/SequenceRenderer.java index d708902..81bb386 100644 --- a/src/jalview/api/SequenceRenderer.java +++ b/src/jalview/api/SequenceRenderer.java @@ -22,13 +22,11 @@ package jalview.api; import jalview.datamodel.SequenceI; -import java.awt.Color; - public interface SequenceRenderer { - Color getResidueBoxColour(SequenceI sequenceI, int r); + ColorI getResidueBoxColour(SequenceI sequenceI, int r); - Color getResidueColour(SequenceI seq, int position, FeatureRenderer fr); + ColorI getResidueColour(SequenceI seq, int position, FeatureRenderer fr); } diff --git a/src/jalview/api/ViewStyleI.java b/src/jalview/api/ViewStyleI.java index db82dcf..2375a72 100644 --- a/src/jalview/api/ViewStyleI.java +++ b/src/jalview/api/ViewStyleI.java @@ -20,8 +20,6 @@ */ package jalview.api; -import java.awt.Color; - public interface ViewStyleI { @@ -148,9 +146,9 @@ public interface ViewStyleI */ void setColourByReferenceSeq(boolean colourByReferenceSeq); - Color getTextColour(); + ColorI getTextColour(); - Color getTextColour2(); + ColorI getTextColour2(); int getThresholdTextColour(); @@ -166,11 +164,11 @@ public interface ViewStyleI void setShowColourText(boolean showColourText); - void setTextColour(Color textColour); + void setTextColour(ColorI textColour); void setThresholdTextColour(int thresholdTextColour); - void setTextColour2(Color textColour2); + void setTextColour2(ColorI textColour2); boolean isSeqNameItalics(); diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index e5f0053..8f1f2fd 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -25,6 +25,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; import jalview.api.FeatureRenderer; import jalview.api.FeatureSettingsControllerI; import jalview.api.SequenceStructureBinding; @@ -367,7 +368,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, boolean featuresFile = false; try { - Map colours = alignPanel.seqPanel.seqCanvas + Map colours = alignPanel.seqPanel.seqCanvas .getFeatureRenderer().getFeatureColours(); boolean relaxedIdMatching = viewport.applet.getDefaultParameter( "relaxedidmatch", false); @@ -1399,7 +1400,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return annotation; } - private Map getDisplayedFeatureCols() + private Map getDisplayedFeatureCols() { if (alignPanel.getFeatureRenderer() != null && viewport.getFeaturesDisplayed() != null) diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index 57b182c..15346a3 100644 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -309,6 +309,7 @@ public class AnnotationColourChooser extends Panel implements Checkbox thresholdIsMin = new Checkbox(); + @Override public void actionPerformed(ActionEvent evt) { if (evt.getSource() == thresholdValue) @@ -351,6 +352,7 @@ public class AnnotationColourChooser extends Panel implements } } + @Override public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == currentColours) @@ -368,6 +370,7 @@ public class AnnotationColourChooser extends Panel implements changeColour(); } + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { if (!adjusting) @@ -552,23 +555,28 @@ public class AnnotationColourChooser extends Panel implements } + @Override public void mouseClicked(MouseEvent evt) { } + @Override public void mousePressed(MouseEvent evt) { } + @Override public void mouseReleased(MouseEvent evt) { ap.paintAlignment(true); } + @Override public void mouseEntered(MouseEvent evt) { } + @Override public void mouseExited(MouseEvent evt) { } diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java index 46a67c4..7638b3b 100644 --- a/src/jalview/appletgui/FeatureColourChooser.java +++ b/src/jalview/appletgui/FeatureColourChooser.java @@ -20,9 +20,12 @@ */ package jalview.appletgui; +import jalview.api.FeatureColourI; import jalview.datamodel.GraphLine; import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +import jalview.schemes.Colour; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import java.awt.Checkbox; @@ -60,9 +63,9 @@ public class FeatureColourChooser extends Panel implements ActionListener, // AlignmentPanel ap; - GraduatedColor cs; + FeatureColourI cs; - Object oldcs; + FeatureColourI oldcs; Hashtable oldgroupColours; @@ -91,29 +94,30 @@ public class FeatureColourChooser extends Panel implements ActionListener, { this.type = type; fr = frenderer; - float mm[] = ((float[][]) fr.getMinMax().get(type))[0]; + float mm[] = fr.getMinMax().get(type)[0]; min = mm[0]; max = mm[1]; oldcs = fr.getFeatureColours().get(type); - if (oldcs instanceof GraduatedColor) + if (oldcs.isGraduatedColour()) { - cs = new GraduatedColor((GraduatedColor) oldcs, min, max); + cs = new FeatureColour((FeatureColour) oldcs, min, max); } else { // promote original color to a graduated color Color bl = Color.black; - if (oldcs instanceof Color) + if (oldcs.isSimpleColour()) { - bl = (Color) oldcs; + bl = ColorUtils.getColor(oldcs.getColour()); } // original colour becomes the maximum colour - cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]); + cs = new FeatureColour(new Colour(Color.white), new Colour(bl), + mm[0], mm[1]); } - minColour.setBackground(cs.getMinColor()); - maxColour.setBackground(cs.getMaxColor()); - minColour.setForeground(cs.getMinColor()); - maxColour.setForeground(cs.getMaxColor()); + minColour.setBackground(ColorUtils.getColor(cs.getMinColour())); + maxColour.setBackground(ColorUtils.getColor(cs.getMaxColour())); + minColour.setForeground(ColorUtils.getColor(cs.getMinColour())); + maxColour.setForeground(ColorUtils.getColor(cs.getMaxColour())); colourFromLabel.setState(cs.isColourByLabel()); adjusting = true; @@ -123,10 +127,8 @@ public class FeatureColourChooser extends Panel implements ActionListener, } catch (Exception ex) { } - threshold - .select(cs.getThreshType() == AnnotationColourGradient.NO_THRESHOLD ? 0 - : cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1 - : 2); + threshold.select(cs.isAboveThreshold() ? 1 : (cs.isBelowThreshold() ? 2 + : 0)); adjusting = false; changeColour(); @@ -259,6 +261,7 @@ public class FeatureColourChooser extends Panel implements ActionListener, private GraphLine threshline; + @Override public void actionPerformed(ActionEvent evt) { if (evt.getSource() == thresholdValue) @@ -286,6 +289,7 @@ public class FeatureColourChooser extends Panel implements ActionListener, } } + @Override public void itemStateChanged(ItemEvent evt) { maxColour.setEnabled(!colourFromLabel.getState()); @@ -293,27 +297,28 @@ public class FeatureColourChooser extends Panel implements ActionListener, changeColour(); } + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { if (!adjusting) { - thresholdValue.setText(((float) slider.getValue() / 1000f) + ""); + thresholdValue.setText((slider.getValue() / 1000f) + ""); valueChanged(); } } protected void valueChanged() { - threshline.value = (float) slider.getValue() / 1000f; - cs.setThresh(threshline.value); + threshline.value = slider.getValue() / 1000f; + cs.setThreshold(threshline.value); changeColour(); PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId()); // ap.paintAlignment(false); } - public void minColour_actionPerformed(Color newCol) + public void minColour_actionPerformed(Color c) { - if (newCol == null) + if (c == null) { UserDefinedColours udc = new UserDefinedColours(this, minColour.getBackground(), owner, @@ -321,8 +326,8 @@ public class FeatureColourChooser extends Panel implements ActionListener, } else { - minColour.setBackground(newCol); - minColour.setForeground(newCol); + minColour.setBackground(c); + minColour.setForeground(c); minColour.repaint(); changeColour(); } @@ -369,8 +374,9 @@ public class FeatureColourChooser extends Panel implements ActionListener, slider.setEnabled(true); thresholdValue.setEnabled(true); - GraduatedColor acg = new GraduatedColor(minColour.getBackground(), - maxColour.getBackground(), min, max); + FeatureColour acg = new FeatureColour(new Colour( + minColour.getBackground()), new Colour( + maxColour.getBackground()), min, max); acg.setColourByLabel(colourFromLabel.getState()); maxColour.setEnabled(!colourFromLabel.getState()); @@ -393,7 +399,7 @@ public class FeatureColourChooser extends Panel implements ActionListener, if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD) { adjusting = true; - acg.setThresh(threshline.value); + acg.setThreshold(threshline.value); float range = max * 1000f - min * 1000f; @@ -406,17 +412,17 @@ public class FeatureColourChooser extends Panel implements ActionListener, adjusting = false; } - acg.setThreshType(aboveThreshold); + acg.setAboveThreshold(true); if (thresholdIsMin.getState() && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD) { if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD) { - acg = new GraduatedColor(acg, threshline.value, max); + acg = new FeatureColour(acg, threshline.value, max); } else { - acg = new GraduatedColor(acg, min, threshline.value); + acg = new FeatureColour(acg, min, threshline.value); } } @@ -434,14 +440,17 @@ public class FeatureColourChooser extends Panel implements ActionListener, } + @Override public void mouseClicked(MouseEvent evt) { } + @Override public void mousePressed(MouseEvent evt) { } + @Override public void mouseReleased(MouseEvent evt) { if (evt.getSource() == minColour || evt.getSource() == maxColour) @@ -456,10 +465,12 @@ public class FeatureColourChooser extends Panel implements ActionListener, // ap.paintAlignment(true); } + @Override public void mouseEntered(MouseEvent evt) { } + @Override public void mouseExited(MouseEvent evt) { } diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index 03d4ce6..b979674 100644 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -20,11 +20,15 @@ */ package jalview.appletgui; +import jalview.api.FeatureColourI; import jalview.datamodel.SearchResults; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +import jalview.io.FeaturesFile; +import jalview.schemes.Colour; +import jalview.schemes.FeatureColour; +import jalview.schemes.UserColourScheme; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -43,6 +47,9 @@ import java.awt.TextArea; import java.awt.TextField; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.util.Hashtable; /** * DOCUMENT ME! @@ -88,51 +95,35 @@ public class FeatureRenderer extends /** * render a feature style in the amend feature dialog box */ - public void updateColor(Object newcol) + public void updateColor(FeatureColourI newcol) { - - Color bg, col = null; - GraduatedColor gcol = null; + Color bg = null; String vlabel = ""; - if (newcol instanceof Color) - { - isGcol = false; - col = (Color) newcol; - gcol = null; - } - else if (newcol instanceof GraduatedColor) + if (newcol.isSimpleColour()) { - isGcol = true; - gcol = (GraduatedColor) newcol; - col = null; + bg = ColorUtils.getColor(newcol.getColour()); + setBackground(bg); } else { - throw new Error( - MessageManager - .getString("error.invalid_colour_for_mycheckbox")); - } - if (col != null) - { - setBackground(bg = col); - } - else - { - if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) + if (newcol.isAboveThreshold()) + { + vlabel += " (>)"; + } + else if (newcol.isBelowThreshold()) { - vlabel += " " - + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" - : "(<)"); + vlabel += " (<)"; } - if (isColourByLabel = gcol.isColourByLabel()) + + if (isColourByLabel = newcol.isColourByLabel()) { setBackground(bg = Color.white); vlabel += " (by Label)"; } else { - setBackground(bg = gcol.getMinColor()); - maxCol = gcol.getMaxColor(); + setBackground(bg = ColorUtils.getColor(newcol.getMinColour())); + maxCol = ColorUtils.getColor(newcol.getMaxColour()); } } label = vlabel; @@ -239,11 +230,12 @@ public class FeatureRenderer extends ap.seqPanel.seqCanvas.highlightSearchResults(highlight); } - Object col = getFeatureStyle(name.getText()); + FeatureColourI col = getFeatureStyle(name.getText()); if (col == null) { - col = new jalview.schemes.UserColourScheme() + Color generatedColour = UserColourScheme .createColourFromName(name.getText()); + col = new FeatureColour(new Colour(generatedColour)); } colourPanel.updateColor(col); @@ -351,21 +343,16 @@ public class FeatureRenderer extends start.setText(features[0].getBegin() + ""); end.setText(features[0].getEnd() + ""); description.setText(features[0].getDescription()); - Color col = getColour(name.getText()); - if (col == null) - { - col = new jalview.schemes.UserColourScheme() - .createColourFromName(name.getText()); - } - Object fcol = getFeatureStyle(name.getText()); + // lookup (or generate) the feature colour + FeatureColourI fcol = getFeatureStyle(name.getText()); // simply display the feature color in a box colourPanel.updateColor(fcol); dialog.setResizable(true); // TODO: render the graduated color in the box. - colourPanel.addMouseListener(new java.awt.event.MouseAdapter() + colourPanel.addMouseListener(new MouseAdapter() { @Override - public void mousePressed(java.awt.event.MouseEvent evt) + public void mousePressed(MouseEvent evt) { if (!colourPanel.isGcol) { @@ -373,15 +360,14 @@ public class FeatureRenderer extends } else { - FeatureColourChooser fcc = new FeatureColourChooser( - ap.alignFrame, name.getText()); + new FeatureColourChooser(ap.alignFrame, name.getText()); dialog.transferFocus(); } } }); dialog.setVisible(true); - jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); + FeaturesFile ffile = new FeaturesFile(); if (dialog.accept) { @@ -410,7 +396,9 @@ public class FeatureRenderer extends if (!colourPanel.isGcol) { // update colour - otherwise its already done. - setColour(sf.type, colourPanel.getBackground()); + setColour( + sf.type, + new FeatureColour(new Colour(colourPanel.getBackground()))); } try { @@ -450,7 +438,8 @@ public class FeatureRenderer extends { setGroupVisibility(lastFeatureGroupAdded, true); } - setColour(lastFeatureAdded, newColour); // was fcol + setColour(lastFeatureAdded, + new FeatureColour(new Colour(newColour))); // was fcol setVisible(lastFeatureAdded); findAllFeatures(false); // different to original applet behaviour ? // findAllFeatures(); diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index 7ae318c..e765f31 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -20,11 +20,11 @@ */ package jalview.appletgui; +import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceFeature; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -190,10 +190,10 @@ public class FeatureSettings extends Panel implements ItemListener, int x, int y) { final String type = check.type; - final Object typeCol = fr.getFeatureStyle(type); - java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage( + final FeatureColourI typeCol = fr.getFeatureStyle(type); + PopupMenu men = new PopupMenu(MessageManager.formatMessage( "label.settings_for_type", new String[] { type })); - java.awt.MenuItem scr = new MenuItem( + MenuItem scr = new MenuItem( MessageManager.getString("label.sort_by_score")); men.add(scr); final FeatureSettings me = this; @@ -243,7 +243,7 @@ public class FeatureSettings extends Panel implements ItemListener, // graduated colourschemes for those where minmax exists for the // positional features MenuItem mxcol = new MenuItem( - (typeCol instanceof Color) ? "Graduated Colour" + (typeCol.isSimpleColour()) ? "Graduated Colour" : "Single Colour"); men.add(mxcol); mxcol.addActionListener(new ActionListener() @@ -252,7 +252,7 @@ public class FeatureSettings extends Panel implements ItemListener, @Override public void actionPerformed(ActionEvent e) { - if (typeCol instanceof Color) + if (typeCol.isSimpleColour()) { new FeatureColourChooser(me, type); // write back the current colour object to update the table @@ -260,8 +260,7 @@ public class FeatureSettings extends Panel implements ItemListener, } else { - new UserDefinedColours(me, check.type, - ((GraduatedColor) typeCol)); + new UserDefinedColours(me, check.type, typeCol); } } @@ -637,19 +636,9 @@ public class FeatureSettings extends Panel implements ItemListener, } } - public void setUserColour(String feature, Object originalColour) + public void setUserColour(String feature, FeatureColourI originalColour) { - if (originalColour instanceof Color - || originalColour instanceof GraduatedColor) - { - fr.setColour(feature, originalColour); - } - else - { - throw new Error( - MessageManager - .getString("error.implementation_error_unsupported_feature_colour_object")); - } + fr.setColour(feature, originalColour); refreshTable(); } @@ -686,10 +675,11 @@ public class FeatureSettings extends Panel implements ItemListener, if (evt.getClickCount() > 1) { - Object fcol = fr.getFeatureStyle(check.type); - if (fcol instanceof Color) + FeatureColourI fcol = fr.getFeatureStyle(check.type); + if (fcol.isSimpleColour()) { - new UserDefinedColours(this, check.type, (Color) fcol); + new UserDefinedColours(this, check.type, ColorUtils.getColor(fcol + .getColour())); } else { @@ -721,49 +711,34 @@ public class FeatureSettings extends Panel implements ItemListener, boolean hasLink; - GraduatedColor gcol; - - Color col; + FeatureColourI col; - public void updateColor(Object newcol) + public void updateColor(FeatureColourI newcol) { - if (newcol instanceof Color) - { - col = (Color) newcol; - gcol = null; - } - else if (newcol instanceof GraduatedColor) - { - gcol = (GraduatedColor) newcol; - col = null; - } - else + col = newcol; + if (col.isSimpleColour()) { - throw new Error( - MessageManager - .getString("error.invalid_colour_for_mycheckbox")); - } - if (col != null) - { - setBackground(col); + setBackground(ColorUtils.getColor(col.getColour())); } else { String vlabel = type; - if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) + if (col.isAboveThreshold()) + { + vlabel += " (>)"; + } + else if (col.isBelowThreshold()) { - vlabel += " " - + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" - : "(<)"); + vlabel += " (<)"; } - if (gcol.isColourByLabel()) + if (col.isColourByLabel()) { setBackground(Color.white); vlabel += " (by Label)"; } else { - setBackground(gcol.getMinColor()); + setBackground(ColorUtils.getColor(col.getMinColour())); } this.setLabel(vlabel); } @@ -780,7 +755,7 @@ public class FeatureSettings extends Panel implements ItemListener, } public MyCheckbox(String type, boolean selected, boolean b, - Object featureStyle) + FeatureColourI featureStyle) { this(type, selected, b); updateColor(featureStyle); @@ -790,31 +765,28 @@ public class FeatureSettings extends Panel implements ItemListener, public void paint(Graphics g) { Dimension d = getSize(); - if (gcol != null) + if (col.isColourByLabel()) { - if (gcol.isColourByLabel()) - { - g.setColor(Color.white); - g.fillRect(d.width / 2, 0, d.width / 2, d.height); - /* - * g.setColor(Color.black); Font f=g.getFont().deriveFont(9); - * g.setFont(f); - * - * // g.setFont(g.getFont().deriveFont( // - * AffineTransform.getScaleInstance( // - * width/g.getFontMetrics().stringWidth("Label"), // - * height/g.getFontMetrics().getHeight()))); g.drawString("Label", - * width/2, 0); - */ + g.setColor(Color.white); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + /* + * g.setColor(Color.black); Font f=g.getFont().deriveFont(9); + * g.setFont(f); + * + * // g.setFont(g.getFont().deriveFont( // + * AffineTransform.getScaleInstance( // + * width/g.getFontMetrics().stringWidth("Label"), // + * height/g.getFontMetrics().getHeight()))); g.drawString("Label", + * width/2, 0); + */ - } - else - { - Color maxCol = gcol.getMaxColor(); - g.setColor(maxCol); - g.fillRect(d.width / 2, 0, d.width / 2, d.height); + } + else if (col.isGraduatedColour()) + { + Color maxCol = ColorUtils.getColor(col.getMaxColour()); + g.setColor(maxCol); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); - } } if (hasLink) diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java index d72e91f..4386dee 100755 --- a/src/jalview/appletgui/IdCanvas.java +++ b/src/jalview/appletgui/IdCanvas.java @@ -21,6 +21,7 @@ package jalview.appletgui; import jalview.datamodel.SequenceI; +import jalview.util.ColorUtils; import java.awt.Color; import java.awt.Font; @@ -78,7 +79,7 @@ public class IdCanvas extends Panel } else { - gg.setColor(av.getSequenceColour(s)); + gg.setColor(ColorUtils.getColor(av.getSequenceColour(s))); gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width, charHeight); gg.setColor(Color.black); @@ -293,7 +294,7 @@ public class IdCanvas extends Panel } else { - currentColor = av.getSequenceColour(seq); + currentColor = ColorUtils.getColor(av.getSequenceColour(seq)); currentTextColor = Color.black; } diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index bc64728..edf8645 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -21,6 +21,7 @@ package jalview.appletgui; import jalview.datamodel.AlignmentI; +import jalview.util.ColorUtils; import java.awt.Color; import java.awt.Dimension; @@ -344,11 +345,12 @@ public class OverviewPanel extends Panel implements Runnable, if (seq.getLength() > lastcol) { - color = sr.getResidueBoxColour(seq, lastcol); + color = ColorUtils.getColor(sr.getResidueBoxColour(seq, lastcol)); if (av.isShowSequenceFeatures()) { - color = fr.findFeatureColour(color, seq, lastcol); + color = ColorUtils.getColor(fr.findFeatureColour(color, seq, + lastcol)); } } else diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java index 5c91ea8..615edbd 100755 --- a/src/jalview/appletgui/RotatableCanvas.java +++ b/src/jalview/appletgui/RotatableCanvas.java @@ -25,6 +25,7 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.datamodel.SequencePoint; import jalview.math.RotatableMatrix; +import jalview.util.ColorUtils; import jalview.util.Format; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -126,6 +127,7 @@ public class RotatableCanvas extends Panel implements MouseListener, repaint(); } + @Override public void setPoints(Vector points, int npoint) { this.points = points; @@ -287,7 +289,7 @@ public class RotatableCanvas extends Panel implements MouseListener, dim = height; } - return (float) (dim * scalefactor / (2 * maxwidth)); + return dim * scalefactor / (2 * maxwidth); } public void findCentre() @@ -304,6 +306,7 @@ public class RotatableCanvas extends Panel implements MouseListener, // System.out.println("Centre z " + centre[2]); } + @Override public Dimension getPreferredSize() { if (prefsize != null) @@ -316,16 +319,19 @@ public class RotatableCanvas extends Panel implements MouseListener, } } + @Override public Dimension getMinimumSize() { return getPreferredSize(); } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { if (points == null) @@ -397,8 +403,8 @@ public class RotatableCanvas extends Panel implements MouseListener, for (int i = 0; i < npoint; i++) { SequencePoint sp = (SequencePoint) points.elementAt(i); - int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth; - int y = (int) ((float) (sp.coord[1] - centre[1]) * scale) + int x = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth; + int y = (int) ((sp.coord[1] - centre[1]) * scale) + halfheight; float z = sp.coord[1] - centre[2]; @@ -408,7 +414,7 @@ public class RotatableCanvas extends Panel implements MouseListener, } else { - g.setColor(av.getSequenceColour(sp.sequence)); + g.setColor(ColorUtils.getColor(av.getSequenceColour(sp.sequence))); } if (av.getSelectionGroup() != null) @@ -445,14 +451,17 @@ public class RotatableCanvas extends Panel implements MouseListener, return prefsize; } + @Override public void keyTyped(KeyEvent evt) { } + @Override public void keyReleased(KeyEvent evt) { } + @Override public void keyPressed(KeyEvent evt) { if (evt.getKeyCode() == KeyEvent.VK_UP) @@ -491,22 +500,27 @@ public class RotatableCanvas extends Panel implements MouseListener, } } + @Override public void mouseClicked(MouseEvent evt) { } + @Override public void mouseEntered(MouseEvent evt) { } + @Override public void mouseExited(MouseEvent evt) { } + @Override public void mouseReleased(MouseEvent evt) { } + @Override public void mousePressed(MouseEvent evt) { int x = evt.getX(); @@ -551,6 +565,7 @@ public class RotatableCanvas extends Panel implements MouseListener, repaint(); } + @Override public void mouseMoved(MouseEvent evt) { SequenceI found = findPoint(evt.getX(), evt.getY()); @@ -567,6 +582,7 @@ public class RotatableCanvas extends Panel implements MouseListener, repaint(); } + @Override public void mouseDragged(MouseEvent evt) { mx = evt.getX(); @@ -574,8 +590,8 @@ public class RotatableCanvas extends Panel implements MouseListener, rotmat.setIdentity(); - rotmat.rotate((float) (my - omy), 'x'); - rotmat.rotate((float) (mx - omx), 'y'); + rotmat.rotate(my - omy, 'x'); + rotmat.rotate(mx - omx, 'y'); for (int i = 0; i < npoint; i++) { @@ -609,8 +625,8 @@ public class RotatableCanvas extends Panel implements MouseListener, for (int i = 0; i < npoint; i++) { SequencePoint sp = (SequencePoint) points.elementAt(i); - int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale + (float) getSize().width / 2.0); - int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale + (float) getSize().height / 2.0); + int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale + getSize().width / 2.0); + int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale + getSize().height / 2.0); if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2) { @@ -638,9 +654,9 @@ public class RotatableCanvas extends Panel implements MouseListener, { SequencePoint sp = (SequencePoint) points.elementAt(i); - int px = (int) ((float) (sp.coord[0] - centre[0]) * scale) + int px = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth; - int py = (int) ((float) (sp.coord[1] - centre[1]) * scale) + int py = (int) ((sp.coord[1] - centre[1]) * scale) + halfheight; if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3) diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index 024fdc7..0e5c0e7 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.SearchResults; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.util.ColorUtils; import jalview.viewmodel.AlignmentViewport; import java.awt.Color; @@ -731,7 +732,7 @@ public class SeqCanvas extends Panel } else { - g.setColor(group.getOutlineColour()); + g.setColor(ColorUtils.getColor(group.getOutlineColour())); } } } diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index 09b50c4..a64686a 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -20,9 +20,11 @@ */ package jalview.appletgui; +import jalview.api.ColorI; import jalview.api.FeatureRenderer; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; import java.awt.Color; @@ -67,7 +69,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer this.renderGaps = renderGaps; } - public Color getResidueBoxColour(SequenceI seq, int i) + @Override + public ColorI getResidueBoxColour(SequenceI seq, int i) { allGroups = av.getAlignment().findAllGroups(seq); @@ -83,7 +86,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer getBoxColour(av.getGlobalColourScheme(), seq, i); } - return resBoxColour; + return new Colour(resBoxColour); } /** @@ -97,12 +100,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer * @return */ @Override - public Color getResidueColour(final SequenceI seq, int position, + public ColorI getResidueColour(final SequenceI seq, int position, FeatureRenderer fr) { // TODO replace 8 or so code duplications with calls to this method // (refactored as needed) - Color col = getResidueBoxColour(seq, position); + ColorI col = getResidueBoxColour(seq, position); if (fr != null) { diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index edcd961..626960d 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -27,10 +27,12 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceNode; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; +import jalview.util.ColorUtils; import jalview.util.Format; import jalview.util.MappingUtils; import jalview.viewmodel.AlignmentViewport; @@ -176,7 +178,8 @@ public class TreeCanvas extends Panel implements MouseListener, } else { - g.setColor(av.getSequenceColour(seq).darker()); + g.setColor(ColorUtils.getColor(av.getSequenceColour(seq)) + .darker()); } } @@ -403,7 +406,7 @@ public class TreeCanvas extends Panel implements MouseListener, if (node.element() instanceof SequenceI) { - av.setSequenceColour((SequenceI) node.element(), c); + av.setSequenceColour((SequenceI) node.element(), new Colour(c)); } } else @@ -707,7 +710,7 @@ public class TreeCanvas extends Panel implements MouseListener, for (SequenceI seq : mappedGroup.getSequences()) { // TODO why does gui require col.brighter() here?? - codingComplement.setSequenceColour(seq, col); + codingComplement.setSequenceColour(seq, new Colour(col)); } } } diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java index 57cf669..b1ccd51 100644 --- a/src/jalview/appletgui/UserDefinedColours.java +++ b/src/jalview/appletgui/UserDefinedColours.java @@ -20,11 +20,14 @@ */ package jalview.appletgui; +import jalview.api.FeatureColourI; import jalview.datamodel.SequenceGroup; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; -import jalview.schemes.GraduatedColor; +import jalview.schemes.FeatureColour; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import java.awt.Button; @@ -59,7 +62,7 @@ public class UserDefinedColours extends Panel implements ActionListener, Button selectedButton; - Vector oldColours = new Vector(); + Vector oldColours = new Vector(); ColourSchemeI oldColourScheme; @@ -75,7 +78,7 @@ public class UserDefinedColours extends Panel implements ActionListener, String originalLabel; - Object originalColour; + FeatureColourI originalColour; int R = 0, G = 0, B = 0; @@ -117,7 +120,8 @@ public class UserDefinedColours extends Panel implements ActionListener, public UserDefinedColours(FeatureRenderer fr, Frame alignframe) { caller = fr; - originalColour = fr.colourPanel.getBackground(); + originalColour = new FeatureColour(new Colour( + fr.colourPanel.getBackground())); originalLabel = "Feature Colour"; setForDialog("Select Feature Colour", alignframe); setTargetColour(fr.colourPanel.getBackground()); @@ -134,21 +138,21 @@ public class UserDefinedColours extends Panel implements ActionListener, * * @param caller * - handles events - * @param col1 + * @param col * - original colour * @param alignframe * - the parent Frame for the dialog * @param title * - window title */ - public UserDefinedColours(Component caller, Color col1, Frame alignframe, + public UserDefinedColours(Component caller, Color col, Frame alignframe, String title) { this.caller = caller; - originalColour = col1; + originalColour = new FeatureColour(new Colour(col)); originalLabel = title; setForDialog(title, alignframe); - setTargetColour(col1); + setTargetColour(col); dialog.setVisible(true); } @@ -161,7 +165,7 @@ public class UserDefinedColours extends Panel implements ActionListener, */ public UserDefinedColours(Object caller, String label, Color colour) { - this(caller, label, colour, colour); + this(caller, label, new FeatureColour(new Colour(colour)), colour); } /** @@ -172,13 +176,14 @@ public class UserDefinedColours extends Panel implements ActionListener, * @param graduatedColor */ public UserDefinedColours(FeatureSettings me, String type, - GraduatedColor graduatedColor) + FeatureColourI graduatedColor) { - this(me, type, graduatedColor, graduatedColor.getMaxColor()); + this(me, type, graduatedColor, ColorUtils.getColor(graduatedColor + .getMaxColour())); } - private UserDefinedColours(Object caller, String label, Object ocolour, - Color colour) + private UserDefinedColours(Object caller, String label, + FeatureColourI ocolour, Color colour) { this.caller = caller; originalColour = ocolour; @@ -228,6 +233,7 @@ public class UserDefinedColours extends Panel implements ActionListener, } + @Override public void actionPerformed(ActionEvent evt) { final Object source = evt.getSource(); @@ -257,6 +263,7 @@ public class UserDefinedColours extends Panel implements ActionListener, } } + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { if (evt.getSource() == rScroller) @@ -420,6 +427,7 @@ public class UserDefinedColours extends Panel implements ActionListener, button.setFont(new java.awt.Font("Verdana", 1, 10)); button.addMouseListener(new java.awt.event.MouseAdapter() { + @Override public void mousePressed(MouseEvent e) { colourButtonPressed(e); @@ -451,7 +459,8 @@ public class UserDefinedColours extends Panel implements ActionListener, { if (caller instanceof FeatureSettings) { - ((FeatureSettings) caller).setUserColour(originalLabel, getColor()); + ((FeatureSettings) caller).setUserColour(originalLabel, + new FeatureColour(new Colour(getColor()))); } else if (caller instanceof AnnotationColourChooser) { @@ -468,7 +477,8 @@ public class UserDefinedColours extends Panel implements ActionListener, } else if (caller instanceof FeatureRenderer) { - ((FeatureRenderer) caller).colourPanel.updateColor(getColor()); + ((FeatureRenderer) caller).colourPanel + .updateColor(new FeatureColour(new Colour(getColor()))); } else if (caller instanceof FeatureColourChooser) { @@ -537,12 +547,14 @@ public class UserDefinedColours extends Panel implements ActionListener, if (originalLabel.equals("Min Colour")) { ((AnnotationColourChooser) caller) - .minColour_actionPerformed((Color) originalColour); + .minColour_actionPerformed(ColorUtils + .getColor(originalColour.getColour())); } else { ((AnnotationColourChooser) caller) - .maxColour_actionPerformed((Color) originalColour); + .maxColour_actionPerformed(ColorUtils + .getColor(originalColour.getColour())); } } else if (caller instanceof FeatureRenderer) @@ -556,12 +568,14 @@ public class UserDefinedColours extends Panel implements ActionListener, if (originalLabel.indexOf("inimum") > -1) { ((FeatureColourChooser) caller) - .minColour_actionPerformed((Color) originalColour); + .minColour_actionPerformed(ColorUtils + .getColor(originalColour.getColour())); } else { ((FeatureColourChooser) caller) - .maxColour_actionPerformed((Color) originalColour); + .maxColour_actionPerformed(ColorUtils + .getColor(originalColour.getColour())); } } if (dialog != null) @@ -576,7 +590,7 @@ public class UserDefinedColours extends Panel implements ActionListener, Color[] newColours = new Color[24]; for (int i = 0; i < 24; i++) { - newColours[i] = (Color) oldColours.elementAt(i); + newColours[i] = oldColours.elementAt(i); buttonPanel.getComponent(i).setBackground(newColours[i]); } diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index 24439ca..5ab522e 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -25,6 +25,7 @@ import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.ColorI; import jalview.api.FeatureRenderer; import jalview.commands.OrderCommand; import jalview.datamodel.AlignmentI; @@ -34,6 +35,7 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.FeaturesFile; +import jalview.schemes.Colour; import jalview.util.MessageManager; import java.awt.Color; @@ -112,10 +114,10 @@ public class AlignViewController implements AlignViewControllerI viewport.getAlignment().addGroup(gps[g]); Color col = new Color((int) (Math.random() * 255), (int) (Math.random() * 255), (int) (Math.random() * 255)); - col = col.brighter(); + ColorI newcol = new Colour(col.brighter()); for (SequenceI sq : gps[g].getSequences(null)) { - viewport.setSequenceColour(sq, col); + viewport.setSequenceColour(sq, newcol); } } return true; diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 0e8fa17..b9cdf0e 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -22,6 +22,8 @@ package jalview.datamodel; import jalview.analysis.AAFrequency; import jalview.analysis.Conservation; +import jalview.api.ColorI; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; @@ -82,15 +84,15 @@ public class SequenceGroup implements AnnotatedCollectionI // end column (base 0) int endRes = 0; - public Color outlineColour = Color.black; + public ColorI outlineColour = Colour.black; - public Color idColour = null; + public ColorI idColour = null; public int thresholdTextColour = 0; - public Color textColour = Color.black; + public ColorI textColour = Colour.black; - public Color textColour2 = Color.white; + public ColorI textColour2 = Colour.white; /** * consensus calculation property @@ -796,7 +798,7 @@ public class SequenceGroup implements AnnotatedCollectionI */ public void setOutlineColour(Color c) { - outlineColour = c; + outlineColour = new Colour(c); } /** @@ -804,7 +806,7 @@ public class SequenceGroup implements AnnotatedCollectionI * * @return DOCUMENT ME! */ - public Color getOutlineColour() + public ColorI getOutlineColour() { return outlineColour; } @@ -877,7 +879,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * @return the idColour */ - public Color getIdColour() + public ColorI getIdColour() { return idColour; } @@ -888,12 +890,13 @@ public class SequenceGroup implements AnnotatedCollectionI */ public void setIdColour(Color idColour) { - this.idColour = idColour; + this.idColour = new Colour(idColour); } /** * @return the representative sequence for this group */ + @Override public SequenceI getSeqrep() { return seqrep; @@ -906,6 +909,7 @@ public class SequenceGroup implements AnnotatedCollectionI * @param seqrep * the seqrep to set (null means no sequence representative) */ + @Override public void setSeqrep(SequenceI seqrep) { this.seqrep = seqrep; @@ -915,6 +919,7 @@ public class SequenceGroup implements AnnotatedCollectionI * * @return true if group has a sequence representative */ + @Override public boolean hasSeqrep() { return seqrep != null; diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index 4dd1bba..b320e83 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -1,5 +1,6 @@ package jalview.ext.ensembl; +import jalview.api.ColorI; import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsModelI; import jalview.datamodel.AlignmentI; @@ -8,11 +9,11 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; +import jalview.schemes.Colour; import jalview.schemes.FeatureColourAdapter; import jalview.schemes.FeatureSettingsAdapter; import jalview.util.MapList; -import java.awt.Color; import java.io.UnsupportedEncodingException; import java.net.URLDecoder; import java.util.ArrayList; @@ -551,9 +552,9 @@ public class EnsemblGene extends EnsemblSeqProxy { @Override - public Color getColour() + public ColorI getColour() { - return Color.RED; + return Colour.red; } }; } diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java index d5676c5..0114d1c 100644 --- a/src/jalview/ext/jmol/JmolCommands.java +++ b/src/jalview/ext/jmol/JmolCommands.java @@ -20,6 +20,7 @@ */ package jalview.ext.jmol; +import jalview.api.ColorI; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.datamodel.AlignmentI; @@ -28,7 +29,6 @@ import jalview.structure.StructureMapping; import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; -import java.awt.Color; import java.util.ArrayList; /** @@ -93,7 +93,7 @@ public class JmolCommands lastPos = pos; - Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r); + ColorI col = sr.getResidueBoxColour(sequence[pdbfnum][s], r); if (fr != null) { diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index a551ca2..930d6fe 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -20,6 +20,7 @@ */ package jalview.ext.rbvi.chimera; +import jalview.api.ColorI; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.datamodel.AlignmentI; @@ -30,7 +31,6 @@ import jalview.structure.StructureSelectionManager; import jalview.util.ColorUtils; import jalview.util.Comparison; -import java.awt.Color; import java.util.ArrayList; import java.util.LinkedHashMap; import java.util.List; @@ -58,7 +58,7 @@ public class ChimeraCommands SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment) { - Map>>> colourMap = buildColoursMap( + Map>>> colourMap = buildColoursMap( ssm, files, sequence, sr, fr, alignment); List colourCommands = buildColourCommands(colourMap); @@ -86,7 +86,7 @@ public class ChimeraCommands * @return */ protected static List buildColourCommands( - Map>>> colourMap) + Map>>> colourMap) { /* * This version concatenates all commands into a single String (semi-colon @@ -96,7 +96,7 @@ public class ChimeraCommands List commands = new ArrayList(); StringBuilder sb = new StringBuilder(256); boolean firstColour = true; - for (Color colour : colourMap.keySet()) + for (ColorI colour : colourMap.keySet()) { String colourCode = ColorUtils.toTkCode(colour); if (!firstColour) @@ -161,13 +161,13 @@ public class ChimeraCommands * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains) * */ - protected static Map>>> buildColoursMap( + protected static Map>>> buildColoursMap( StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment) { - Map>>> colourMap = new LinkedHashMap>>>(); - Color lastColour = null; + Map>>> colourMap = new LinkedHashMap>>>(); + ColorI lastColour = null; for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); @@ -202,7 +202,7 @@ public class ChimeraCommands continue; } - Color colour = sr.getResidueColour(seq, r, fr); + ColorI colour = sr.getResidueColour(seq, r, fr); final String chain = mapping[m].getChain(); /* @@ -251,8 +251,8 @@ public class ChimeraCommands * @param chain */ protected static void addColourRange( - Map>>> colourMap, - Color colour, int model, int startPos, int endPos, String chain) + Map>>> colourMap, + ColorI colour, int model, int startPos, int endPos, String chain) { /* * Get/initialize map of data for the colour diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java index a41e10e..d0d0b5b 100644 --- a/src/jalview/ext/varna/VarnaCommands.java +++ b/src/jalview/ext/varna/VarnaCommands.java @@ -20,6 +20,7 @@ */ package jalview.ext.varna; +import jalview.api.ColorI; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.datamodel.AlignmentI; @@ -27,7 +28,6 @@ import jalview.datamodel.SequenceI; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; -import java.awt.Color; import java.util.ArrayList; /** @@ -58,7 +58,9 @@ public class VarnaCommands StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); if (mapping == null || mapping.length < 1) + { continue; + } int lastPos = -1; for (int s = 0; s < sequence[pdbfnum].length; s++) @@ -79,14 +81,18 @@ public class VarnaCommands int pos = mapping[m].getPDBResNum(asp.findPosition(r)); if (pos < 1 || pos == lastPos) + { continue; + } lastPos = pos; - Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r); + ColorI col = sr.getResidueBoxColour(sequence[pdbfnum][s], r); if (fr != null) + { col = fr.findFeatureColour(col, sequence[pdbfnum][s], r); + } String newSelcom = (mapping[m].getChain() != " " ? ":" + mapping[m].getChain() : "") + "/" diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index f06ca94..7b0d717 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -33,6 +33,7 @@ import jalview.jbgui.GAlignmentPanel; import jalview.math.AlignmentDimension; import jalview.schemes.ResidueProperties; import jalview.structure.StructureSelectionManager; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import jalview.util.Platform; @@ -1068,7 +1069,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - currentColor = av.getSequenceColour(seq); + currentColor = ColorUtils.getColor(av.getSequenceColour(seq)); currentTextColor = Color.black; } diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java index d688ddd..cffc52f 100644 --- a/src/jalview/gui/AnnotationExporter.java +++ b/src/jalview/gui/AnnotationExporter.