X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=d898398dcb079accd934d187c92d021b9b42e10b;hb=f6996637c284c21faf5a5d2d9f1335e8718b3da0;hp=b5472141ee6f30c50dd2f5c230acaae4de6633a6;hpb=217274a8e9ea2ae20d5a6d21989b8b16840ca6f0;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index b547214..d898398 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -20,15 +20,6 @@ */ package jalview.gui; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentAnnotation; -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 java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -48,13 +39,20 @@ 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") public class AnnotationColourChooser extends AnnotationRowFilter { - private static final int ONETHOUSAND = 1000; - private ColourSchemeI oldcs; private JButton defColours; @@ -75,6 +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) @@ -89,6 +91,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter } } frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); Desktop.addInternalFrame(frame, @@ -107,11 +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()); @@ -126,10 +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()) { @@ -147,15 +171,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter "error.implementation_error_dont_know_about_threshold_setting")); } thresholdIsMin.setSelected(acg.isThresholdIsMinMax()); - thresholdValue.setText("" + acg.getAnnotationThreshold()); + thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold())); } - - jbInit(); - adjusting = false; - - updateView(); - frame.invalidate(); - frame.pack(); } @Override @@ -308,7 +325,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void reset() { - av.setGlobalColourScheme(oldcs); + this.ap.alignFrame.changeColour(oldcs); if (av.getAlignment().getGroups() != null) { @@ -329,7 +346,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter { updateView(); } - getCurrentAnnotation().threshold.value = slider.getValue() / 1000f; + getCurrentAnnotation().threshold.value = getSliderValue(); propagateSeqAssociatedThreshold(updateAllAnnotation, getCurrentAnnotation()); ap.paintAlignment(false, false); @@ -358,9 +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()); @@ -369,6 +388,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter thresholdValue.setEnabled(true); thresholdIsMin.setEnabled(!useOriginalColours.isSelected()); + final AlignmentAnnotation currentAnnotation = getCurrentAnnotation(); if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD) { slider.setEnabled(false); @@ -377,33 +397,26 @@ public class AnnotationColourChooser extends AnnotationRowFilter thresholdIsMin.setEnabled(false); } else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD - && getCurrentAnnotation().threshold == null) + && currentAnnotation.threshold == null) { - getCurrentAnnotation().setThreshold(new GraphLine( - (getCurrentAnnotation().graphMax - - getCurrentAnnotation().graphMin) / 2f, + currentAnnotation.setThreshold(new GraphLine( + (currentAnnotation.graphMax - currentAnnotation.graphMin) + / 2f, "Threshold", Color.black)); } if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD) { adjusting = true; - float range = getCurrentAnnotation().graphMax * ONETHOUSAND - - getCurrentAnnotation().graphMin * ONETHOUSAND; - - slider.setMinimum( - (int) (getCurrentAnnotation().graphMin * ONETHOUSAND)); - slider.setMaximum( - (int) (getCurrentAnnotation().graphMax * ONETHOUSAND)); - slider.setValue( - (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND)); - thresholdValue.setText(getCurrentAnnotation().threshold.value + ""); - slider.setMajorTickSpacing((int) (range / 10f)); + setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax, + currentAnnotation.threshold.value); slider.setEnabled(true); + + setThresholdValueText(); thresholdValue.setEnabled(true); adjusting = false; } - colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem); + colorAlignmentContaining(currentAnnotation, selectedThresholdItem); ap.alignmentChanged(); } @@ -433,7 +446,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter acg.setThresholdIsMinMax(thresholdIsMin.isSelected()); - av.setGlobalColourScheme(acg); + this.ap.alignFrame.changeColour(acg); if (av.getAlignment().getGroups() != null) { @@ -444,8 +457,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter { continue; } - sg.setColourScheme( - acg.getInstance(sg, ap.av.getHiddenRepSequences())); + sg.setColourScheme(acg.getInstance(av, sg)); } } } @@ -457,4 +469,32 @@ public class AnnotationColourChooser extends AnnotationRowFilter 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