X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=d898398dcb079accd934d187c92d021b9b42e10b;hb=ca160187a050f6d4e50158cd5b51f75c83a7179e;hp=7ed178b4bdde183a24ec7b9f71966ec35767d20f;hpb=b645f92e338a4eea33bd2813c27917fb0fe5cc4d;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index 7ed178b..d898398 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -20,14 +20,6 @@ */ package jalview.gui; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.GraphLine; -import jalview.datamodel.SequenceGroup; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.ColourSchemeI; -import jalview.util.MessageManager; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -42,12 +34,20 @@ import java.util.Vector; import javax.swing.BorderFactory; import javax.swing.JButton; import javax.swing.JCheckBox; -import javax.swing.JColorChooser; import javax.swing.JComboBox; import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.JPanel; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.GraphLine; +import jalview.datamodel.SequenceGroup; +import jalview.gui.JalviewColourChooser.ColourChooserListener; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.ColourSchemeI; +import jalview.util.MessageManager; import net.miginfocom.swing.MigLayout; @SuppressWarnings("serial") @@ -61,9 +61,9 @@ public class AnnotationColourChooser extends AnnotationRowFilter private JCheckBox useOriginalColours = new JCheckBox(); - private JPanel minColour = new JPanel(); + JPanel minColour = new JPanel(); - private JPanel maxColour = new JPanel(); + JPanel maxColour = new JPanel(); private JCheckBox thresholdIsMin = new JCheckBox(); @@ -73,6 +73,10 @@ public class AnnotationColourChooser extends AnnotationRowFilter public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap) { + this(av,ap,null); + } + public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,AnnotationColourGradient initSettings) + { super(av, ap); oldcs = av.getGlobalColourScheme(); if (av.getAlignment().getGroups() != null) @@ -87,6 +91,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter } } frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); Desktop.addInternalFrame(frame, @@ -105,11 +110,28 @@ public class AnnotationColourChooser extends AnnotationRowFilter setDefaultMinMax(); adjusting = true; - if (oldcs instanceof AnnotationColourGradient) + if (oldcs instanceof AnnotationColourGradient && initSettings==null) + { + // init from oldcs + initialiseFrom((AnnotationColourGradient) oldcs); + } else { + // use initial colour gradient - if any.. + initialiseFrom(initSettings); + } + + jbInit(); + adjusting = false; + + updateView(); + frame.invalidate(); + frame.pack(); + } + private void initialiseFrom(AnnotationColourGradient acg) + { + if (acg!=null) { - AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; useOriginalColours.setSelected( - acg.isPredefinedColours() || acg.getBaseColour() != null); + acg.isPredefinedColours() || acg.getBaseColour() != null); if (!acg.isPredefinedColours() && acg.getBaseColour() == null) { minColour.setBackground(acg.getMinColour()); @@ -124,10 +146,14 @@ public class AnnotationColourChooser extends AnnotationRowFilter populateThresholdComboBox(threshold); - if (oldcs instanceof AnnotationColourGradient) + if (acg!=null) { - AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; String label = getAnnotationMenuLabel(acg.getAnnotation()); + // TODO: workaround below shouldn't be necessary - there's a bug in getAnnotationMenuLabel! + if (acg.isSeqAssociated()) + { + label = acg.getAnnotation().label; + } annotations.setSelectedItem(label); switch (acg.getAboveThreshold()) { @@ -145,16 +171,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter "error.implementation_error_dont_know_about_threshold_setting")); } thresholdIsMin.setSelected(acg.isThresholdIsMinMax()); - thresholdValue - .setText(String.valueOf(acg.getAnnotationThreshold())); + thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold())); } - - jbInit(); - adjusting = false; - - updateView(); - frame.invalidate(); - frame.pack(); } @Override @@ -173,7 +191,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter { if (minColour.isEnabled()) { - minColour_actionPerformed(); + showColourChooser(minColour, "label.select_colour_minimum_value"); } } }); @@ -188,7 +206,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter { if (maxColour.isEnabled()) { - maxColour_actionPerformed(); + showColourChooser(maxColour, "label.select_colour_maximum_value"); } } }); @@ -287,30 +305,21 @@ public class AnnotationColourChooser extends AnnotationRowFilter Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); } - public void minColour_actionPerformed() + protected void showColourChooser(JPanel colourPanel, String titleKey) { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_minimum_value"), - minColour.getBackground()); - if (col != null) + String ttl = MessageManager.getString(titleKey); + ColourChooserListener listener = new ColourChooserListener() { - minColour.setBackground(col); - } - minColour.repaint(); - updateView(); - } - - public void maxColour_actionPerformed() - { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_maximum_value"), - maxColour.getBackground()); - if (col != null) - { - maxColour.setBackground(col); - } - maxColour.repaint(); - updateView(); + @Override + public void colourSelected(Color c) + { + colourPanel.setBackground(c); + colourPanel.repaint(); + updateView(); + } + }; + JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl, + colourPanel.getBackground(), listener); } @Override @@ -366,9 +375,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter return; } + int selIndex = annotations + .getSelectedIndex(); + int annIndex = annmap[selIndex]; setCurrentAnnotation( - av.getAlignment().getAlignmentAnnotation()[annmap[annotations - .getSelectedIndex()]]); + av.getAlignment().getAlignmentAnnotation()[annIndex]); int selectedThresholdItem = getSelectedThresholdItem( getThreshold().getSelectedIndex()); @@ -446,8 +457,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter { continue; } - sg.setColourScheme( - acg.getInstance(av, sg)); + sg.setColourScheme(acg.getInstance(av, sg)); } } } @@ -458,4 +468,33 @@ public class AnnotationColourChooser extends AnnotationRowFilter super.sliderDragReleased(); ap.paintAlignment(true, true); } + + /** + * construct and display a colourchooser for a given annotation row + * + * @param av + * @param ap + * @param alignmentAnnotation + * @param perseq - when true, enable per-sequence if alignment annotation is per sequence + */ + public static void displayFor(AlignViewport av, AlignmentPanel ap, + AlignmentAnnotation alignmentAnnotation, boolean perSeq) + { + ColourSchemeI global = av.getGlobalColourScheme(); + AnnotationColourGradient newCS = new AnnotationColourGradient(alignmentAnnotation, global, alignmentAnnotation.threshold!=null ? AnnotationColourGradient.ABOVE_THRESHOLD:AnnotationColourGradient.NO_THRESHOLD); + if (alignmentAnnotation.sequenceRef!=null) + { + newCS.setSeqAssociated(perSeq); + } + for (int i=0;i