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.api.FeatureColourI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.SequenceI; import jalview.io.AnnotationFile; @@ -157,7 +158,7 @@ public class AnnotationExporter extends JPanel { FeaturesFile formatter = new FeaturesFile(); SequenceI[] sequences = ap.av.getAlignment().getSequencesArray(); - Map featureColours = ap.getFeatureRenderer() + Map featureColours = ap.getFeatureRenderer() .getDisplayedFeatureCols(); boolean includeNonPositional = ap.av.isShowNPFeats(); if (GFFFormat.isSelected()) diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index f4a4f4d..e754adf 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -32,6 +32,7 @@ import jalview.structure.SelectionListener; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; +import jalview.util.ColorUtils; import jalview.util.Comparison; import jalview.util.MessageManager; import jalview.util.ShiftList; @@ -424,7 +425,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener, } selectionHighlighter.highlightRegion(rna, start, end); selectionHighlighter.getLastHighlight().setOutlineColor( - seqsel.getOutlineColour()); + ColorUtils.getColor(seqsel.getOutlineColour())); // TODO - translate column markings to positions on structure if present. vab.updateSelectedRNA(rna); } diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java index 064d58b..ac22aca 100644 --- a/src/jalview/gui/FeatureColourChooser.java +++ b/src/jalview/gui/FeatureColourChooser.java @@ -20,9 +20,11 @@ */ package jalview.gui; +import jalview.api.FeatureColourI; import jalview.datamodel.GraphLine; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +import jalview.schemes.Colour; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -33,7 +35,6 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; -import java.util.Hashtable; import javax.swing.BorderFactory; import javax.swing.JCheckBox; @@ -52,16 +53,16 @@ public class FeatureColourChooser extends JalviewDialog // FeatureSettings fs; FeatureRenderer fr; - private GraduatedColor cs; + private FeatureColourI cs; - private Object oldcs; + private FeatureColourI oldcs; /** * * @return the last colour setting selected by user - either oldcs (which may * be a java.awt.Color) or the new GraduatedColor */ - public Object getLastColour() + public FeatureColourI getLastColour() { if (cs == null) { @@ -70,8 +71,6 @@ public class FeatureColourChooser extends JalviewDialog return cs; } - Hashtable oldgroupColours; - AlignmentPanel ap; boolean adjusting = false; @@ -127,7 +126,7 @@ public class FeatureColourChooser extends JalviewDialog } }); - float mm[] = ((float[][]) fr.getMinMax().get(type))[0]; + float mm[] = fr.getMinMax().get(type)[0]; min = mm[0]; max = mm[1]; @@ -139,32 +138,35 @@ public class FeatureColourChooser extends JalviewDialog scaleFactor = (max == min) ? 1f : 100f / (max - min); oldcs = fr.getFeatureColours().get(type); - if (oldcs instanceof GraduatedColor) + if (!oldcs.isSimpleColour()) { - if (((GraduatedColor) oldcs).isAutoScale()) + if (oldcs.isAutoScaled()) { // update the scale - cs = new GraduatedColor((GraduatedColor) oldcs, min, max); + cs = new FeatureColour((FeatureColour) oldcs, min, max); } else { - cs = new GraduatedColor((GraduatedColor) oldcs); + cs = new FeatureColour((FeatureColour) oldcs); } } else { // promote original color to a graduated color - Color bl = Color.black; - if (oldcs instanceof Color) + Color bl = ColorUtils.getColor(oldcs.getColour()); + if (bl == null) { - bl = (Color) oldcs; + bl = Color.BLACK; } // original colour becomes the maximum colour - cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]); + cs = new FeatureColour(new Colour(Color.white), new Colour(bl), + mm[0], mm[1]); cs.setColourByLabel(false); } - minColour.setBackground(oldminColour = cs.getMinColor()); - maxColour.setBackground(oldmaxColour = cs.getMaxColor()); + minColour.setBackground(oldminColour = ColorUtils.getColor(cs + .getMinColour())); + maxColour.setBackground(oldmaxColour = ColorUtils.getColor(cs + .getMaxColour())); adjusting = true; try @@ -174,18 +176,15 @@ public class FeatureColourChooser extends JalviewDialog { } // update the gui from threshold state - thresholdIsMin.setSelected(!cs.isAutoScale()); + thresholdIsMin.setSelected(!cs.isAutoScaled()); colourByLabel.setSelected(cs.isColourByLabel()); - if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) + if (cs.hasThreshold()) { // initialise threshold slider and selector - threshold - .setSelectedIndex(cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1 - : 2); + threshold.setSelectedIndex(cs.isAboveThreshold() ? 1 : 2); slider.setEnabled(true); thresholdValue.setEnabled(true); - threshline = new jalview.datamodel.GraphLine((max - min) / 2f, - "Threshold", Color.black); + threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black); } @@ -395,50 +394,52 @@ public class FeatureColourChooser extends JalviewDialog return; } - int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD; + boolean aboveThreshold = false; + boolean belowThreshold = false; if (threshold.getSelectedIndex() == 1) { - aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD; + aboveThreshold = true; } else if (threshold.getSelectedIndex() == 2) { - aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD; + belowThreshold = true; } + boolean hasThreshold = aboveThreshold || belowThreshold; slider.setEnabled(true); thresholdValue.setEnabled(true); - GraduatedColor acg; + FeatureColourI acg; if (cs.isColourByLabel()) { - acg = new GraduatedColor(oldminColour, oldmaxColour, min, max); + acg = new FeatureColour(new Colour(oldminColour), new Colour( + oldmaxColour), min, max); } else { - acg = new GraduatedColor(oldminColour = minColour.getBackground(), - oldmaxColour = maxColour.getBackground(), min, max); + acg = new FeatureColour(new Colour( + oldminColour = minColour.getBackground()), new Colour( + oldmaxColour = maxColour.getBackground()), min, max); } - if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD) + if (!hasThreshold) { slider.setEnabled(false); thresholdValue.setEnabled(false); thresholdValue.setText(""); thresholdIsMin.setEnabled(false); } - else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD - && threshline == null) + else if (threshline == null) { // todo visual indication of feature threshold - threshline = new jalview.datamodel.GraphLine((max - min) / 2f, - "Threshold", Color.black); + threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black); } - if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD) + if (hasThreshold) { adjusting = true; - acg.setThresh(threshline.value); + acg.setThreshold(threshline.value); float range = (max - min) * scaleFactor; @@ -453,18 +454,18 @@ public class FeatureColourChooser extends JalviewDialog adjusting = false; } - acg.setThreshType(aboveThreshold); - if (thresholdIsMin.isSelected() - && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD) + acg.setAboveThreshold(aboveThreshold); + acg.setBelowThreshold(belowThreshold); + if (thresholdIsMin.isSelected() && hasThreshold) { acg.setAutoScaled(false); - if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD) + if (aboveThreshold) { - acg = new GraduatedColor(acg, threshline.value, max); + acg = new FeatureColour((FeatureColour) acg, threshline.value, max); } else { - acg = new GraduatedColor(acg, min, threshline.value); + acg = new FeatureColour((FeatureColour) acg, min, threshline.value); } } else @@ -554,7 +555,7 @@ public class FeatureColourChooser extends JalviewDialog public void valueChanged() { threshline.value = slider.getValue() / scaleFactor; - cs.setThresh(threshline.value); + cs.setThreshold(threshline.value); changeColour(); ap.paintAlignment(false); } diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 1cf15ac..0284105 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -20,10 +20,14 @@ */ package jalview.gui; +import jalview.api.FeatureColourI; import jalview.datamodel.SearchResults; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; -import jalview.schemes.GraduatedColor; +import jalview.schemes.Colour; +import jalview.schemes.FeatureColour; +import jalview.schemes.UserColourScheme; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -94,7 +98,7 @@ public class FeatureRenderer extends static String lastDescriptionAdded; - Object oldcol, fcol; + FeatureColourI oldcol, fcol; int featureIndex = 0; @@ -126,20 +130,19 @@ public class FeatureRenderer extends @Override public void mousePressed(MouseEvent evt) { - if (fcol instanceof Color) + if (fcol.isSimpleColour()) { Color col = JColorChooser.showDialog(Desktop.desktop, MessageManager.getString("label.select_feature_colour"), - ((Color) fcol)); + ColorUtils.getColor(fcol.getColour())); if (col != null) { - fcol = col; - updateColourButton(bigPanel, colour, col); + fcol = new FeatureColour(new Colour(col)); + updateColourButton(bigPanel, colour, fcol); } } else { - if (fcc == null) { final String type = features[featureIndex].getType(); @@ -206,11 +209,11 @@ public class FeatureRenderer extends ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight); } - Object col = getFeatureStyle(name.getText()); + FeatureColourI col = getFeatureStyle(name.getText()); if (col == null) { - col = new jalview.schemes.UserColourScheme() - .createColourFromName(name.getText()); + col = new FeatureColour(new Colour(UserColourScheme + .createColourFromName(name.getText()))); } oldcol = fcol = col; updateColourButton(bigPanel, colour, col); @@ -420,27 +423,26 @@ public class FeatureRenderer extends * update the amend feature button dependent on the given style * * @param bigPanel + * @param colour * @param col - * @param col2 */ protected void updateColourButton(JPanel bigPanel, JLabel colour, - Object col2) + FeatureColourI col) { colour.removeAll(); colour.setIcon(null); colour.setToolTipText(null); colour.setText(""); - if (col2 instanceof Color) + if (col.isSimpleColour()) { - colour.setBackground((Color) col2); + colour.setBackground(ColorUtils.getColor(col.getColour())); } else { colour.setBackground(bigPanel.getBackground()); colour.setForeground(Color.black); - FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2); - // colour.setForeground(colour.getBackground()); + FeatureSettings.renderGraduatedColor(colour, col); } } diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 40635c0..187d3d0 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,15 +20,21 @@ */ package jalview.gui; +import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; import jalview.bin.Cache; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.Help.HelpId; import jalview.io.JalviewFileChooser; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +import jalview.schemabinding.version2.JalviewUserColours; +import jalview.schemes.Colour; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; +import jalview.util.Format; import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.QuickSort; import jalview.viewmodel.AlignmentViewport; import jalview.ws.dbsources.das.api.jalviewSourceI; @@ -160,8 +166,8 @@ public class FeatureSettings extends JPanel implements table.setDefaultEditor(Color.class, new ColorEditor(this)); - table.setDefaultEditor(GraduatedColor.class, new ColorEditor(this)); - table.setDefaultRenderer(GraduatedColor.class, new ColorRenderer()); + table.setDefaultEditor(FeatureColour.class, new ColorEditor(this)); + table.setDefaultRenderer(FeatureColour.class, new ColorRenderer()); table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); table.addMouseListener(new MouseAdapter() @@ -251,7 +257,7 @@ public class FeatureSettings extends JPanel implements frame = new JInternalFrame(); frame.setContentPane(this); - if (new jalview.util.Platform().isAMac()) + if (Platform.isAMac()) { Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), @@ -281,6 +287,8 @@ public class FeatureSettings extends JPanel implements final Object typeCol, final Map minmax, int x, int y) { + final FeatureColourI featureColour = (FeatureColourI) typeCol; + JPopupMenu men = new JPopupMenu(MessageManager.formatMessage( "label.settings_for_param", new String[] { type })); JMenuItem scr = new JMenuItem( @@ -336,7 +344,7 @@ public class FeatureSettings extends JPanel implements // positional features final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem( "Graduated Colour"); - mxcol.setSelected(!(typeCol instanceof Color)); + mxcol.setSelected(!featureColour.isSimpleColour()); men.add(mxcol); mxcol.addActionListener(new ActionListener() { @@ -347,7 +355,7 @@ public class FeatureSettings extends JPanel implements { if (e.getSource() == mxcol) { - if (typeCol instanceof Color) + if (featureColour.isSimpleColour()) { FeatureColourChooser fc = new FeatureColourChooser(me.fr, type); @@ -361,8 +369,8 @@ public class FeatureSettings extends JPanel implements "Select new Colour", true, // modal colorChooser, this, // OK button handler null); // no CANCEL button handler - colorChooser.setColor(((GraduatedColor) typeCol) - .getMaxColor()); + colorChooser.setColor(ColorUtils.getColor(featureColour + .getMaxColour())); dialog.setVisible(true); } } @@ -447,13 +455,13 @@ public class FeatureSettings extends JPanel implements /** * contains a float[3] for each feature type string. created by setTableData */ - Hashtable typeWidth = null; + Map typeWidth = null; @Override synchronized public void discoverAllFeatureData() { - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); + Vector allFeatures = new Vector(); + Vector allGroups = new Vector(); SequenceFeature[] tmpfeatures; String group; for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++) @@ -559,13 +567,13 @@ public class FeatureSettings extends JPanel implements return; } resettingTable = true; - typeWidth = new Hashtable(); + typeWidth = new Hashtable(); // TODO: change avWidth calculation to 'per-sequence' average and use long // rather than float float[] avWidth = null; SequenceFeature[] tmpfeatures; String group = null, type; - Vector visibleChecks = new Vector(); + Vector visibleChecks = new Vector(); // Find out which features should be visible depending on which groups // are selected / deselected @@ -606,7 +614,7 @@ public class FeatureSettings extends JPanel implements } else { - avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType()); + avWidth = typeWidth.get(tmpfeatures[index].getType()); } avWidth[0]++; if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd()) @@ -751,8 +759,7 @@ public class FeatureSettings extends JPanel implements InputStreamReader in = new InputStreamReader(new FileInputStream( file), "UTF-8"); - jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours(); - jucs = jucs.unmarshal(in); + JalviewUserColours jucs = JalviewUserColours.unmarshal(in); for (int i = jucs.getColourCount() - 1; i >= 0; i--) { @@ -771,7 +778,8 @@ public class FeatureSettings extends JPanel implements Cache.log.warn("Couldn't parse out graduated feature color.", e); } - GraduatedColor gcol = new GraduatedColor(mincol, maxcol, + FeatureColourI gcol = new FeatureColour(new Colour(mincol), + new Colour(maxcol), newcol.getMin(), newcol.getMax()); if (newcol.hasAutoScale()) { @@ -783,31 +791,28 @@ public class FeatureSettings extends JPanel implements } if (newcol.hasThreshold()) { - gcol.setThresh(newcol.getThreshold()); - gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default + gcol.setThreshold(newcol.getThreshold()); } if (newcol.getThreshType().length() > 0) { String ttyp = newcol.getThreshType(); - if (ttyp.equalsIgnoreCase("NONE")) - { - gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); - } if (ttyp.equalsIgnoreCase("ABOVE")) { - gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); + gcol.setAboveThreshold(true); } if (ttyp.equalsIgnoreCase("BELOW")) { - gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); + gcol.setBelowThreshold(true); } } fr.setColour(name = newcol.getName(), gcol); } else { - fr.setColour(name = jucs.getColour(i).getName(), new Color( - Integer.parseInt(jucs.getColour(i).getRGB(), 16))); + Color color = new Color( + Integer.parseInt(jucs.getColour(i).getRGB(), 16)); + fr.setColour(name = jucs.getColour(i).getName(), + new FeatureColour(new Colour(color))); } fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount()); } @@ -851,50 +856,40 @@ public class FeatureSettings extends JPanel implements PrintWriter out = new PrintWriter(new OutputStreamWriter( new FileOutputStream(choice), "UTF-8")); - Set fr_colours = fr.getAllFeatureColours(); - Iterator e = fr_colours.iterator(); + Set fr_colours = fr.getAllFeatureColours(); + Iterator e = fr_colours.iterator(); float[] sortOrder = new float[fr_colours.size()]; String[] sortTypes = new String[fr_colours.size()]; int i = 0; while (e.hasNext()) { - sortTypes[i] = e.next().toString(); + sortTypes[i] = e.next(); sortOrder[i] = fr.getOrder(sortTypes[i]); i++; } - jalview.util.QuickSort.sort(sortOrder, sortTypes); + QuickSort.sort(sortOrder, sortTypes); sortOrder = null; - Object fcol; - GraduatedColor gcol; for (i = 0; i < sortTypes.length; i++) { jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); col.setName(sortTypes[i]); - col.setRGB(jalview.util.Format.getHexString(fr.getColour(col - .getName()))); - fcol = fr.getFeatureStyle(sortTypes[i]); - if (fcol instanceof GraduatedColor) + FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]); + if (fcol.isSimpleColour()) { - gcol = (GraduatedColor) fcol; - col.setMin(gcol.getMin()); - col.setMax(gcol.getMax()); - col.setMinRGB(jalview.util.Format.getHexString(gcol - .getMinColor())); - col.setAutoScale(gcol.isAutoScale()); - col.setThreshold(gcol.getThresh()); - col.setColourByLabel(gcol.isColourByLabel()); - switch (gcol.getThreshType()) - { - case AnnotationColourGradient.NO_THRESHOLD: - col.setThreshType("NONE"); - break; - case AnnotationColourGradient.ABOVE_THRESHOLD: - col.setThreshType("ABOVE"); - break; - case AnnotationColourGradient.BELOW_THRESHOLD: - col.setThreshType("BELOW"); - break; - } + col.setRGB(Format.getHexString(fcol.getColour())); + } + else + { + col.setRGB(Format.getHexString(fcol.getMaxColour())); + col.setMin(fcol.getMin()); + col.setMax(fcol.getMax()); + col.setMinRGB(jalview.util.Format.getHexString(fcol + .getMinColour())); + col.setAutoScale(fcol.isAutoScaled()); + col.setThreshold(fcol.getThreshold()); + col.setColourByLabel(fcol.isColourByLabel()); + col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" : (fcol + .isBelowThreshold() ? "BELOW" : "NONE")); } ucs.addColour(col); } @@ -930,7 +925,7 @@ public class FeatureSettings extends JPanel implements int num = 0; for (int i = 0; i < data.length; i++) { - awidth = (float[]) typeWidth.get(data[i][0]); + awidth = typeWidth.get(data[i][0]); if (awidth[0] > 0) { width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better @@ -1253,7 +1248,8 @@ public class FeatureSettings extends JPanel implements fetchDAS.setEnabled(false); cancelDAS.setEnabled(true); dassourceBrowser.setGuiEnabled(false); - Vector selectedSources = dassourceBrowser.getSelectedSources(); + Vector selectedSources = dassourceBrowser + .getSelectedSources(); doDasFeatureFetch(selectedSources, true, true); } @@ -1312,7 +1308,7 @@ public class FeatureSettings extends JPanel implements * Vector of Strings to resolve to DAS source nicknames. * @return sources that are present in source list. */ - public List resolveSourceNicknames(Vector sources) + public List resolveSourceNicknames(Vector sources) { return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources); } @@ -1323,7 +1319,7 @@ public class FeatureSettings extends JPanel implements * * @return vector of selected das source nicknames */ - public Vector getSelectedSources() + public Vector getSelectedSources() { return dassourceBrowser.getSelectedSources(); } @@ -1337,7 +1333,7 @@ public class FeatureSettings extends JPanel implements * if true then runs in same thread, otherwise passes to the Swing * executor */ - public void fetchDasFeatures(Vector sources, boolean block) + public void fetchDasFeatures(Vector sources, boolean block) { initDasSources(); List resolved = dassourceBrowser.sourceRegistry @@ -1503,10 +1499,11 @@ public class FeatureSettings extends JPanel implements } @Override - public Component getTableCellRendererComponent(JTable table, + public Component getTableCellRendererComponent(JTable tbl, Object color, boolean isSelected, boolean hasFocus, int row, int column) { + FeatureColourI cellColour = (FeatureColourI) color; // JLabel comp = new JLabel(); // comp. setOpaque(true); @@ -1514,11 +1511,11 @@ public class FeatureSettings extends JPanel implements // setBounds(getBounds()); Color newColor; setToolTipText(baseTT); - setBackground(table.getBackground()); - if (color instanceof GraduatedColor) + setBackground(tbl.getBackground()); + if (!cellColour.isSimpleColour()) { - Rectangle cr = table.getCellRect(row, column, false); - FeatureSettings.renderGraduatedColor(this, (GraduatedColor) color, + Rectangle cr = tbl.getCellRect(row, column, false); + FeatureSettings.renderGraduatedColor(this, cellColour, (int) cr.getWidth(), (int) cr.getHeight()); } @@ -1526,8 +1523,7 @@ public class FeatureSettings extends JPanel implements { this.setText(""); this.setIcon(null); - newColor = (Color) color; - // comp. + newColor = ColorUtils.getColor(cellColour.getColour()); setBackground(newColor); // comp.setToolTipText("RGB value: " + newColor.getRed() + ", " // + newColor.getGreen() + ", " + newColor.getBlue()); @@ -1537,9 +1533,8 @@ public class FeatureSettings extends JPanel implements if (selectedBorder == null) { selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getSelectionBackground()); + tbl.getSelectionBackground()); } - // comp. setBorder(selectedBorder); } else @@ -1547,9 +1542,8 @@ public class FeatureSettings extends JPanel implements if (unselectedBorder == null) { unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5, - table.getBackground()); + tbl.getBackground()); } - // comp. setBorder(unselectedBorder); } @@ -1563,7 +1557,7 @@ public class FeatureSettings extends JPanel implements * @param comp * @param gcol */ - public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol) + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol) { int w = comp.getWidth(), h = comp.getHeight(); if (w < 20) @@ -1579,23 +1573,23 @@ public class FeatureSettings extends JPanel implements renderGraduatedColor(comp, gcol, w, h); } - public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol, + public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol, int w, int h) { boolean thr = false; String tt = ""; String tx = ""; - if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) + if (gcol.isAboveThreshold()) { thr = true; tx += ">"; - tt += "Thresholded (Above " + gcol.getThresh() + ") "; + tt += "Thresholded (Above " + gcol.getThreshold() + ") "; } - if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD) + if (gcol.isBelowThreshold()) { thr = true; tx += "<"; - tt += "Thresholded (Below " + gcol.getThresh() + ") "; + tt += "Thresholded (Below " + gcol.getThreshold() + ") "; } if (gcol.isColourByLabel()) { @@ -1609,7 +1603,7 @@ public class FeatureSettings extends JPanel implements } else { - Color newColor = gcol.getMaxColor(); + Color newColor = ColorUtils.getColor(gcol.getMaxColour()); comp.setBackground(newColor); // System.err.println("Width is " + w / 2); Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr); @@ -1637,7 +1631,7 @@ public class FeatureSettings extends JPanel implements class FeatureIcon implements Icon { - GraduatedColor gcol; + FeatureColourI gcol; Color backg; @@ -1649,7 +1643,7 @@ class FeatureIcon implements Icon Color mpcolour = Color.white; - FeatureIcon(GraduatedColor gfc, Color bg, int w, int h, boolean mspace) + FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace) { gcol = gfc; backg = bg; @@ -1689,7 +1683,7 @@ class FeatureIcon implements Icon g.setColor(backg); g.fillRect(0, 0, width, height); // need an icon here. - g.setColor(gcol.getMaxColor()); + g.setColor(ColorUtils.getColor(gcol.getMaxColour())); g.setFont(new Font("Verdana", Font.PLAIN, 9)); @@ -1703,7 +1697,7 @@ class FeatureIcon implements Icon } else { - Color minCol = gcol.getMinColor(); + Color minCol = ColorUtils.getColor(gcol.getMinColour()); g.setColor(minCol); g.fillRect(0, 0, s1, height); if (midspace) @@ -1711,7 +1705,7 @@ class FeatureIcon implements Icon g.setColor(Color.white); g.fillRect(s1, 0, e1 - s1, height); } - g.setColor(gcol.getMaxColor()); + g.setColor(ColorUtils.getColor(gcol.getMaxColour())); g.fillRect(0, e1, width - e1, height); } } @@ -1722,14 +1716,12 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, { FeatureSettings me; - GraduatedColor currentGColor; + FeatureColourI currentColor; FeatureColourChooser chooser; String type; - Color currentColor; - JButton button; JColorChooser colorChooser; @@ -1769,11 +1761,12 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, { // The user has clicked the cell, so // bring up the dialog. - if (currentColor != null) + if (currentColor.isSimpleColour()) { // bring up simple color chooser - button.setBackground(currentColor); - colorChooser.setColor(currentColor); + button.setBackground(ColorUtils.getColor(currentColor.getColour())); + colorChooser + .setColor(ColorUtils.getColor(currentColor.getColour())); dialog.setVisible(true); } else @@ -1790,15 +1783,14 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, } else { // User pressed dialog's "OK" button. - if (currentColor != null) + if (currentColor.isSimpleColour()) { - currentColor = colorChooser.getColor(); + currentColor = new FeatureColour( + new Colour(colorChooser.getColor())); } else { - // class cast exceptions may be raised if the chooser created on a - // non-graduated color - currentGColor = (GraduatedColor) chooser.getLastColour(); + currentColor = chooser.getLastColour(); } me.table.setValueAt(getCellEditorValue(), selectedRow, 1); fireEditingStopped(); @@ -1810,10 +1802,6 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, @Override public Object getCellEditorValue() { - if (currentColor == null) - { - return currentGColor; - } return currentColor; } @@ -1822,18 +1810,16 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row, int column) { - currentGColor = null; - currentColor = null; + currentColor = (FeatureColourI) value; this.selectedRow = row; type = me.table.getValueAt(row, 0).toString(); button.setOpaque(true); button.setBackground(me.getBackground()); - if (value instanceof GraduatedColor) + if (!currentColor.isSimpleColour()) { - currentGColor = (GraduatedColor) value; JLabel btn = new JLabel(); btn.setSize(button.getSize()); - FeatureSettings.renderGraduatedColor(btn, currentGColor); + FeatureSettings.renderGraduatedColor(btn, currentColor); button.setBackground(btn.getBackground()); button.setIcon(btn.getIcon()); button.setText(btn.getText()); @@ -1842,8 +1828,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor, { button.setText(""); button.setIcon(null); - currentColor = (Color) value; - button.setBackground(currentColor); + button.setBackground(ColorUtils.getColor(currentColor.getColour())); } return button; } diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index 37be8bc..2cb5bcd 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -21,6 +21,7 @@ package jalview.gui; import jalview.datamodel.SequenceI; +import jalview.util.ColorUtils; import java.awt.BorderLayout; import java.awt.Color; @@ -121,7 +122,7 @@ public class IdCanvas extends JPanel } else { - gg.setColor(av.getSequenceColour(s)); + gg.setColor(ColorUtils.getColor(av.getSequenceColour(s))); gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); gg.setColor(Color.black); @@ -383,7 +384,8 @@ public class IdCanvas extends JPanel } else { - currentColor = av.getSequenceColour(sequence); + currentColor = ColorUtils + .getColor(av.getSequenceColour(sequence)); currentTextColor = Color.black; } diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 2799a7e..ef5802e 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.api.FeatureColourI; import jalview.api.ViewStyleI; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; @@ -69,9 +70,10 @@ import jalview.schemabinding.version2.Tree; import jalview.schemabinding.version2.UserColours; import jalview.schemabinding.version2.Viewport; import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.GraduatedColor; +import jalview.schemes.FeatureColour; import jalview.schemes.ResidueColourScheme; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; @@ -90,6 +92,7 @@ import jalview.ws.params.ArgumentI; import jalview.ws.params.AutoCalcSetting; import jalview.ws.params.WsParamSetI; +import java.awt.Color; import java.awt.Rectangle; import java.io.BufferedReader; import java.io.DataInputStream; @@ -1194,34 +1197,32 @@ public class Jalview2XML .getFeatureRenderer().getRenderOrder() .toArray(new String[0]); - Vector settingsAdded = new Vector(); - Object gstyle = null; - GraduatedColor gcol = null; + Vector settingsAdded = new Vector(); if (renderOrder != null) { for (int ro = 0; ro < renderOrder.length; ro++) { - gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer() + FeatureColourI gstyle = ap.getSeqPanel().seqCanvas + .getFeatureRenderer() .getFeatureStyle(renderOrder[ro]); Setting setting = new Setting(); setting.setType(renderOrder[ro]); - if (gstyle instanceof GraduatedColor) + if (!gstyle.isSimpleColour()) { - gcol = (GraduatedColor) gstyle; - setting.setColour(gcol.getMaxColor().getRGB()); - setting.setMincolour(gcol.getMinColor().getRGB()); - setting.setMin(gcol.getMin()); - setting.setMax(gcol.getMax()); - setting.setColourByLabel(gcol.isColourByLabel()); - setting.setAutoScale(gcol.isAutoScale()); - setting.setThreshold(gcol.getThresh()); - setting.setThreshstate(gcol.getThreshType()); + setting.setColour(gstyle.getMaxColour().getRGB()); + setting.setMincolour(gstyle.getMinColour().getRGB()); + setting.setMin(gstyle.getMin()); + setting.setMax(gstyle.getMax()); + setting.setColourByLabel(gstyle.isColourByLabel()); + setting.setAutoScale(gstyle.isAutoScaled()); + setting.setThreshold(gstyle.getThreshold()); + // -1 = No threshold, 0 = Below, 1 = Above + setting.setThreshstate(gstyle.isAboveThreshold() ? 1 + : (gstyle.isBelowThreshold() ? 0 : -1)); } else { - setting.setColour(ap.getSeqPanel().seqCanvas - .getFeatureRenderer().getColour(renderOrder[ro]) - .getRGB()); + setting.setColour(gstyle.getColour().getRGB()); } setting.setDisplay(av.getFeaturesDisplayed().isVisible( @@ -1237,36 +1238,11 @@ public class Jalview2XML } } - // Make sure we save none displayed feature settings - Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getFeatureColours().keySet().iterator(); - while (en.hasNext()) - { - String key = en.next().toString(); - if (settingsAdded.contains(key)) - { - continue; - } - - Setting setting = new Setting(); - setting.setType(key); - setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getColour(key).getRGB()); - - setting.setDisplay(false); - float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getOrder(key); - if (rorder > -1) - { - setting.setOrder(rorder); - } - fs.addSetting(setting); - settingsAdded.addElement(key); - } // is groups actually supposed to be a map here ? - en = ap.getSeqPanel().seqCanvas.getFeatureRenderer() + Iterator en = ap.getSeqPanel().seqCanvas + .getFeatureRenderer() .getFeatureGroups().iterator(); - Vector groupsAdded = new Vector(); + Vector groupsAdded = new Vector(); while (en.hasNext()) { String grp = en.next().toString(); @@ -1283,7 +1259,6 @@ public class Jalview2XML groupsAdded.addElement(grp); } jms.setFeatureSettings(fs); - } if (av.hasHiddenColumns()) @@ -3147,8 +3122,8 @@ public class Jalview2XML sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour())); - sg.textColour = new java.awt.Color(jGroup.getTextCol1()); - sg.textColour2 = new java.awt.Color(jGroup.getTextCol2()); + sg.textColour = new Colour(jGroup.getTextCol1()); + sg.textColour2 = new Colour(jGroup.getTextCol2()); sg.setShowNonconserved(jGroup.hasShowUnconserved() ? jGroup .isShowUnconserved() : false); sg.thresholdTextColour = jGroup.getTextColThreshold(); @@ -4148,7 +4123,7 @@ public class Jalview2XML for (int i = 0; i < JSEQ.length; i++) { af.viewport.setSequenceColour(af.viewport.getAlignment() - .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour())); + .getSequenceAt(i), new Colour(JSEQ[i].getColour())); } af.viewport.setGatherViewsHere(view.getGatheredViews()); @@ -4234,8 +4209,8 @@ public class Jalview2XML af.viewport.setShowText(view.getShowText()); - af.viewport.setTextColour(new java.awt.Color(view.getTextCol1())); - af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2())); + af.viewport.setTextColour(new Colour(view.getTextCol1())); + af.viewport.setTextColour2(new Colour(view.getTextCol2())); af.viewport.setThresholdTextColour(view.getTextColThreshold()); af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view .isShowUnconserved() : false); @@ -4354,25 +4329,34 @@ public class Jalview2XML af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); String[] renderOrder = new String[jms.getFeatureSettings() .getSettingCount()]; - Hashtable featureGroups = new Hashtable(); - Hashtable featureColours = new Hashtable(); - Hashtable featureOrder = new Hashtable(); + Map featureColours = new Hashtable(); + Map featureOrder = new Hashtable(); for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); if (setting.hasMincolour()) { - GraduatedColor gc = setting.hasMin() ? new GraduatedColor( - new java.awt.Color(setting.getMincolour()), - new java.awt.Color(setting.getColour()), - setting.getMin(), setting.getMax()) : new GraduatedColor( - new java.awt.Color(setting.getMincolour()), - new java.awt.Color(setting.getColour()), 0, 1); + FeatureColourI gc = setting.hasMin() ? new FeatureColour( + new Colour(new Color(setting.getMincolour())), + new Colour(new Color(setting.getColour())), + setting.getMin(), setting.getMax()) : new FeatureColour( + new Colour(new Color(setting.getMincolour())), + new Colour(new Color(setting.getColour())), + 0, 1); if (setting.hasThreshold()) { - gc.setThresh(setting.getThreshold()); - gc.setThreshType(setting.getThreshstate()); + gc.setThreshold(setting.getThreshold()); + int threshstate = setting.getThreshstate(); + // -1 = None, 0 = Below, 1 = Above threshold + if (threshstate == 0) + { + gc.setBelowThreshold(true); + } + else if (threshstate == 1) + { + gc.setAboveThreshold(true); + } } gc.setAutoScaled(true); // default if (setting.hasAutoScale()) @@ -4388,8 +4372,8 @@ public class Jalview2XML } else { - featureColours.put(setting.getType(), - new java.awt.Color(setting.getColour())); + featureColours.put(setting.getType(), new FeatureColour( + new Colour(new Color(setting.getColour())))); } renderOrder[fs] = setting.getType(); if (setting.hasOrder()) @@ -4406,7 +4390,7 @@ public class Jalview2XML fdi.setVisible(setting.getType()); } } - Hashtable fgtable = new Hashtable(); + Map fgtable = new Hashtable(); for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) { Group grp = jms.getFeatureSettings().getGroup(gs); diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index 61e20fa..fb27e19 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -35,6 +35,7 @@ import jalview.binding.Tree; import jalview.binding.UserColours; import jalview.binding.Viewport; import jalview.datamodel.PDBEntry; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.ResidueProperties; @@ -310,7 +311,7 @@ public class Jalview2XML_V1 for (int i = 0; i < JSEQ.length; i++) { af.viewport.setSequenceColour(af.viewport.getAlignment() - .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour())); + .getSequenceAt(i), new Colour(JSEQ[i].getColour())); } // af.changeColour() ); diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java index 0719fa0..cd2ecfe 100755 --- a/src/jalview/gui/RotatableCanvas.java +++ b/src/jalview/gui/RotatableCanvas.java @@ -25,6 +25,7 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.datamodel.SequencePoint; import jalview.math.RotatableMatrix; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -136,6 +137,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, addMouseWheelListener(new MouseWheelListener() { + @Override public void mouseWheelMoved(MouseWheelEvent e) { if (e.getWheelRotation() > 0) @@ -162,6 +164,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, boolean first = true; + @Override public void setPoints(Vector points, int npoint) { this.points = points; @@ -327,7 +330,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, dim = height; } - return (float) ((dim * scalefactor) / (2 * maxwidth)); + return (dim * scalefactor) / (2 * maxwidth); } /** @@ -352,6 +355,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * * @return DOCUMENT ME! */ + @Override public Dimension getPreferredSize() { if (prefsize != null) @@ -369,6 +373,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * * @return DOCUMENT ME! */ + @Override public Dimension getMinimumSize() { return getPreferredSize(); @@ -380,6 +385,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * @param g * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g1) { @@ -474,8 +480,8 @@ public class RotatableCanvas extends JPanel implements MouseListener, for (int i = 0; i < npoint; i++) { SequencePoint sp = (SequencePoint) points.elementAt(i); - int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth; - int y = (int) ((float) (sp.coord[1] - centre[1]) * scale) + int x = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth; + int y = (int) ((sp.coord[1] - centre[1]) * scale) + halfheight; float z = sp.coord[1] - centre[2]; @@ -485,7 +491,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, } else { - g.setColor(av.getSequenceColour(sp.sequence)); + g.setColor(ColorUtils.getColor(av.getSequenceColour(sp.sequence))); } if (av.getSelectionGroup() != null) @@ -546,6 +552,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void keyTyped(KeyEvent evt) { } @@ -556,6 +563,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void keyReleased(KeyEvent evt) { } @@ -566,6 +574,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void keyPressed(KeyEvent evt) { if (evt.getKeyCode() == KeyEvent.VK_UP) @@ -597,6 +606,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseClicked(MouseEvent evt) { } @@ -607,6 +617,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent evt) { } @@ -617,6 +628,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent evt) { } @@ -627,6 +639,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent evt) { } @@ -637,6 +650,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent evt) { int x = evt.getX(); @@ -689,6 +703,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, // controller.handleSequenceSelectionEvent(new // SequenceSelectionEvent(this,sel)); // } + @Override public void mouseMoved(MouseEvent evt) { SequenceI found = findPoint(evt.getX(), evt.getY()); @@ -709,6 +724,7 @@ public class RotatableCanvas extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent evt) { mx = evt.getX(); @@ -724,8 +740,8 @@ public class RotatableCanvas extends JPanel implements MouseListener, { rotmat.setIdentity(); - rotmat.rotate((float) (my - omy), 'x'); - rotmat.rotate((float) (mx - omx), 'y'); + rotmat.rotate(my - omy, 'x'); + rotmat.rotate(mx - omx, 'y'); for (int i = 0; i < npoint; i++) { @@ -772,8 +788,8 @@ public class RotatableCanvas extends JPanel implements MouseListener, for (int i = 0; i < npoint; i++) { SequencePoint sp = (SequencePoint) points.elementAt(i); - int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale) + ((float) getWidth() / 2.0)); - int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale) + ((float) getHeight() / 2.0)); + int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale) + (getWidth() / 2.0)); + int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale) + (getHeight() / 2.0)); if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2)) { @@ -813,9 +829,9 @@ public class RotatableCanvas extends JPanel implements MouseListener, for (int i = 0; i < npoint; i++) { SequencePoint sp = (SequencePoint) points.elementAt(i); - int px = (int) ((float) (sp.coord[0] - centre[0]) * scale) + int px = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth; - int py = (int) ((float) (sp.coord[1] - centre[1]) * scale) + int py = (int) ((sp.coord[1] - centre[1]) * scale) + halfheight; if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3)) diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 0f24b4b..8a120c5 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.SearchResults; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.util.ColorUtils; import java.awt.BasicStroke; import java.awt.BorderLayout; @@ -844,7 +845,7 @@ public class SeqCanvas extends JComponent else { g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); + g.setColor(ColorUtils.getColor(group.getOutlineColour())); } } } diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 258a229..f215f9d 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -20,10 +20,13 @@ */ package jalview.gui; +import jalview.api.ColorI; import jalview.api.FeatureRenderer; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; +import jalview.util.ColorUtils; import java.awt.Color; import java.awt.FontMetrics; @@ -89,7 +92,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } @Override - public Color getResidueBoxColour(SequenceI seq, int i) + public ColorI getResidueBoxColour(SequenceI seq, int i) { allGroups = av.getAlignment().findAllGroups(seq); @@ -105,7 +108,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer getBoxColour(av.getGlobalColourScheme(), seq, i); } - return resBoxColour; + return new Colour(resBoxColour); } /** @@ -119,12 +122,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer * @return */ @Override - public Color getResidueColour(final SequenceI seq, int position, + public ColorI getResidueColour(final SequenceI seq, int position, FeatureRenderer fr) { // TODO replace 8 or so code duplications with calls to this method // (refactored as needed) - Color col = getResidueBoxColour(seq, position); + ColorI col = getResidueBoxColour(seq, position); if (fr != null) { @@ -303,7 +306,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { end = seq.getLength() - 1; } - graphics.setColor(av.getTextColour()); + graphics.setColor(ColorUtils.getColor(av.getTextColour())); if (monospacedFont && av.getShowText() && allGroups.length == 0 && !av.getColourText() && av.getThresholdTextColour() == 0) @@ -330,7 +333,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer for (int i = start; i <= end; i++) { - graphics.setColor(av.getTextColour()); + graphics.setColor(ColorUtils.getColor(av.getTextColour())); getboxColour = false; s = seq.getCharAt(i); @@ -362,13 +365,13 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (resBoxColour.getRed() + resBoxColour.getBlue() + resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour) { - graphics.setColor(currentSequenceGroup.textColour2); + graphics.setColor(ColorUtils.getColor(currentSequenceGroup.textColour2)); } } } else { - graphics.setColor(currentSequenceGroup.textColour); + graphics.setColor(ColorUtils.getColor(currentSequenceGroup.textColour)); } if (!isarep && !isgrep && currentSequenceGroup.getShowNonconserved()) // todo @@ -412,7 +415,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (resBoxColour.getRed() + resBoxColour.getBlue() + resBoxColour.getGreen() < av.getThresholdTextColour()) { - graphics.setColor(av.getTextColour2()); + graphics.setColor(ColorUtils.getColor(av.getTextColour2())); } } if (!isarep && av.getShowUnconserved()) diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java index 6bac6df..2ec1c18 100644 --- a/src/jalview/gui/TextColourChooser.java +++ b/src/jalview/gui/TextColourChooser.java @@ -21,6 +21,7 @@ package jalview.gui; import jalview.datamodel.SequenceGroup; +import jalview.schemes.Colour; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -89,6 +90,7 @@ public class TextColourChooser col1.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent e) { Color col = JColorChooser.showDialog(bigpanel, @@ -104,6 +106,7 @@ public class TextColourChooser col2.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent e) { Color col = JColorChooser.showDialog(bigpanel, @@ -119,6 +122,7 @@ public class TextColourChooser slider.addChangeListener(new ChangeListener() { + @Override public void stateChanged(ChangeEvent evt) { thresholdChanged(slider.getValue()); @@ -138,14 +142,14 @@ public class TextColourChooser { if (sg == null) { - ap.av.setTextColour(new Color(original1)); - ap.av.setTextColour2(new Color(original2)); + ap.av.setTextColour(new Colour(original1)); + ap.av.setTextColour2(new Colour(original2)); ap.av.setThresholdTextColour(originalThreshold); } else { - sg.textColour = new Color(original1); - sg.textColour2 = new Color(original2); + sg.textColour = new Colour(original1); + sg.textColour2 = new Colour(original2); sg.thresholdTextColour = originalThreshold; } } @@ -155,7 +159,7 @@ public class TextColourChooser { if (sg == null) { - ap.av.setTextColour(col); + ap.av.setTextColour(new Colour(col)); if (ap.av.getColourAppliesToAllGroups()) { setGroupTextColour(); @@ -163,7 +167,7 @@ public class TextColourChooser } else { - sg.textColour = col; + sg.textColour = new Colour(col); } ap.paintAlignment(true); @@ -173,7 +177,7 @@ public class TextColourChooser { if (sg == null) { - ap.av.setTextColour2(col); + ap.av.setTextColour2(new Colour(col)); if (ap.av.getColourAppliesToAllGroups()) { setGroupTextColour(); @@ -181,7 +185,7 @@ public class TextColourChooser } else { - sg.textColour2 = col; + sg.textColour2 = new Colour(col); } ap.paintAlignment(true); diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index f21c5e7..149a587 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -27,11 +27,13 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceNode; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; import jalview.structure.SelectionSource; +import jalview.util.ColorUtils; import jalview.util.Format; import jalview.util.MappingUtils; import jalview.util.MessageManager; @@ -245,7 +247,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - g.setColor(av.getSequenceColour(seq).darker()); + g.setColor(ColorUtils.getColor(av.getSequenceColour(seq)) + .darker()); } } else @@ -522,7 +525,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, for (int a = 0; a < aps.length; a++) { final SequenceI seq = (SequenceI) node.element(); - aps[a].av.setSequenceColour(seq, c); + aps[a].av.setSequenceColour(seq, new Colour(c)); } } } @@ -1002,7 +1005,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, codingComplement.getAlignment().addGroup(mappedGroup); for (SequenceI seq : mappedGroup.getSequences()) { - codingComplement.setSequenceColour(seq, col.brighter()); + codingComplement.setSequenceColour(seq, + new Colour(col.brighter())); } } } diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 8b3aa98..9ef9ee8 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -30,6 +30,7 @@ import jalview.datamodel.GraphLine; import jalview.datamodel.HiddenSequences; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.ResidueProperties; @@ -1670,11 +1671,13 @@ public class AnnotationFile } else if (key.equalsIgnoreCase("textCol1")) { - sg.textColour = new UserColourScheme(value).findColour('A'); + sg.textColour = new Colour( + new UserColourScheme(value).findColour('A')); } else if (key.equalsIgnoreCase("textCol2")) { - sg.textColour2 = new UserColourScheme(value).findColour('A'); + sg.textColour2 = new Colour( + new UserColourScheme(value).findColour('A')); } else if (key.equalsIgnoreCase("textColThreshold")) { diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index 2dd5f26..40f83d3 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -23,6 +23,7 @@ package jalview.io; import jalview.analysis.AlignmentUtils; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; import jalview.api.FeaturesSourceI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; @@ -33,15 +34,13 @@ import jalview.datamodel.SequenceI; import jalview.io.gff.GffHelperBase; import jalview.io.gff.GffHelperFactory; import jalview.io.gff.GffHelperI; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +import jalview.schemes.FeatureColour; import jalview.schemes.UserColourScheme; import jalview.util.Format; import jalview.util.MapList; import jalview.util.ParseHtmlBodyAndLinks; import jalview.util.StringUtils; -import java.awt.Color; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; @@ -140,7 +139,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * - process html strings into plain text * @return true if features were added */ - public boolean parse(AlignmentI align, Map colours, + public boolean parse(AlignmentI align, + Map colours, boolean removeHTML) { return parse(align, colours, removeHTML, false); @@ -177,7 +177,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * - when true, ID matches to compound sequence IDs are allowed * @return true if features were added */ - public boolean parse(AlignmentI align, Map colours, + public boolean parse(AlignmentI align, + Map colours, boolean removeHTML, boolean relaxedIdmatching) { Map gffProps = new HashMap(); @@ -297,7 +298,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @param featureGroup */ protected boolean parseJalviewFeature(String line, String[] gffColumns, - AlignmentI alignment, Map featureColours, + AlignmentI alignment, Map featureColours, boolean removeHTML, boolean relaxedIdMatching, String featureGroup) { /* @@ -350,7 +351,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * synthesize a colour from the feature type */ UserColourScheme ucs = new UserColourScheme(ft); - featureColours.put(ft, ucs.findColour('A')); + featureColours.put(ft, new FeatureColour(ucs.findColour('A'))); } SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos, endPos, featureGroup); @@ -393,9 +394,9 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * map to which to add derived colour specification */ protected void parseFeatureColour(String line, String featureType, - String[] gffColumns, Map colours) + String[] gffColumns, Map colours) { - Object colour = null; + FeatureColourI colour = null; String colscheme = gffColumns[1]; if (colscheme.indexOf("|") > -1 || colscheme.trim().equalsIgnoreCase("label")) @@ -405,7 +406,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI else { UserColourScheme ucs = new UserColourScheme(colscheme); - colour = ucs.findColour('A'); + colour = new FeatureColour(ucs.findColour('A')); } if (colour != null) { @@ -420,7 +421,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @param colourDescriptor * @return */ - protected GraduatedColor parseGraduatedColourScheme(String line, + protected FeatureColourI parseGraduatedColourScheme(String line, String colourDescriptor) { // Parse '|' separated graduated colourscheme fields: @@ -530,10 +531,10 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI maxcol = "000000"; } - GraduatedColor colour = null; + FeatureColourI colour = null; try { - colour = new GraduatedColor( + colour = new FeatureColour( new UserColourScheme(mincol).findColour('A'), new UserColourScheme(maxcol).findColour('A'), min, max); } catch (Exception e) @@ -548,21 +549,23 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI colour.setAutoScaled(abso == null); // add in any additional parameters String ttype = null, tval = null; + boolean hasThreshold = false; if (gcol.hasMoreTokens()) { // threshold type and possibly a threshold value ttype = gcol.nextToken(); if (ttype.toLowerCase().startsWith("below")) { - colour.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); + colour.setBelowThreshold(true); + hasThreshold = true; } else if (ttype.toLowerCase().startsWith("above")) { - colour.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); + colour.setAboveThreshold(true); + hasThreshold = true; } else { - colour.setThreshType(AnnotationColourGradient.NO_THRESHOLD); if (!ttype.toLowerCase().startsWith("no")) { System.err.println("Ignoring unrecognised threshold type : " @@ -570,13 +573,13 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } } } - if (colour.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) + if (hasThreshold) { try { gcol.nextToken(); tval = gcol.nextToken(); - colour.setThresh(new Float(tval).floatValue()); + colour.setThreshold(new Float(tval).floatValue()); } catch (Exception e) { System.err.println("Couldn't parse threshold value as a float: (" @@ -703,7 +706,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @return features file contents */ public String printJalviewFormat(SequenceI[] sequences, - Map visible) + Map visible) { return printJalviewFormat(sequences, visible, true, true); } @@ -713,7 +716,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * * @param sequences * source of features - * @param visible + * @param featureColours * hash of Colours for each feature type * @param visOnly * when true only feature types in 'visible' will be output @@ -723,68 +726,62 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @return features file contents */ public String printJalviewFormat(SequenceI[] sequences, - Map visible, boolean visOnly, boolean nonpos) + Map featureColours, boolean visOnly, + boolean nonpos) { StringBuilder out = new StringBuilder(256); boolean featuresGen = false; - if (visOnly && !nonpos && (visible == null || visible.size() < 1)) + if (visOnly && !nonpos + && (featureColours == null || featureColours.size() < 1)) { // no point continuing. return "No Features Visible"; } - if (visible != null && visOnly) + if (featureColours != null && visOnly) { // write feature colours only if we're given them and we are generating // viewed features // TODO: decide if feature links should also be written here ? - Iterator en = visible.keySet().iterator(); + Iterator en = featureColours.keySet().iterator(); String featureType, color; while (en.hasNext()) { - featureType = en.next().toString(); - - if (visible.get(featureType) instanceof GraduatedColor) + featureType = en.next(); + FeatureColourI fc = featureColours.get(featureType); + if (fc.isSimpleColour()) { - GraduatedColor gc = (GraduatedColor) visible.get(featureType); - color = (gc.isColourByLabel() ? "label|" : "") - + Format.getHexString(gc.getMinColor()) + "|" - + Format.getHexString(gc.getMaxColor()) - + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|" - + gc.getMax() + "|"; - if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) - { - if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD) + color = Format.getHexString(fc.getColour()); + } + else + { + color = (fc.isColourByLabel() ? "label|" : "") + + Format.getHexString(fc.getMinColour()) + "|" + + Format.getHexString(fc.getMaxColour()) + + (fc.isAutoScaled() ? "|" : "|abso|") + fc.getMin() + "|" + + fc.getMax() + "|"; + if (fc.isBelowThreshold()) { color += "below"; } - else + else if (fc.isAboveThreshold()) { - if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD) - { - System.err.println("WARNING: Unsupported threshold type (" - + gc.getThreshType() + ") : Assuming 'above'"); - } color += "above"; } // add the value - color += "|" + gc.getThresh(); + color += "|" + fc.getThreshold(); } - else - { - color += "none"; - } - } - else if (visible.get(featureType) instanceof Color) - { - color = Format.getHexString((Color) visible.get(featureType)); - } - else - { - // legacy support for integer objects containing colour triplet values - color = Format.getHexString(new Color(Integer.parseInt(visible - .get(featureType).toString()))); - } +// else +// { +// color += "none"; +// } + // else + // { + // // legacy support for integer objects containing colour triplet + // values + // color = Format.getHexString(new Color(Integer + // .parseInt(fc.toString()))); + // } out.append(featureType); out.append(TAB); out.append(color); @@ -806,7 +803,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI { isnonpos = features[j].begin == 0 && features[j].end == 0; if ((!nonpos && isnonpos) - || (!isnonpos && visOnly && !visible + || (!isnonpos && visOnly && !featureColours .containsKey(features[j].type))) { continue; @@ -846,7 +843,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI { isnonpos = features[j].begin == 0 && features[j].end == 0; if ((!nonpos && isnonpos) - || (!isnonpos && visOnly && !visible + || (!isnonpos && visOnly && !featureColours .containsKey(features[j].type))) { // skip if feature is nonpos and we ignore them or if we only @@ -1003,7 +1000,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @return */ public String printGffFormat(SequenceI[] sequences, - Map visible) + Map visible) { return printGffFormat(sequences, visible, true, true); } @@ -1013,14 +1010,15 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * * @param sequences * the sequences whose features are to be output - * @param visible + * @param featureColours * a map whose keys are the type names of visible features * @param outputVisibleOnly * @param includeNonPositionalFeatures * @return */ public String printGffFormat(SequenceI[] sequences, - Map visible, boolean outputVisibleOnly, + Map featureColours, + boolean outputVisibleOnly, boolean includeNonPositionalFeatures) { StringBuilder out = new StringBuilder(256); @@ -1045,7 +1043,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI // TODO why the test !isnonpos here? // what about not visible non-positional features? if (!isnonpos && outputVisibleOnly - && !visible.containsKey(sf.type)) + && !featureColours.containsKey(sf.type)) { /* * ignore not visible features if not wanted diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java index df0dc06..6c6224c 100755 --- a/src/jalview/io/HTMLOutput.java +++ b/src/jalview/io/HTMLOutput.java @@ -20,15 +20,16 @@ */ package jalview.io; +import jalview.api.ColorI; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.gui.AlignViewport; import jalview.gui.AlignmentPanel; import jalview.gui.FeatureRenderer; import jalview.gui.SequenceRenderer; +import jalview.schemes.Colour; import jalview.util.MessageManager; -import java.awt.Color; import java.awt.Font; import java.io.PrintWriter; @@ -40,7 +41,7 @@ public class HTMLOutput jalview.renderer.seqfeatures.FeatureRenderer fr; - Color color; + ColorI color; public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1) @@ -155,7 +156,7 @@ public class HTMLOutput } else { - color = Color.white; + color = Colour.white; } if (color.getRGB() < -1) @@ -257,7 +258,7 @@ public class HTMLOutput } else { - color = Color.white; + color = Colour.white; } if (color.getRGB() < -1) diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java index e554b8e..79c055e 100644 --- a/src/jalview/io/HtmlSvgOutput.java +++ b/src/jalview/io/HtmlSvgOutput.java @@ -30,6 +30,7 @@ import jalview.gui.HTMLOptions; import jalview.gui.IProgressIndicator; import jalview.gui.OOMWarning; import jalview.math.AlignmentDimension; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import java.awt.Color; @@ -308,7 +309,7 @@ public class HtmlSvgOutput } else { - currentColor = av.getSequenceColour(seq); + currentColor = ColorUtils.getColor(av.getSequenceColour(seq)); currentTextColor = Color.black; } pg[0].setColor(currentColor); diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java index 36980f8..dfd351a 100644 --- a/src/jalview/io/JSONFile.java +++ b/src/jalview/io/JSONFile.java @@ -46,6 +46,7 @@ import jalview.json.binding.biojson.v1.ColourSchemeMapper; import jalview.json.binding.biojson.v1.SequenceFeaturesPojo; import jalview.json.binding.biojson.v1.SequenceGrpPojo; import jalview.json.binding.biojson.v1.SequencePojo; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.UserColourScheme; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; @@ -344,7 +345,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile String.valueOf(seq.hashCode())); String featureColour = (fr == null) ? null : jalview.util.Format - .getHexString(fr.findFeatureColour(Color.white, seq, + .getHexString(fr.findFeatureColour(Colour.white, seq, seq.findIndex(sf.getBegin()))); jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1); jsonFeature.setXend(seq.findIndex(sf.getEnd())); diff --git a/src/jalview/io/PDBFeatureSettings.java b/src/jalview/io/PDBFeatureSettings.java index 83bb37e..0c2f030 100644 --- a/src/jalview/io/PDBFeatureSettings.java +++ b/src/jalview/io/PDBFeatureSettings.java @@ -1,11 +1,11 @@ package jalview.io; +import jalview.api.ColorI; import jalview.api.FeatureColourI; +import jalview.schemes.Colour; import jalview.schemes.FeatureColourAdapter; import jalview.schemes.FeatureSettingsAdapter; -import java.awt.Color; - public class PDBFeatureSettings extends FeatureSettingsAdapter { @@ -29,9 +29,9 @@ public class PDBFeatureSettings extends FeatureSettingsAdapter { @Override - public Color getColour() + public ColorI getColour() { - return Color.RED; + return Colour.red; } }; } diff --git a/src/jalview/io/packed/JalviewDataset.java b/src/jalview/io/packed/JalviewDataset.java index 817ba9c..63263d2 100644 --- a/src/jalview/io/packed/JalviewDataset.java +++ b/src/jalview/io/packed/JalviewDataset.java @@ -20,6 +20,7 @@ */ package jalview.io.packed; +import jalview.api.FeatureColourI; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.io.NewickFile; @@ -57,7 +58,7 @@ public class JalviewDataset /** * @return the featureColours */ - public Map getFeatureColours() + public Map getFeatureColours() { return featureColours; } @@ -66,7 +67,7 @@ public class JalviewDataset * @param featureColours * the featureColours to set */ - public void setFeatureColours(Map featureColours) + public void setFeatureColours(Map featureColours) { this.featureColours = featureColours; } @@ -187,7 +188,7 @@ public class JalviewDataset /** * current set of feature colours */ - Map featureColours; + Map featureColours; /** * original identity of each sequence in results @@ -201,7 +202,7 @@ public class JalviewDataset seqDetails = new Hashtable(); al = new ArrayList(); parentDataset = null; - featureColours = new HashMap(); + featureColours = new HashMap(); } /** @@ -209,7 +210,8 @@ public class JalviewDataset * * @param parentAlignment */ - public JalviewDataset(AlignmentI aldataset, Map fc, + public JalviewDataset(AlignmentI aldataset, + Map fc, Hashtable seqDets) { // TODO not used - remove? @@ -231,7 +233,8 @@ public class JalviewDataset * (may be null) alignment to associate new annotation and trees * with. */ - public JalviewDataset(AlignmentI aldataset, Map fc, + public JalviewDataset(AlignmentI aldataset, + Map fc, Hashtable seqDets, AlignmentI parentAlignment) { this(); diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java index 01369b9..71999f0 100644 --- a/src/jalview/io/packed/ParsePackedSet.java +++ b/src/jalview/io/packed/ParsePackedSet.java @@ -20,6 +20,7 @@ */ package jalview.io.packed; +import jalview.api.FeatureColourI; import jalview.datamodel.AlignmentI; import jalview.io.AppletFormatAdapter; import jalview.io.FileParse; @@ -157,7 +158,7 @@ public class ParsePackedSet // if not, create one. if (context.featureColours == null) { - context.featureColours = new HashMap(); + context.featureColours = new HashMap(); } try { diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index 0d14cd9..e6e3071 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -20,8 +20,10 @@ */ package jalview.renderer.seqfeatures; +import jalview.api.ColorI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.schemes.Colour; import jalview.viewmodel.seqfeatures.FeatureRendererModel; import java.awt.AlphaComposite; @@ -169,14 +171,19 @@ public class FeatureRenderer extends FeatureRendererModel BufferedImage offscreenImage; @Override - public Color findFeatureColour(Color initialCol, SequenceI seq, int res) + public ColorI findFeatureColour(ColorI initialCol, SequenceI seq, int res) { - return new Color(findFeatureColour(initialCol.getRGB(), seq, res)); + return new Colour(findFeatureColour(initialCol.getRGB(), seq, res)); + } + + public ColorI findFeatureColour(Color initialCol, SequenceI seq, int res) + { + return findFeatureColour(new Colour(initialCol), seq, res); } /** - * This is used by the Molecule Viewer and Overview to get the accurate - * colourof the rendered sequence + * This is used by the Molecule Viewer and Overview to get the accurate colour + * of the rendered sequence */ public synchronized int findFeatureColour(int initialCol, final SequenceI seq, int column) @@ -246,7 +253,7 @@ public class FeatureRenderer extends FeatureRendererModel } else { - return ((Integer) currentColour).intValue(); + return currentColour.intValue(); } } @@ -262,6 +269,8 @@ public class FeatureRenderer extends FeatureRendererModel int epos; + private Integer currentColour; + public synchronized void drawSequence(Graphics g, final SequenceI seq, int start, int end, int y1) { diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java new file mode 100644 index 0000000..37c85d4 --- /dev/null +++ b/src/jalview/schemes/FeatureColour.java @@ -0,0 +1,684 @@ +package jalview.schemes; + +import jalview.api.ColorI; +import jalview.api.FeatureColourI; +import jalview.datamodel.SequenceFeature; +import jalview.util.Format; + +import java.awt.Color; +import java.util.StringTokenizer; + +/** + * A class that wraps either a simple colour or a graduated colour + */ +public class FeatureColour implements FeatureColourI +{ + private static final String BAR = "|"; + + final private ColorI colour; + + final private ColorI minColour; + + final private ColorI maxColour; + + private boolean graduatedColour; + + private boolean colourByLabel; + + private float threshold; + + private float base; + + private float range; + + private boolean belowThreshold; + + private boolean aboveThreshold; + + private boolean thresholdIsMinOrMax; + + private boolean isHighToLow; + + private boolean autoScaled; + + final private float minRed; + + final private float minGreen; + + final private float minBlue; + + final private float deltaRed; + + final private float deltaGreen; + + final private float deltaBlue; + + /** + * Parses a Jalview features file format colour descriptor + * [label|][mincolour|maxcolour + * |[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue] Examples: + *
    + *
  • red
    • + *
  • a28bbb
    • + *
  • 25,125,213
    • + *
  • label
    • + *
  • label|||0.0|0.0|above|12.5
    • + *
  • label|||0.0|0.0|below|12.5
    • + *
  • red|green|12.0|26.0|none
    • + *
  • a28bbb|3eb555|12.0|26.0|above|12.5
    • + *
  • a28bbb|3eb555|abso|12.0|26.0|below|12.5
    • + *
+ * + * @param descriptor + * @return + * @throws IllegalArgumentException + * if not parseable + */ + public static FeatureColour parseJalviewFeatureColour(String descriptor) + { + StringTokenizer gcol = new StringTokenizer(descriptor, "|", true); + float min = Float.MIN_VALUE; + float max = Float.MAX_VALUE; + boolean labelColour = false; + + String mincol = gcol.nextToken(); + if (mincol == "|") + { + throw new IllegalArgumentException( + "Expected either 'label' or a colour specification in the line: " + + descriptor); + } + String maxcol = null; + if (mincol.toLowerCase().indexOf("label") == 0) + { + labelColour = true; + mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); + // skip '|' + mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); + } + + if (!labelColour && !gcol.hasMoreTokens()) + { + /* + * only a simple colour specification - parse it + */ + Color colour = UserColourScheme.getColourFromString(descriptor); + if (colour == null) + { + throw new IllegalArgumentException("Invalid colour descriptor: " + + descriptor); + } + return new FeatureColour(new Colour(colour)); + } + + /* + * autoScaled == true: colours range over actual score range; autoScaled == + * false ('abso'): colours range over min/max range + */ + boolean autoScaled = false; + String tok = null, minval, maxval; + if (mincol != null) + { + // at least four more tokens + if (mincol.equals("|")) + { + mincol = ""; + } + else + { + gcol.nextToken(); // skip next '|' + } + maxcol = gcol.nextToken(); + if (maxcol.equals("|")) + { + maxcol = ""; + } + else + { + gcol.nextToken(); // skip next '|' + } + tok = gcol.nextToken(); + gcol.nextToken(); // skip next '|' + if (tok.toLowerCase().indexOf("abso") != 0) + { + minval = tok; + autoScaled = true; + } + else + { + minval = gcol.nextToken(); + gcol.nextToken(); // skip next '|' + } + maxval = gcol.nextToken(); + if (gcol.hasMoreTokens()) + { + gcol.nextToken(); // skip next '|' + } + try + { + if (minval.length() > 0) + { + min = new Float(minval).floatValue(); + } + } catch (Exception e) + { + throw new IllegalArgumentException( + "Couldn't parse the minimum value for graduated colour (" + + descriptor + ")"); + } + try + { + if (maxval.length() > 0) + { + max = new Float(maxval).floatValue(); + } + } catch (Exception e) + { + throw new IllegalArgumentException( + "Couldn't parse the maximum value for graduated colour (" + + descriptor + ")"); + } + } + else + { + // add in some dummy min/max colours for the label-only + // colourscheme. + mincol = "FFFFFF"; + maxcol = "000000"; + } + + /* + * construct the FeatureColour + */ + FeatureColour featureColour; + try + { + featureColour = new FeatureColour(new Colour(new UserColourScheme( + mincol).findColour('A')), new Colour(new UserColourScheme( + maxcol).findColour('A')), min, max); + featureColour.setColourByLabel(labelColour); + featureColour.setAutoScaled(autoScaled); + // add in any additional parameters + String ttype = null, tval = null; + if (gcol.hasMoreTokens()) + { + // threshold type and possibly a threshold value + ttype = gcol.nextToken(); + if (ttype.toLowerCase().startsWith("below")) + { + featureColour.setBelowThreshold(true); + } + else if (ttype.toLowerCase().startsWith("above")) + { + featureColour.setAboveThreshold(true); + } + else + { + if (!ttype.toLowerCase().startsWith("no")) + { + System.err.println("Ignoring unrecognised threshold type : " + + ttype); + } + } + } + if (featureColour.hasThreshold()) + { + try + { + gcol.nextToken(); + tval = gcol.nextToken(); + featureColour.setThreshold(new Float(tval).floatValue()); + } catch (Exception e) + { + System.err.println("Couldn't parse threshold value as a float: (" + + tval + ")"); + } + } + if (gcol.hasMoreTokens()) + { + System.err + .println("Ignoring additional tokens in parameters in graduated colour specification\n"); + while (gcol.hasMoreTokens()) + { + System.err.println("|" + gcol.nextToken()); + } + System.err.println("\n"); + } + return featureColour; + } catch (Exception e) + { + throw new IllegalArgumentException(e.getMessage()); + } + } + + /** + * Default constructor + */ + public FeatureColour() + { + this((ColorI) null); + } + + /** + * Constructor given a simple colour + * + * @param c + */ + public FeatureColour(ColorI c) + { + minColour = new Colour(Color.WHITE); + maxColour = new Colour(Color.BLACK); + minRed = 0f; + minGreen = 0f; + minBlue = 0f; + deltaRed = 0f; + deltaGreen = 0f; + deltaBlue = 0f; + colour = c; + } + + public FeatureColour(Color c) + { + this(new Colour(c)); + } + + /** + * Constructor given a colour range and a score range + * + * @param low + * @param high + * @param min + * @param max + */ + public FeatureColour(ColorI low, ColorI high, float min, float max) + { + graduatedColour = true; + colour = null; + minColour = low; + maxColour = high; + threshold = Float.NaN; + isHighToLow = min >= max; + minRed = low.getRed() / 255f; + minGreen = low.getGreen() / 255f; + minBlue = low.getBlue() / 255f; + deltaRed = (high.getRed() / 255f) - minRed; + deltaGreen = (high.getGreen() / 255f) - minGreen; + deltaBlue = (high.getBlue() / 255f) - minBlue; + if (isHighToLow) + { + base = max; + range = min - max; + } + else + { + base = min; + range = max - min; + } + } + + public FeatureColour(Color low, Color high, float min, float max) + { + this(new Colour(low), new Colour(high), min, max); + } + /** + * Copy constructor + * + * @param fc + */ + public FeatureColour(FeatureColour fc) + { + colour = fc.colour; + minColour = fc.minColour; + maxColour = fc.maxColour; + minRed = fc.minRed; + minGreen = fc.minGreen; + minBlue = fc.minBlue; + deltaRed = fc.deltaRed; + deltaGreen = fc.deltaGreen; + deltaBlue = fc.deltaBlue; + base = fc.base; + range = fc.range; + isHighToLow = fc.isHighToLow; + setAboveThreshold(fc.isAboveThreshold()); + setBelowThreshold(fc.isBelowThreshold()); + setThreshold(fc.getThreshold()); + setAutoScaled(fc.isAutoScaled()); + setColourByLabel(fc.isColourByLabel()); + } + + /** + * Copy constructor with new min/max ranges + * @param fc + * @param min + * @param max + */ + public FeatureColour(FeatureColour fc, float min, float max) + { + this(fc); + graduatedColour = true; + updateBounds(min, max); + } + + @Override + public boolean isGraduatedColour() + { + return graduatedColour; + } + + /** + * Sets the 'graduated colour' flag. If true, also sets 'colour by label' to + * false. + */ + @Override + public void setGraduatedColour(boolean b) + { + graduatedColour = b; + if (b) + { + setColourByLabel(false); + } + } + + @Override + public ColorI getColour() + { + return colour; + } + + @Override + public ColorI getMinColour() + { + return minColour; + } + + @Override + public ColorI getMaxColour() + { + return maxColour; + } + + @Override + public boolean isColourByLabel() + { + return colourByLabel; + } + + /** + * Sets the 'colour by label' flag. If true, also sets 'graduated colour' to + * false. + */ + @Override + public void setColourByLabel(boolean b) + { + colourByLabel = b; + if (b) + { + setGraduatedColour(false); + } + } + @Override + public boolean isBelowThreshold() + { + return belowThreshold; + } + + @Override + public void setBelowThreshold(boolean b) + { + belowThreshold = b; + if (b) + { + setAboveThreshold(false); + } + } + + @Override + public boolean isAboveThreshold() + { + return aboveThreshold; + } + + @Override + public void setAboveThreshold(boolean b) + { + aboveThreshold = b; + if (b) + { + setBelowThreshold(false); + } + } + + @Override + public boolean isThresholdMinMax() + { + return thresholdIsMinOrMax; + } + + @Override + public void setThresholdMinMax(boolean b) + { + thresholdIsMinOrMax = b; + } + + @Override + public float getThreshold() + { + return threshold; + } + + @Override + public void setThreshold(float f) + { + threshold = f; + } + + @Override + public boolean isAutoScaled() + { + return autoScaled; + } + + @Override + public void setAutoScaled(boolean b) + { + this.autoScaled = b; + } + + /** + * Updates the base and range appropriately for the given minmax range + * + * @param min + * @param max + */ + @Override + public void updateBounds(float min, float max) + { + if (max < min) + { + base = max; + range = min - max; + isHighToLow = true; + } + else + { + base = min; + range = max - min; + isHighToLow = false; + } + } + + /** + * Returns the colour for the given instance of the feature. This may be a + * simple colour, a colour generated from the feature description (if + * isColourByLabel()), or a colour derived from the feature score (if + * isGraduatedColour()). + * + * @param feature + * @return + */ + @Override + public ColorI getColor(SequenceFeature feature) + { + if (isColourByLabel()) + { + return new Colour(UserColourScheme.createColourFromName(feature + .getDescription())); + } + + if (!isGraduatedColour()) + { + return getColour(); + } + + // todo should we check for above/below threshold here? + if (range == 0.0) + { + return getMaxColour(); + } + float scr = feature.getScore(); + if (Float.isNaN(scr)) + { + return getMinColour(); + } + float scl = (scr - base) / range; + if (isHighToLow) + { + scl = -scl; + } + if (scl < 0f) + { + scl = 0f; + } + if (scl > 1f) + { + scl = 1f; + } + return new Colour(new Color(minRed + scl * deltaRed, minGreen + scl + * deltaGreen, minBlue + scl * deltaBlue)); + } + + /** + * Returns the maximum score of the graduated colour range + * + * @return + */ + @Override + public float getMax() + { + // regenerate the original values passed in to the constructor + return (isHighToLow) ? base : (base + range); + } + + /** + * Returns the minimum score of the graduated colour range + * + * @return + */ + @Override + public float getMin() + { + // regenerate the original value passed in to the constructor + return (isHighToLow) ? (base + range) : base; + } + + /** + * Answers true if the feature has a simple colour, or is coloured by label, + * or has a graduated colour and the score of this feature instance is within + * the range to render (if any), i.e. does not lie below or above any + * threshold set. + * + * @param feature + * @return + */ + @Override + public boolean isColored(SequenceFeature feature) + { + if (isColourByLabel() || !isGraduatedColour()) + { + return true; + } + + float val = feature.getScore(); + if (Float.isNaN(val)) + { + return true; + } + if (Float.isNaN(this.threshold)) + { + return true; + } + + if (isAboveThreshold() && val <= threshold) + { + return false; + } + if (isBelowThreshold() && val >= threshold) + { + return false; + } + return true; + } + + @Override + public boolean isSimpleColour() + { + return (!isColourByLabel() && !isGraduatedColour()); + } + + @Override + public boolean hasThreshold() + { + return isAboveThreshold() || isBelowThreshold(); + } + + @Override + public String toJalviewFormat(String featureType) + { + String colourString = null; + if (isSimpleColour()) + { + colourString = Format.getHexString(getColour()); + } + else + { + StringBuilder sb = new StringBuilder(32); + if (isColourByLabel()) + { + sb.append("label"); + if (hasThreshold()) + { + sb.append(BAR).append(BAR).append(BAR); + } + } + if (isGraduatedColour()) + { + sb.append(Format.getHexString(getMinColour())).append(BAR); + sb.append(Format.getHexString(getMaxColour())).append(BAR); + if (isAutoScaled()) + { + sb.append("abso").append(BAR); + } + } + if (hasThreshold() || isGraduatedColour()) + { + sb.append(getMin()).append(BAR); + sb.append(getMax()).append(BAR); + if (isBelowThreshold()) + { + sb.append("below").append(BAR).append(getThreshold()); + } + else if (isAboveThreshold()) + { + sb.append("above").append(BAR).append(getThreshold()); + } + else + { + sb.append("none"); + } + } + colourString = sb.toString(); + } + return String.format("%s\t%s", featureType, colourString); + } + +} diff --git a/src/jalview/schemes/FeatureColourAdapter.java b/src/jalview/schemes/FeatureColourAdapter.java index a86bee4..cc03dd3 100644 --- a/src/jalview/schemes/FeatureColourAdapter.java +++ b/src/jalview/schemes/FeatureColourAdapter.java @@ -1,8 +1,8 @@ package jalview.schemes; +import jalview.api.ColorI; import jalview.api.FeatureColourI; - -import java.awt.Color; +import jalview.datamodel.SequenceFeature; /** * A convenience class with implementations of FeatureColourI methods. Override @@ -17,21 +17,21 @@ public class FeatureColourAdapter implements FeatureColourI } @Override - public Color getColour() + public ColorI getColour() { - return Color.BLACK; + return Colour.black; } @Override - public Color getMinColour() + public ColorI getMinColour() { - return Color.WHITE; + return Colour.white; } @Override - public Color getMaxColour() + public ColorI getMaxColour() { - return Color.BLACK; + return Colour.black; } @Override @@ -65,9 +65,91 @@ public class FeatureColourAdapter implements FeatureColourI } @Override - public boolean isLowToHigh() + public float getMax() + { + return 0; + } + + @Override + public float getMin() + { + return 0; + } + + @Override + public boolean hasThreshold() + { + return false; + } + + @Override + public ColorI getColor(SequenceFeature feature) + { + return null; + } + + @Override + public boolean isColored(SequenceFeature feature) + { + return false; + } + + @Override + public void updateBounds(float min, float max) + { + } + + @Override + public String toJalviewFormat(String featureType) + { + return null; + } + + @Override + public void setThreshold(float f) + { + } + + @Override + public boolean isAutoScaled() + { + return false; + } + + @Override + public void setAutoScaled(boolean b) + { + } + + @Override + public boolean isSimpleColour() + { + return false; + } + + @Override + public void setAboveThreshold(boolean b) + { + } + + @Override + public void setThresholdMinMax(boolean b) + { + } + + @Override + public void setBelowThreshold(boolean b) + { + } + + @Override + public void setColourByLabel(boolean b) + { + } + + @Override + public void setGraduatedColour(boolean b) { - return true; } } diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java index b1e4d58..2bc2d26 100755 --- a/src/jalview/schemes/UserColourScheme.java +++ b/src/jalview/schemes/UserColourScheme.java @@ -136,7 +136,7 @@ public class UserColourScheme extends ResidueColourScheme } - public Color createColourFromName(String name) + public static Color createColourFromName(String name) { int r, g, b; diff --git a/src/jalview/util/ColorUtils.java b/src/jalview/util/ColorUtils.java index 31d1ded..4ba17d5 100644 --- a/src/jalview/util/ColorUtils.java +++ b/src/jalview/util/ColorUtils.java @@ -24,12 +24,18 @@ package jalview.util; +import jalview.api.ColorI; + import java.awt.Color; import java.util.Random; public class ColorUtils { + public static Color getColor(ColorI c) + { + return new Color(c.getRed(), c.getGreen(), c.getBlue()); + } /** * Generates a random color, will mix with input color. Code taken from * http://stackoverflow @@ -68,7 +74,7 @@ public class ColorUtils * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/colortool.html# * tkcode */ - public static final String toTkCode(Color colour) + public static final String toTkCode(ColorI colour) { String colstring = "#" + ((colour.getRed() < 16) ? "0" : "") + Integer.toHexString(colour.getRed()) diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java index d14e4ad..44963f3 100755 --- a/src/jalview/util/Format.java +++ b/src/jalview/util/Format.java @@ -26,6 +26,10 @@ */ package jalview.util; +import jalview.api.ColorI; + +import java.awt.Color; + /** * DOCUMENT ME! * @@ -270,7 +274,37 @@ public class Format * if bad format * */ - public static String getHexString(java.awt.Color color) + public static String getHexString(final Color c) + { + return getHexString(new ColorI() + { + + @Override + public int getRed() + { + return c.getRed(); + } + + @Override + public int getGreen() + { + return c.getGreen(); + } + + @Override + public int getBlue() + { + return c.getBlue(); + } + + @Override + public int getRGB() + { + return c.getRGB(); + } + }); + } + public static String getHexString(ColorI color) { String r; String g; diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index fbd1622..1a42611 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -25,6 +25,7 @@ import jalview.analysis.Conservation; import jalview.api.AlignCalcManagerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.ColorI; import jalview.api.FeaturesDisplayedI; import jalview.api.ViewStyleI; import jalview.commands.CommandI; @@ -42,6 +43,7 @@ import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; import jalview.schemes.PIDColourScheme; import jalview.schemes.ResidueProperties; @@ -57,7 +59,6 @@ import jalview.workers.ComplementConsensusThread; import jalview.workers.ConsensusThread; import jalview.workers.StrucConsensusThread; -import java.awt.Color; import java.util.ArrayDeque; import java.util.ArrayList; import java.util.BitSet; @@ -1237,7 +1238,7 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean showConsensus = true; - private Map sequenceColours = new HashMap(); + private Map sequenceColours = new HashMap(); protected SequenceAnnotationOrder sortAnnotationsBy = null; @@ -2059,14 +2060,14 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public Color getSequenceColour(SequenceI seq) + public ColorI getSequenceColour(SequenceI seq) { - Color sqc = sequenceColours.get(seq); - return (sqc == null ? Color.white : sqc); + ColorI sqc = sequenceColours.get(seq); + return (sqc == null ? Colour.white : sqc); } @Override - public void setSequenceColour(SequenceI seq, Color col) + public void setSequenceColour(SequenceI seq, ColorI col) { if (col == null) { @@ -2223,7 +2224,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @see jalview.api.ViewStyleI#getTextColour() */ @Override - public Color getTextColour() + public ColorI getTextColour() { return viewStyle.getTextColour(); } @@ -2233,7 +2234,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @see jalview.api.ViewStyleI#getTextColour2() */ @Override - public Color getTextColour2() + public ColorI getTextColour2() { return viewStyle.getTextColour2(); } @@ -2304,7 +2305,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color) */ @Override - public void setTextColour(Color textColour) + public void setTextColour(ColorI textColour) { viewStyle.setTextColour(textColour); } @@ -2324,7 +2325,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color) */ @Override - public void setTextColour2(Color textColour2) + public void setTextColour2(ColorI textColour2) { viewStyle.setTextColour2(textColour2); } diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 848f565..52cfb50 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -27,7 +27,10 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.renderer.seqfeatures.FeatureRenderer; -import jalview.schemes.GraduatedColor; +import jalview.schemes.Colour; +import jalview.schemes.FeatureColour; +import jalview.schemes.UserColourScheme; +import jalview.util.ColorUtils; import jalview.viewmodel.AlignmentViewport; import java.awt.Color; @@ -52,17 +55,14 @@ public abstract class FeatureRendererModel implements */ protected float transparency = 1.0f; - protected Map featureColours = new ConcurrentHashMap(); + protected Map featureColours = new ConcurrentHashMap(); protected Map featureGroups = new ConcurrentHashMap(); - protected Object currentColour; - - /* - * feature types in ordering of rendering, where last means on top - */ protected String[] renderOrder; + Map featureOrder = null; + protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( this); @@ -449,7 +449,6 @@ public abstract class FeatureRendererModel implements List allfeatures = new ArrayList(allFeatures); String[] oldRender = renderOrder; renderOrder = new String[allfeatures.size()]; - Object mmrange, fc = null; boolean initOrders = (featureOrder == null); int opos = 0; if (oldRender != null && oldRender.length > 0) @@ -469,16 +468,13 @@ public abstract class FeatureRendererModel implements allfeatures.remove(oldRender[j]); if (minmax != null) { - mmrange = minmax.get(oldRender[j]); + float[][] mmrange = minmax.get(oldRender[j]); if (mmrange != null) { - fc = featureColours.get(oldRender[j]); - if (fc != null && fc instanceof GraduatedColor - && ((GraduatedColor) fc).isAutoScale()) + FeatureColourI fc = featureColours.get(oldRender[j]); + if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()) { - ((GraduatedColor) fc).updateBounds( - ((float[][]) mmrange)[0][0], - ((float[][]) mmrange)[0][1]); + fc.updateBounds(mmrange[0][0], mmrange[0][1]); } } } @@ -502,15 +498,13 @@ public abstract class FeatureRendererModel implements if (minmax != null) { // update from new features minmax if necessary - mmrange = minmax.get(newf[i]); + float[][] mmrange = minmax.get(newf[i]); if (mmrange != null) { - fc = featureColours.get(newf[i]); - if (fc != null && fc instanceof GraduatedColor - && ((GraduatedColor) fc).isAutoScale()) + FeatureColourI fc = featureColours.get(newf[i]); + if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()) { - ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0], - ((float[][]) mmrange)[0][1]); + fc.updateBounds(mmrange[0][0], mmrange[0][1]); } } } @@ -522,7 +516,7 @@ public abstract class FeatureRendererModel implements setOrder(newf[i], i / (float) denom); } // set order from newly found feature from persisted ordering. - sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue(); + sortOrder[i] = 2 - featureOrder.get(newf[i]).floatValue(); if (i < iSize) { // only sort if we need to @@ -540,52 +534,25 @@ public abstract class FeatureRendererModel implements /** * get a feature style object for the given type string. Creates a - * java.awt.Color for a featureType with no existing colourscheme. TODO: - * replace return type with object implementing standard abstract colour/style - * interface + * java.awt.Color for a featureType with no existing colourscheme. * * @param featureType - * @return java.awt.Color or GraduatedColor + * @return */ @Override - public Object getFeatureStyle(String featureType) + public FeatureColourI getFeatureStyle(String featureType) { - Object fc = featureColours.get(featureType); + FeatureColourI fc = featureColours.get(featureType); if (fc == null) { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); - Color col = ucs.createColourFromName(featureType); - featureColours.put(featureType, fc = col); + Color col = UserColourScheme.createColourFromName(featureType); + fc = new FeatureColour(new Colour(col)); + featureColours.put(featureType, fc); } return fc; } /** - * return a nominal colour for this feature - * - * @param featureType - * @return standard color, or maximum colour for graduated colourscheme - */ - public Color getColour(String featureType) - { - Object fc = getFeatureStyle(featureType); - - if (fc instanceof Color) - { - return (Color) fc; - } - else - { - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).getMaxColor(); - } - } - throw new Error("Implementation Error: Unrecognised render object " - + fc.getClass() + " for features of type " + featureType); - } - - /** * calculate the render colour for a specific feature using current feature * settings. * @@ -594,33 +561,14 @@ public abstract class FeatureRendererModel implements */ public Color getColour(SequenceFeature feature) { - Object fc = getFeatureStyle(feature.getType()); - if (fc instanceof Color) - { - return (Color) fc; - } - else - { - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).findColor(feature); - } - } - throw new Error("Implementation Error: Unrecognised render object " - + fc.getClass() + " for features of type " + feature.getType()); + FeatureColourI fc = getFeatureStyle(feature.getType()); + return ColorUtils.getColor(fc.getColor(feature)); } protected boolean showFeature(SequenceFeature sequenceFeature) { - Object fc = getFeatureStyle(sequenceFeature.type); - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).isColored(sequenceFeature); - } - else - { - return true; - } + FeatureColourI fc = getFeatureStyle(sequenceFeature.type); + return fc.isColored(sequenceFeature); } protected boolean showFeatureOfType(String type) @@ -629,26 +577,9 @@ public abstract class FeatureRendererModel implements } @Override - public void setColour(String featureType, Object col) + public void setColour(String featureType, FeatureColourI col) { - // overwrite - // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof - // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null; - // Object c = featureColours.get(featureType); - // if (c == null || c instanceof Color || (c instanceof GraduatedColor && - // !((GraduatedColor)c).getMaxColor().equals(_col))) - if (col instanceof FeatureColourI) - { - if (((FeatureColourI) col).isGraduatedColour()) - { - col = new GraduatedColor((FeatureColourI) col); - } - else - { - col = ((FeatureColourI) col).getColour(); - } - } - featureColours.put(featureType, col); + featureColours.put(featureType, col); } public void setTransparency(float value) @@ -661,8 +592,6 @@ public abstract class FeatureRendererModel implements return transparency; } - Map featureOrder = null; - /** * analogous to colour - store a normalized ordering for all feature types in * this rendering context. @@ -677,7 +606,7 @@ public abstract class FeatureRendererModel implements { if (featureOrder == null) { - featureOrder = new Hashtable(); + featureOrder = new Hashtable(); } featureOrder.put(type, new Float(position)); return position; @@ -695,14 +624,14 @@ public abstract class FeatureRendererModel implements { if (featureOrder.containsKey(type)) { - return ((Float) featureOrder.get(type)).floatValue(); + return featureOrder.get(type).floatValue(); } } return -1; } @Override - public Map getFeatureColours() + public Map getFeatureColours() { return featureColours; } @@ -768,8 +697,7 @@ public abstract class FeatureRendererModel implements for (int i = 0; i < data.length; i++) { String type = data[i][0].toString(); - setColour(type, data[i][1]); // todo : typesafety - feature color - // interface object + setColour(type, (FeatureColourI) data[i][1]); if (((Boolean) data[i][2]).booleanValue()) { av_featuresdisplayed.setVisible(type); @@ -887,13 +815,13 @@ public abstract class FeatureRendererModel implements * @return list of groups */ @Override - public List getGroups(boolean visible) + public List getGroups(boolean visible) { if (featureGroups != null) { - ArrayList gp = new ArrayList(); + List gp = new ArrayList(); - for (Object grp : featureGroups.keySet()) + for (String grp : featureGroups.keySet()) { Boolean state = featureGroups.get(grp); if (state.booleanValue() == visible) @@ -935,19 +863,19 @@ public abstract class FeatureRendererModel implements } @Override - public Hashtable getDisplayedFeatureCols() + public Map getDisplayedFeatureCols() { - Hashtable fcols = new Hashtable(); + Map fcols = new Hashtable(); if (getViewport().getFeaturesDisplayed() == null) { return fcols; } - Iterator en = getViewport().getFeaturesDisplayed() + Iterator features = getViewport().getFeaturesDisplayed() .getVisibleFeatures(); - while (en.hasNext()) + while (features.hasNext()) { - String col = en.next(); - fcols.put(col, getColour(col)); + String feature = features.next(); + fcols.put(feature, getFeatureStyle(feature)); } return fcols; } @@ -958,10 +886,6 @@ public abstract class FeatureRendererModel implements return av.getFeaturesDisplayed(); } - /** - * Returns a (possibly empty) list of visible feature types, in render order - * (last is on top) - */ @Override public List getDisplayedFeatureTypes() { diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java index 1985b6d..908b5b4 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java @@ -20,10 +20,10 @@ */ package jalview.viewmodel.seqfeatures; -import jalview.schemes.GraduatedColor; +import jalview.api.FeatureColourI; +import jalview.schemes.FeatureColour; import java.util.Arrays; -import java.util.Hashtable; import java.util.Iterator; import java.util.Map; import java.util.concurrent.ConcurrentHashMap; @@ -32,24 +32,27 @@ public class FeatureRendererSettings implements Cloneable { String[] renderOrder; - Map featureGroups; + Map featureGroups; - Map featureColours; + Map featureColours; float transparency; - Map featureOrder; + Map featureOrder; public FeatureRendererSettings(String[] renderOrder, - Hashtable featureGroups, Hashtable featureColours, - float transparency, Hashtable featureOrder) + Map featureGroups, + Map featureColours, float transparency, + Map featureOrder) { super(); this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length); - this.featureGroups = new ConcurrentHashMap(featureGroups); - this.featureColours = new ConcurrentHashMap(featureColours); + this.featureGroups = new ConcurrentHashMap( + featureGroups); + this.featureColours = new ConcurrentHashMap( + featureColours); this.transparency = transparency; - this.featureOrder = new ConcurrentHashMap(featureOrder); + this.featureOrder = new ConcurrentHashMap(featureOrder); } /** @@ -61,9 +64,9 @@ public class FeatureRendererSettings implements Cloneable jalview.viewmodel.seqfeatures.FeatureRendererModel fr) { renderOrder = null; - featureGroups = new ConcurrentHashMap(); - featureColours = new ConcurrentHashMap(); - featureOrder = new ConcurrentHashMap(); + featureGroups = new ConcurrentHashMap(); + featureColours = new ConcurrentHashMap(); + featureOrder = new ConcurrentHashMap(); if (fr.renderOrder != null) { this.renderOrder = new String[fr.renderOrder.length]; @@ -72,26 +75,29 @@ public class FeatureRendererSettings implements Cloneable } if (fr.featureGroups != null) { - this.featureGroups = new ConcurrentHashMap(fr.featureGroups); + this.featureGroups = new ConcurrentHashMap( + fr.featureGroups); } if (fr.featureColours != null) { - this.featureColours = new ConcurrentHashMap(fr.featureColours); + this.featureColours = new ConcurrentHashMap( + fr.featureColours); } - Iterator en = fr.featureColours.keySet().iterator(); + Iterator en = fr.featureColours.keySet().iterator(); while (en.hasNext()) { - Object next = en.next(); - Object val = featureColours.get(next); - if (val instanceof GraduatedColor) + String next = en.next(); + FeatureColourI val = featureColours.get(next); + if (!val.isSimpleColour()) { - featureColours.put(next, new GraduatedColor((GraduatedColor) val)); + featureColours.put(next, new FeatureColour((FeatureColour) val)); } } this.transparency = fr.transparency; if (fr.featureOrder != null) { - this.featureOrder = new ConcurrentHashMap(fr.featureOrder); + this.featureOrder = new ConcurrentHashMap( + fr.featureOrder); } } } diff --git a/src/jalview/viewmodel/styles/ViewStyle.java b/src/jalview/viewmodel/styles/ViewStyle.java index 14a1bde..0e66de1 100644 --- a/src/jalview/viewmodel/styles/ViewStyle.java +++ b/src/jalview/viewmodel/styles/ViewStyle.java @@ -20,9 +20,9 @@ */ package jalview.viewmodel.styles; +import jalview.api.ColorI; import jalview.api.ViewStyleI; - -import java.awt.Color; +import jalview.schemes.Colour; /** * A container for holding alignment view properties. View properties are @@ -133,9 +133,9 @@ public class ViewStyle implements ViewStyleI */ protected boolean showUnconserved = false; - Color textColour = Color.black; + ColorI textColour = Colour.black; - Color textColour2 = Color.white; + ColorI textColour2 = Colour.white; /** * PID or consensus threshold @@ -519,7 +519,7 @@ public class ViewStyle implements ViewStyleI * @return the textColour */ @Override - public Color getTextColour() + public ColorI getTextColour() { return textColour; } @@ -528,7 +528,7 @@ public class ViewStyle implements ViewStyleI * @return the textColour2 */ @Override - public Color getTextColour2() + public ColorI getTextColour2() { return textColour2; } @@ -906,7 +906,7 @@ public class ViewStyle implements ViewStyleI * the textColour to set */ @Override - public void setTextColour(Color textColour) + public void setTextColour(ColorI textColour) { this.textColour = textColour; } @@ -916,7 +916,7 @@ public class ViewStyle implements ViewStyleI * the textColour2 to set */ @Override - public void setTextColour2(Color textColour2) + public void setTextColour2(ColorI textColour2) { this.textColour2 = textColour2; } diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java index b2e9b35..66fddd1 100644 --- a/src/jalview/ws/jws1/SeqSearchWSThread.java +++ b/src/jalview/ws/jws1/SeqSearchWSThread.java @@ -21,6 +21,7 @@ package jalview.ws.jws1; import jalview.analysis.AlignSeq; +import jalview.api.FeatureColourI; import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentView; @@ -172,7 +173,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI * @return null or { Alignment(+features and annotation), NewickFile)} */ public Object[] getAlignment(Alignment dataset, - Map featureColours) + Map featureColours) { if (result != null && result.isFinished()) @@ -622,7 +623,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI // NewickFile nf[] = new NewickFile[jobs.length]; for (int j = 0; j < jobs.length; j++) { - Map featureColours = new HashMap(); + Map featureColours = new HashMap(); Alignment al = null; NewickFile nf = null; if (jobs[j].hasResults()) diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java index f4b1c31..ea6310a 100644 --- a/src/jalview/ws/jws2/AADisorderClient.java +++ b/src/jalview/ws/jws2/AADisorderClient.java @@ -20,13 +20,15 @@ */ package jalview.ws.jws2; +import jalview.api.FeatureColourI; import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.GraphLine; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; -import jalview.schemes.GraduatedColor; +import jalview.schemes.Colour; +import jalview.schemes.FeatureColour; import jalview.schemes.UserColourScheme; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.WsParamSetI; @@ -306,8 +308,8 @@ public class AADisorderClient extends JabawsCalcWorker annot.description += "
" + threshNote; } annot.description += ""; - Color col = new UserColourScheme(typeName) - .createColourFromName(typeName + scr.getMethod()); + Color col = UserColourScheme.createColourFromName(typeName + + scr.getMethod()); for (int p = 0, ps = annot.annotations.length; p < ps; p++) { if (annot.annotations[p] != null) @@ -335,13 +337,14 @@ public class AADisorderClient extends JabawsCalcWorker .cloneFeatureRenderer(); for (String ft : fc.keySet()) { - Object gc = fr.getFeatureStyle(ft); - if (gc instanceof Color) + FeatureColourI gc = fr.getFeatureStyle(ft); + if (gc.isSimpleColour()) { // set graduated color as fading to white for minimum, and // autoscaling to values on alignment - GraduatedColor ggc = new GraduatedColor(Color.white, - (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE); + FeatureColourI ggc = new FeatureColour( + new Colour(Color.white), + gc.getColour(), Float.MIN_VALUE, Float.MAX_VALUE); ggc.setAutoScaled(true); fr.setColour(ft, ggc); } diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java index ff745ac..6ee688f 100644 --- a/test/MCview/PDBChainTest.java +++ b/test/MCview/PDBChainTest.java @@ -26,10 +26,12 @@ import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; import jalview.analysis.AlignSeq; +import jalview.api.ColorI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.schemes.Colour; import jalview.schemes.ColourSchemeI; import jalview.schemes.TaylorColourScheme; import jalview.structure.StructureViewSettings; @@ -138,10 +140,10 @@ public class PDBChainTest c.makeBond(a2, a3); c.setChainColours(Color.PINK); assertEquals(2, c.bonds.size()); - assertEquals(Color.PINK, c.bonds.get(0).startCol); - assertEquals(Color.PINK, c.bonds.get(0).endCol); - assertEquals(Color.PINK, c.bonds.get(1).startCol); - assertEquals(Color.PINK, c.bonds.get(1).endCol); + assertEquals(Colour.pink, c.bonds.get(0).startCol); + assertEquals(Colour.pink, c.bonds.get(0).endCol); + assertEquals(Colour.pink, c.bonds.get(1).startCol); + assertEquals(Colour.pink, c.bonds.get(1).endCol); } /** @@ -151,8 +153,8 @@ public class PDBChainTest @Test(groups = { "Functional" }) public void testSetChainColours_colourScheme() { - Color alaColour = new Color(204, 255, 0); - Color glyColour = new Color(255, 153, 0); + ColorI alaColour = new Colour(204, 255, 0); + ColorI glyColour = new Colour(255, 153, 0); a1.resName = "ALA"; a2.resName = "GLY"; a3.resName = "XXX"; // no colour defined @@ -172,20 +174,20 @@ public class PDBChainTest // bond a2 to a3 - no colour found for a3 // exception handling defaults to gray b = c.bonds.get(2); - assertEquals(Color.gray, b.startCol); - assertEquals(Color.gray, b.endCol); + assertEquals(Colour.gray, b.startCol); + assertEquals(Colour.gray, b.endCol); } @Test(groups = { "Functional" }) public void testGetChargeColour() { - assertEquals(Color.red, PDBChain.getChargeColour("ASP")); - assertEquals(Color.red, PDBChain.getChargeColour("GLU")); - assertEquals(Color.blue, PDBChain.getChargeColour("LYS")); - assertEquals(Color.blue, PDBChain.getChargeColour("ARG")); - assertEquals(Color.yellow, PDBChain.getChargeColour("CYS")); - assertEquals(Color.lightGray, PDBChain.getChargeColour("ALA")); - assertEquals(Color.lightGray, PDBChain.getChargeColour(null)); + assertEquals(Colour.red, PDBChain.getChargeColour("ASP")); + assertEquals(Colour.red, PDBChain.getChargeColour("GLU")); + assertEquals(Colour.blue, PDBChain.getChargeColour("LYS")); + assertEquals(Colour.blue, PDBChain.getChargeColour("ARG")); + assertEquals(Colour.yellow, PDBChain.getChargeColour("CYS")); + assertEquals(Colour.lightGray, PDBChain.getChargeColour("ALA")); + assertEquals(Colour.lightGray, PDBChain.getChargeColour(null)); } /** @@ -205,16 +207,16 @@ public class PDBChainTest assertEquals(3, c.bonds.size()); // bond a1 to a2 Bond b = c.bonds.get(0); - assertEquals(Color.red, b.startCol); - assertEquals(Color.blue, b.endCol); + assertEquals(Colour.red, b.startCol); + assertEquals(Colour.blue, b.endCol); // bond a2 to a3 b = c.bonds.get(1); - assertEquals(Color.blue, b.startCol); - assertEquals(Color.yellow, b.endCol); + assertEquals(Colour.blue, b.startCol); + assertEquals(Colour.yellow, b.endCol); // bond a3 to a4 b = c.bonds.get(2); - assertEquals(Color.yellow, b.startCol); - assertEquals(Color.lightGray, b.endCol); + assertEquals(Colour.yellow, b.startCol); + assertEquals(Colour.lightGray, b.endCol); } /** diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index 29c7d16..6e11a88 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -23,7 +23,9 @@ package jalview.ext.rbvi.chimera; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertTrue; -import java.awt.Color; +import jalview.api.ColorI; +import jalview.schemes.Colour; + import java.util.Arrays; import java.util.LinkedHashMap; import java.util.List; @@ -36,47 +38,47 @@ public class ChimeraCommandsTest @Test(groups = { "Functional" }) public void testAddColourRange() { - Map>>> map = new LinkedHashMap>>>(); - ChimeraCommands.addColourRange(map, Color.pink, 1, 2, 4, "A"); - ChimeraCommands.addColourRange(map, Color.pink, 1, 8, 8, "A"); - ChimeraCommands.addColourRange(map, Color.pink, 1, 5, 7, "B"); - ChimeraCommands.addColourRange(map, Color.red, 1, 3, 5, "A"); - ChimeraCommands.addColourRange(map, Color.red, 0, 1, 4, "B"); - ChimeraCommands.addColourRange(map, Color.orange, 0, 5, 9, "C"); + Map>>> map = new LinkedHashMap>>>(); + ChimeraCommands.addColourRange(map, Colour.pink, 1, 2, 4, "A"); + ChimeraCommands.addColourRange(map, Colour.pink, 1, 8, 8, "A"); + ChimeraCommands.addColourRange(map, Colour.pink, 1, 5, 7, "B"); + ChimeraCommands.addColourRange(map, Colour.red, 1, 3, 5, "A"); + ChimeraCommands.addColourRange(map, Colour.red, 0, 1, 4, "B"); + ChimeraCommands.addColourRange(map, Colour.orange, 0, 5, 9, "C"); // three colours mapped assertEquals(3, map.keySet().size()); // Red has two models, Pink and Orange one each - assertEquals(2, map.get(Color.red).keySet().size()); - assertEquals(1, map.get(Color.orange).keySet().size()); - assertEquals(1, map.get(Color.pink).keySet().size()); + assertEquals(2, map.get(Colour.red).keySet().size()); + assertEquals(1, map.get(Colour.orange).keySet().size()); + assertEquals(1, map.get(Colour.pink).keySet().size()); // pink model 1 has two chains, red.0 / red.1 / orange.0 one each - assertEquals(2, map.get(Color.pink).get(1).keySet().size()); - assertEquals(1, map.get(Color.red).get(0).keySet().size()); - assertEquals(1, map.get(Color.red).get(1).keySet().size()); - assertEquals(1, map.get(Color.orange).get(0).keySet().size()); + assertEquals(2, map.get(Colour.pink).get(1).keySet().size()); + assertEquals(1, map.get(Colour.red).get(0).keySet().size()); + assertEquals(1, map.get(Colour.red).get(1).keySet().size()); + assertEquals(1, map.get(Colour.orange).get(0).keySet().size()); // inspect positions - List posList = map.get(Color.pink).get(1).get("A"); + List posList = map.get(Colour.pink).get(1).get("A"); assertEquals(2, posList.size()); assertTrue(Arrays.equals(new int[] { 2, 4 }, posList.get(0))); assertTrue(Arrays.equals(new int[] { 8, 8 }, posList.get(1))); - posList = map.get(Color.pink).get(1).get("B"); + posList = map.get(Colour.pink).get(1).get("B"); assertEquals(1, posList.size()); assertTrue(Arrays.equals(new int[] { 5, 7 }, posList.get(0))); - posList = map.get(Color.red).get(0).get("B"); + posList = map.get(Colour.red).get(0).get("B"); assertEquals(1, posList.size()); assertTrue(Arrays.equals(new int[] { 1, 4 }, posList.get(0))); - posList = map.get(Color.red).get(1).get("A"); + posList = map.get(Colour.red).get(1).get("A"); assertEquals(1, posList.size()); assertTrue(Arrays.equals(new int[] { 3, 5 }, posList.get(0))); - posList = map.get(Color.orange).get(0).get("C"); + posList = map.get(Colour.orange).get(0).get("C"); assertEquals(1, posList.size()); assertTrue(Arrays.equals(new int[] { 5, 9 }, posList.get(0))); } @@ -85,15 +87,15 @@ public class ChimeraCommandsTest public void testBuildColourCommands() { - Map>>> map = new LinkedHashMap>>>(); - ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A"); - ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B"); - ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A"); - ChimeraCommands.addColourRange(map, Color.blue, 1, 1, 1, "A"); - ChimeraCommands.addColourRange(map, Color.blue, 1, 4, 7, "B"); - ChimeraCommands.addColourRange(map, Color.yellow, 1, 8, 8, "A"); - ChimeraCommands.addColourRange(map, Color.yellow, 1, 3, 5, "A"); - ChimeraCommands.addColourRange(map, Color.red, 0, 3, 5, "A"); + Map>>> map = new LinkedHashMap>>>(); + ChimeraCommands.addColourRange(map, Colour.blue, 0, 2, 5, "A"); + ChimeraCommands.addColourRange(map, Colour.blue, 0, 7, 7, "B"); + ChimeraCommands.addColourRange(map, Colour.blue, 0, 9, 23, "A"); + ChimeraCommands.addColourRange(map, Colour.blue, 1, 1, 1, "A"); + ChimeraCommands.addColourRange(map, Colour.blue, 1, 4, 7, "B"); + ChimeraCommands.addColourRange(map, Colour.yellow, 1, 8, 8, "A"); + ChimeraCommands.addColourRange(map, Colour.yellow, 1, 3, 5, "A"); + ChimeraCommands.addColourRange(map, Colour.red, 0, 3, 5, "A"); // Colours should appear in the Chimera command in the order in which // they were added; within colour, by model, by chain, and positions as diff --git a/test/jalview/gui/SequenceRendererTest.java b/test/jalview/gui/SequenceRendererTest.java index aa3b756..7a9e744 100644 --- a/test/jalview/gui/SequenceRendererTest.java +++ b/test/jalview/gui/SequenceRendererTest.java @@ -26,10 +26,9 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.schemes.Colour; import jalview.schemes.ZappoColourScheme; -import java.awt.Color; - import org.testng.annotations.Test; public class SequenceRendererTest @@ -45,10 +44,10 @@ public class SequenceRendererTest av.setGlobalColourScheme(new ZappoColourScheme()); // @see ResidueProperties.zappo - assertEquals(Color.pink, sr.getResidueColour(seq, 0, null)); // M - assertEquals(Color.green, sr.getResidueColour(seq, 2, null)); // T - assertEquals(Color.magenta, sr.getResidueColour(seq, 5, null)); // G - assertEquals(Color.orange, sr.getResidueColour(seq, 12, null)); // F + assertEquals(Colour.pink, sr.getResidueColour(seq, 0, null)); // M + assertEquals(Colour.green, sr.getResidueColour(seq, 2, null)); // T + assertEquals(Colour.magenta, sr.getResidueColour(seq, 5, null)); // G + assertEquals(Colour.orange, sr.getResidueColour(seq, 12, null)); // F } // TODO more tests for getResidueBoxColour covering groups, feature rendering, // gaps, overview... diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 385e049..6bd06cd 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -26,16 +26,15 @@ import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertTrue; +import jalview.api.FeatureColourI; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceDummy; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +import jalview.schemes.Colour; -import java.awt.Color; import java.io.File; import java.io.IOException; import java.util.Map; @@ -53,7 +52,7 @@ public class FeaturesFileTest File f = new File("examples/uniref50.fa"); AlignmentI al = readAlignmentFile(f); AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() + Map colours = af.getFeatureRenderer() .getFeatureColours(); FeaturesFile featuresFile = new FeaturesFile( "examples/exampleFeatures.txt", FormatAdapter.FILE); @@ -67,8 +66,8 @@ public class FeaturesFileTest */ colours = af.getFeatureRenderer().getFeatureColours(); assertEquals("26 feature group colours not found", 26, colours.size()); - assertEquals(colours.get("Cath"), new Color(0x93b1d1)); - assertEquals(colours.get("ASX-MOTIF"), new Color(0x6addbb)); + assertEquals(colours.get("Cath").getColour(), new Colour(0x93b1d1)); + assertEquals(colours.get("ASX-MOTIF").getColour(), new Colour(0x6addbb)); /* * verify (some) features on sequences @@ -140,7 +139,7 @@ public class FeaturesFileTest File f = new File("examples/uniref50.fa"); AlignmentI al = readAlignmentFile(f); AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() + Map colours = af.getFeatureRenderer() .getFeatureColours(); // GFF2 uses space as name/value separator in column 9 String gffData = "METAL\tcc9900\n" + "GFF\n" @@ -154,7 +153,7 @@ public class FeaturesFileTest // verify colours read or synthesized colours = af.getFeatureRenderer().getFeatureColours(); assertEquals("1 feature group colours not found", 1, colours.size()); - assertEquals(colours.get("METAL"), new Color(0xcc9900)); + assertEquals(colours.get("METAL").getColour(), new Colour(0xcc9900)); // verify feature on FER_CAPAA SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() @@ -205,32 +204,31 @@ public class FeaturesFileTest FeaturesFile ff = new FeaturesFile(); // colour by label: - GraduatedColor gc = ff.parseGraduatedColourScheme( + FeatureColourI gc = ff.parseGraduatedColourScheme( "BETA-TURN-IR\t9a6a94", "label"); assertTrue(gc.isColourByLabel()); - assertEquals(Color.white, gc.getMinColor()); - assertEquals(Color.black, gc.getMaxColor()); - assertTrue(gc.isAutoScale()); + assertEquals(Colour.white, gc.getMinColour()); + assertEquals(Colour.black, gc.getMaxColour()); + assertTrue(gc.isAutoScaled()); // using colour name, rgb, etc: String spec = "blue|255,0,255|absolute|20.0|95.0|below|66.0"; gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec); assertFalse(gc.isColourByLabel()); - assertEquals(Color.blue, gc.getMinColor()); - assertEquals(new Color(255, 0, 255), gc.getMaxColor()); - assertFalse(gc.isAutoScale()); - assertFalse(gc.getTolow()); + assertEquals(Colour.blue, gc.getMinColour()); + assertEquals(new Colour(255, 0, 255), gc.getMaxColour()); + assertFalse(gc.isAutoScaled()); + // assertFalse(gc.getTolow()); assertEquals(20.0f, gc.getMin(), 0.001f); assertEquals(95.0f, gc.getMax(), 0.001f); - assertEquals(AnnotationColourGradient.BELOW_THRESHOLD, - gc.getThreshType()); - assertEquals(66.0f, gc.getThresh(), 0.001f); + assertTrue(gc.isBelowThreshold()); + assertEquals(66.0f, gc.getThreshold(), 0.001f); // inverse gradient high to low: spec = "blue|255,0,255|95.0|20.0|below|66.0"; gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec); - assertTrue(gc.isAutoScale()); - assertTrue(gc.getTolow()); + assertTrue(gc.isAutoScaled()); + // assertTrue(gc..getTolow()); } /** @@ -244,7 +242,7 @@ public class FeaturesFileTest File f = new File("examples/uniref50.fa"); AlignmentI al = readAlignmentFile(f); AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() + Map colours = af.getFeatureRenderer() .getFeatureColours(); // GFF3 uses '=' separator for name/value pairs in colum 9 String gffData = "##gff-version 3\n" @@ -296,7 +294,7 @@ public class FeaturesFileTest File f = new File("examples/uniref50.fa"); AlignmentI al = readAlignmentFile(f); AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() + Map colours = af.getFeatureRenderer() .getFeatureColours(); /* diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java new file mode 100644 index 0000000..ccae3e8 --- /dev/null +++ b/test/jalview/schemes/FeatureColourTest.java @@ -0,0 +1,314 @@ +package jalview.schemes; + +import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertFalse; +import static org.testng.AssertJUnit.assertTrue; +import static org.testng.AssertJUnit.fail; + +import jalview.api.ColorI; +import jalview.datamodel.SequenceFeature; +import jalview.util.Format; + +import java.awt.Color; + +import org.testng.annotations.Test; + +public class FeatureColourTest +{ + @Test(groups = { "Functional" }) + public void testIsColored_simpleColour() + { + FeatureColour fc = new FeatureColour(Color.RED); + assertTrue(fc.isColored(new SequenceFeature())); + } + + @Test(groups = { "Functional" }) + public void testIsColored_colourByLabel() + { + FeatureColour fc = new FeatureColour(); + fc.setColourByLabel(true); + assertTrue(fc.isColored(new SequenceFeature())); + } + + @Test(groups = { "Functional" }) + public void testIsColored_aboveThreshold() + { + // graduated colour range from score 20 to 100 + FeatureColour fc = new FeatureColour(new Colour(Color.WHITE), + new Colour(Color.BLACK), 20f, 100f); + + // score 0 is adjusted to bottom of range + SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 0f, + null); + assertTrue(fc.isColored(sf)); + assertEquals(fc.getColor(sf), Colour.white); + + // score 120 is adjusted to top of range + sf.setScore(120f); + assertEquals(fc.getColor(sf), Colour.black); + + // value below threshold is still rendered + // setting threshold has no effect yet... + fc.setThreshold(60f); + sf.setScore(36f); + assertTrue(fc.isColored(sf)); + assertEquals(fc.getColor(sf), new Colour(204, 204, 204)); + + // now apply threshold: + fc.setAboveThreshold(true); + assertFalse(fc.isColored(sf)); + // colour is still returned though ?!? + assertEquals(fc.getColor(sf), new Colour(204, 204, 204)); + + sf.setScore(84); // above threshold now + assertTrue(fc.isColored(sf)); + assertEquals(fc.getColor(sf), new Colour(51, 51, 51)); + } + + @Test(groups = { "Functional" }) + public void testGetColor_simpleColour() + { + FeatureColour fc = new FeatureColour(Colour.red); + assertEquals(fc.getColor(new SequenceFeature()), Colour.red); + } + + @Test(groups = { "Functional" }) + public void testGetColor_colourByLabel() + { + FeatureColour fc = new FeatureColour(); + fc.setColourByLabel(true); + SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f, + null); + ColorI expected = new Colour( + UserColourScheme.createColourFromName("desc")); + assertEquals(fc.getColor(sf), expected); + // assertEquals(expected, fc.getColor(sf)); + } + + @Test(groups = { "Functional" }) + public void testGetColor_Graduated() + { + // graduated colour from score 0 to 100, gray(128, 128, 128) to red(255, 0, 0) + FeatureColour fc = new FeatureColour(Color.GRAY, Color.RED, 0f, 100f); + // feature score is 75 which is 3/4 of the way from GRAY to RED + SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f, + null); + // the colour gradient is computed in float values from 0-1 (where 1 == 255) + float red = 128 / 255f + 3 / 4f * (255 - 128) / 255f; + float green = 128 / 255f + 3 / 4f * (0 - 128) / 255f; + float blue = 128 / 255f + 3 / 4f * (0 - 128) / 255f; + Colour expected = new Colour(red, green, blue); + assertEquals(fc.getColor(sf), expected); + // assertEquals(expected, fc.getColor(sf)); + } + + @Test(groups = { "Functional" }) + public void testGetColor_belowThreshold() + { + // gradient from [50, 150] from WHITE(255, 255, 255) to BLACK(0, 0, 0) + FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 50f, + 150f); + SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 70f, + null); + fc.setThreshold(100f); // ignore for now + assertTrue(fc.isColored(sf)); + assertEquals(fc.getColor(sf), new Colour(204, 204, 204)); + // assertEquals(new Color(204, 204, 204), fc.getColor(sf)); + + fc.setAboveThreshold(true); // feature lies below threshold + assertFalse(fc.isColored(sf)); + assertEquals(fc.getColor(sf), new Colour(204, 204, 204)); + // assertEquals(new Color(204, 204, 204), fc.getColor(sf)); + } + + /** + * Test output of feature colours to Jalview features file format + */ + @Test(groups = { "Functional" }) + public void testToJalviewFormat() + { + /* + * plain colour - to RGB hex code + */ + FeatureColour fc = new FeatureColour(Color.RED); + String redHex = Format.getHexString(Color.RED); + String hexColour = redHex; + assertEquals("domain\t" + hexColour, fc.toJalviewFormat("domain")); + + /* + * colour by label (no threshold) + */ + fc = new FeatureColour(); + fc.setColourByLabel(true); + assertEquals("domain\tlabel", fc.toJalviewFormat("domain")); + + /* + * colour by label (autoscaled) (an odd state you can reach by selecting + * 'above threshold', then deselecting 'threshold is min/max' then 'colour + * by label') + */ + fc.setAutoScaled(true); + assertEquals("domain\tlabel", fc.toJalviewFormat("domain")); + + /* + * colour by label (above threshold) (min/max values are output though not + * used by this scheme) + */ + fc.setAutoScaled(false); + fc.setThreshold(12.5f); + fc.setAboveThreshold(true); + assertEquals("domain\tlabel|||0.0|0.0|above|12.5", + fc.toJalviewFormat("domain")); + + /* + * colour by label (below threshold) + */ + fc.setBelowThreshold(true); + assertEquals("domain\tlabel|||0.0|0.0|below|12.5", + fc.toJalviewFormat("domain")); + + /* + * graduated colour, no threshold + */ + fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f); + String greenHex = Format.getHexString(Color.GREEN); + String expected = String.format("domain\t%s|%s|12.0|25.0|none", + greenHex, redHex); + assertEquals(expected, fc.toJalviewFormat("domain")); + + /* + * colour ranges over the actual score ranges (not min/max) + */ + fc.setAutoScaled(true); + expected = String.format("domain\t%s|%s|abso|12.0|25.0|none", greenHex, + redHex); + assertEquals(expected, fc.toJalviewFormat("domain")); + + /* + * graduated colour below threshold + */ + fc.setThreshold(12.5f); + fc.setBelowThreshold(true); + expected = String.format("domain\t%s|%s|abso|12.0|25.0|below|12.5", + greenHex, redHex); + assertEquals(expected, fc.toJalviewFormat("domain")); + + /* + * graduated colour above threshold + */ + fc.setThreshold(12.5f); + fc.setAboveThreshold(true); + expected = String.format("domain\t%s|%s|abso|12.0|25.0|above|12.5", + greenHex, redHex); + assertEquals(expected, fc.toJalviewFormat("domain")); + } + + /** + * Test parsing of feature colours from Jalview features file format + */ + @Test(groups = { "Functional" }) + public void testParseJalviewFeatureColour() + { + /* + * simple colour by name + */ + FeatureColour fc = FeatureColour.parseJalviewFeatureColour("red"); + assertTrue(fc.isSimpleColour()); + assertEquals(fc.getColour(), Colour.red); + + /* + * simple colour by hex code + */ + fc = FeatureColour.parseJalviewFeatureColour(Format + .getHexString(Color.RED)); + assertTrue(fc.isSimpleColour()); + assertEquals(fc.getColour(), Colour.red); + // assertEquals(Color.RED, fc.getColour()); + + /* + * simple colour by rgb triplet + */ + fc = FeatureColour.parseJalviewFeatureColour("255,0,0"); + assertTrue(fc.isSimpleColour()); + assertEquals(fc.getColour(), Colour.red); + // assertEquals(Color.RED, fc.getColour()); + + /* + * malformed colour + */ + try + { + fc = FeatureColour.parseJalviewFeatureColour("oops"); + fail("expected exception"); + } catch (IllegalArgumentException e) + { + assertEquals("Invalid colour descriptor: oops", e.getMessage()); + } + + /* + * colour by label (no threshold) + */ + fc = FeatureColour.parseJalviewFeatureColour("label"); + assertTrue(fc.isColourByLabel()); + assertFalse(fc.hasThreshold()); + + /* + * colour by label (with threshold) + */ + fc = FeatureColour + .parseJalviewFeatureColour("label|||0.0|0.0|above|12.0"); + assertTrue(fc.isColourByLabel()); + assertTrue(fc.isAboveThreshold()); + assertEquals(12.0f, fc.getThreshold()); + + /* + * graduated colour (by name) (no threshold) + */ + fc = FeatureColour.parseJalviewFeatureColour("red|green|10.0|20.0"); + assertTrue(fc.isGraduatedColour()); + assertFalse(fc.hasThreshold()); + assertEquals(fc.getMinColour(), Colour.red); + // assertEquals(Color.RED, fc.getMinColour()); + assertEquals(fc.getMaxColour(), Colour.green); + // assertEquals(Color.GREEN, fc.getMaxColour()); + assertEquals(10f, fc.getMin()); + assertEquals(20f, fc.getMax()); + assertTrue(fc.isAutoScaled()); + + /* + * graduated colour (by hex code) (above threshold) + */ + String descriptor = String.format("%s|%s|10.0|20.0|above|15", + Format.getHexString(Color.RED), + Format.getHexString(Color.GREEN)); + fc = FeatureColour.parseJalviewFeatureColour(descriptor); + assertTrue(fc.isGraduatedColour()); + assertTrue(fc.hasThreshold()); + assertTrue(fc.isAboveThreshold()); + assertEquals(15f, fc.getThreshold()); + assertEquals(fc.getMinColour(), Colour.red); + // assertEquals(Color.RED, fc.getMinColour()); + assertEquals(fc.getMaxColour(), Colour.green); + // assertEquals(Color.GREEN, fc.getMaxColour()); + assertEquals(10f, fc.getMin()); + assertEquals(20f, fc.getMax()); + assertTrue(fc.isAutoScaled()); + + /* + * graduated colour (by RGB triplet) (below threshold), absolute scale + */ + descriptor = String.format("255,0,0|0,255,0|abso|10.0|20.0|below|15"); + fc = FeatureColour.parseJalviewFeatureColour(descriptor); + assertTrue(fc.isGraduatedColour()); + assertFalse(fc.isAutoScaled()); + assertTrue(fc.hasThreshold()); + assertTrue(fc.isBelowThreshold()); + assertEquals(15f, fc.getThreshold()); + assertEquals(fc.getMinColour(), Colour.red); + // assertEquals(Color.RED, fc.getMinColour()); + assertEquals(fc.getMaxColour(), Colour.green); + // assertEquals(Color.GREEN, fc.getMaxColour()); + assertEquals(10f, fc.getMin()); + assertEquals(20f, fc.getMax()); + } +} diff --git a/test/jalview/util/ColorUtilsTest.java b/test/jalview/util/ColorUtilsTest.java index a82b9c0..e20fc5c 100644 --- a/test/jalview/util/ColorUtilsTest.java +++ b/test/jalview/util/ColorUtilsTest.java @@ -23,6 +23,8 @@ package jalview.util; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertNull; +import jalview.schemes.Colour; + import java.awt.Color; import org.testng.annotations.Test; @@ -66,11 +68,11 @@ public class ColorUtilsTest @Test(groups = { "Functional" }) public void testToTkCode() { - assertEquals("#fffafa", ColorUtils.toTkCode(new Color(255, 250, 250))); // snow - assertEquals("#e6e6fa", ColorUtils.toTkCode(new Color(230, 230, 250))); // lavender - assertEquals("#dda0dd", ColorUtils.toTkCode(new Color(221, 160, 221))); // plum - assertEquals("#800080", ColorUtils.toTkCode(new Color(128, 0, 128))); // purple - assertEquals("#00ff00", ColorUtils.toTkCode(new Color(0, 255, 0))); // lime + assertEquals("#fffafa", ColorUtils.toTkCode(new Colour(255, 250, 250))); // snow + assertEquals("#e6e6fa", ColorUtils.toTkCode(new Colour(230, 230, 250))); // lavender + assertEquals("#dda0dd", ColorUtils.toTkCode(new Colour(221, 160, 221))); // plum + assertEquals("#800080", ColorUtils.toTkCode(new Colour(128, 0, 128))); // purple + assertEquals("#00ff00", ColorUtils.toTkCode(new Colour(0, 255, 0))); // lime } @Test(groups = { "Functional" }) diff --git a/test/jalview/viewmodel/styles/ViewStyleTest.java b/test/jalview/viewmodel/styles/ViewStyleTest.java index 200cfbb..1262587 100644 --- a/test/jalview/viewmodel/styles/ViewStyleTest.java +++ b/test/jalview/viewmodel/styles/ViewStyleTest.java @@ -24,7 +24,9 @@ import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; -import java.awt.Color; +import jalview.api.ColorI; +import jalview.schemes.Colour; + import java.lang.reflect.Field; import java.util.Random; @@ -150,10 +152,10 @@ public class ViewStyleTest { field.set(vs, "Joe" + field.get(vs)); } - else if (type.equals(Color.class)) + else if (type.equals(ColorI.class)) { - field.set(vs, Color.RED.equals(field.get(vs)) ? Color.BLACK - : Color.RED); + field.set(vs, Colour.red.equals(field.get(vs)) ? Colour.black + : Colour.red); } else { -- 1.7.10.2