X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=965770ce5a7bbc4f7a57821d2f365b94ca089951;hb=ba1f9fee25b87bdac0c535019252b787939a8f80;hp=7226eb06b6e2cbcfca5d50dd415ae4a64a5182c6;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index 7226eb0..965770c 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,105 +20,88 @@ */ package jalview.gui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import javax.swing.*; -import javax.swing.event.*; - -import net.miginfocom.swing.MigLayout; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.FlowLayout; +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 java.util.Vector; + +import javax.swing.BorderFactory; +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JComboBox; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JPanel; import jalview.bin.Cache; -import jalview.datamodel.*; -import jalview.schemes.*; +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; -import java.awt.Dimension; - -public class AnnotationColourChooser extends JPanel +@SuppressWarnings("serial") +public class AnnotationColourChooser extends AnnotationRowFilter { - JInternalFrame frame; + private ColourSchemeI oldcs; - AlignViewport av; + private JButton defColours; - AlignmentPanel ap; + private Hashtable oldgroupColours; - ColourSchemeI oldcs; + private JCheckBox useOriginalColours = new JCheckBox(); - Hashtable oldgroupColours; + JPanel minColour = new JPanel(); - jalview.datamodel.AlignmentAnnotation currentAnnotation; + JPanel maxColour = new JPanel(); - boolean adjusting = false; + private JCheckBox thresholdIsMin = new JCheckBox(); - /** - * enabled if the user is dragging the slider - try to keep updates to a - * minimun - */ - boolean sliderDragging = false; + protected static final int MIN_WIDTH = 500; + + protected static final int MIN_HEIGHT = 240; 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) { - oldgroupColours = new Hashtable(); + oldgroupColours = new Hashtable<>(); for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - if (sg.cs != null) + if (sg.getColourScheme() != null) { - oldgroupColours.put(sg, sg.cs); + oldgroupColours.put(sg, sg.getColourScheme()); } } } - this.av = av; - this.ap = ap; frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215); - - slider.addChangeListener(new ChangeListener() - { - public void stateChanged(ChangeEvent evt) - { - if (!adjusting) - { - thresholdValue.setText(((float) slider.getValue() / 1000f) + ""); - valueChanged(!sliderDragging); - } - } - }); - slider.addMouseListener(new MouseAdapter() - { - @Override - public void mousePressed(MouseEvent e) - { - sliderDragging = true; - super.mousePressed(e); - } - - @Override - public void mouseDragged(MouseEvent e) - { - sliderDragging = true; - super.mouseDragged(e); - } - - public void mouseReleased(MouseEvent evt) - { - if (sliderDragging) - { - sliderDragging = false; - valueChanged(true); - } - ap.paintAlignment(true); - } - }); + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); + addSliderChangeListener(); + addSliderMouseListeners(); if (av.getAlignment().getAlignmentAnnotation() == null) { @@ -129,11 +112,31 @@ public class AnnotationColourChooser extends JPanel 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; - currentColours.setSelected(acg.isPredefinedColours() - || acg.getBaseColour() != null); + useOriginalColours.setSelected( + acg.isPredefinedColours() || acg.getBaseColour() != null); if (!acg.isPredefinedColours() && acg.getBaseColour() == null) { minColour.setBackground(acg.getMinColour()); @@ -142,126 +145,59 @@ public class AnnotationColourChooser extends JPanel seqAssociated.setSelected(acg.isSeqAssociated()); } - annotations = new JComboBox( - getAnnotationItems(seqAssociated.isSelected())); + Vector annotItems = getAnnotationItems( + seqAssociated.isSelected()); + annotations = new JComboBox<>(annotItems); - threshold.addItem(MessageManager - .getString("label.threshold_feature_no_thereshold")); - threshold.addItem(MessageManager - .getString("label.threshold_feature_above_thereshold")); - threshold.addItem(MessageManager - .getString("label.threshold_feature_below_thereshold")); + populateThresholdComboBox(threshold); - if (oldcs instanceof AnnotationColourGradient) + if (acg != null) { - AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; - annotations.setSelectedItem(acg.getAnnotation()); + 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()) { case AnnotationColourGradient.NO_THRESHOLD: - threshold.setSelectedIndex(0); + getThreshold().setSelectedIndex(0); break; case AnnotationColourGradient.ABOVE_THRESHOLD: - threshold.setSelectedIndex(1); + getThreshold().setSelectedIndex(1); break; case AnnotationColourGradient.BELOW_THRESHOLD: - threshold.setSelectedIndex(2); + getThreshold().setSelectedIndex(2); break; default: - throw new Error(MessageManager.getString("error.implementation_error_dont_know_about_thereshold_setting")); - } - thresholdIsMin.setSelected(acg.thresholdIsMinMax); - thresholdValue.setText("" + acg.getAnnotationThreshold()); - } - - try - { - jbInit(); - } catch (Exception ex) - { - } - - adjusting = false; - - changeColour(); - frame.invalidate(); - frame.pack(); - - } - - private Vector getAnnotationItems(boolean isSeqAssociated) - { - Vector list = new Vector(); - int index = 1; - int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length]; - boolean enableSeqAss = false; - for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) - { - if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null) - { - if (isSeqAssociated) - { - continue; - } - } - else - { - enableSeqAss = true; - } - String label = av.getAlignment().getAlignmentAnnotation()[i].label; - if (!list.contains(label)) - { - anmap[list.size()] = i; - list.addElement(label); - - } - else - { - if (!isSeqAssociated) - { - anmap[list.size()] = i; - list.addElement(label + "_" + (index++)); - } + throw new Error(MessageManager.getString( + "error.implementation_error_dont_know_about_threshold_setting")); } + thresholdIsMin.setSelected(acg.isThresholdIsMinMax()); + thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold())); } - seqAssociated.setEnabled(enableSeqAss); - annmap = new int[list.size()]; - System.arraycopy(anmap, 0, annmap, 0, annmap.length); - return list; } - private void setDefaultMinMax() + @Override + protected void jbInit() { - minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", - Color.orange)); - maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", - Color.red)); - } + super.jbInit(); - public AnnotationColourChooser() - { - try - { - jbInit(); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - private void jbInit() throws Exception - { minColour.setFont(JvSwingUtils.getLabelFont()); minColour.setBorder(BorderFactory.createEtchedBorder()); minColour.setPreferredSize(new Dimension(40, 20)); minColour.setToolTipText(MessageManager.getString("label.min_colour")); minColour.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent e) { if (minColour.isEnabled()) { - minColour_actionPerformed(); + showColourChooser(minColour, "label.select_colour_minimum_value"); } } }); @@ -271,32 +207,17 @@ public class AnnotationColourChooser extends JPanel maxColour.setToolTipText(MessageManager.getString("label.max_colour")); maxColour.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent e) { if (maxColour.isEnabled()) { - maxColour_actionPerformed(); + showColourChooser(maxColour, "label.select_colour_maximum_value"); } } }); - ok.setOpaque(false); - ok.setText(MessageManager.getString("action.ok")); - ok.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - ok_actionPerformed(e); - } - }); - cancel.setOpaque(false); - cancel.setText(MessageManager.getString("action.cancel")); - cancel.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - cancel_actionPerformed(e); - } - }); + + defColours = new JButton(); defColours.setOpaque(false); defColours.setText(MessageManager.getString("action.set_defaults")); defColours.setToolTipText(MessageManager @@ -307,76 +228,51 @@ public class AnnotationColourChooser extends JPanel @Override public void actionPerformed(ActionEvent arg0) { - resetColours_actionPerformed(arg0); + resetColours_actionPerformed(); } }); - annotations.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - annotations_actionPerformed(e); - } - }); - threshold.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - threshold_actionPerformed(e); - } - }); - thresholdValue.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - thresholdValue_actionPerformed(e); - } - }); - slider.setPaintLabels(false); - slider.setPaintTicks(true); - slider.setBackground(Color.white); - slider.setEnabled(false); - slider.setOpaque(false); - slider.setPreferredSize(new Dimension(100, 32)); - thresholdValue.setEnabled(false); - thresholdValue.setColumns(7); - currentColours.setFont(JvSwingUtils.getLabelFont()); - currentColours.setOpaque(false); - currentColours.setText(MessageManager - .getString("label.use_original_colours")); - currentColours.addActionListener(new ActionListener() + useOriginalColours.setFont(JvSwingUtils.getLabelFont()); + useOriginalColours.setOpaque(false); + useOriginalColours.setText( + MessageManager.getString("label.use_original_colours")); + useOriginalColours.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - currentColours_actionPerformed(e); + originalColours_actionPerformed(); } }); thresholdIsMin.setBackground(Color.white); thresholdIsMin.setFont(JvSwingUtils.getLabelFont()); - thresholdIsMin.setText(MessageManager - .getString("label.threshold_minmax")); + thresholdIsMin + .setText(MessageManager.getString("label.threshold_minmax")); thresholdIsMin.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { - thresholdIsMin_actionPerformed(actionEvent); + thresholdIsMin_actionPerformed(); } }); seqAssociated.setBackground(Color.white); seqAssociated.setFont(JvSwingUtils.getLabelFont()); - seqAssociated.setText(MessageManager - .getString("label.per_sequence_only")); + seqAssociated + .setText(MessageManager.getString("label.per_sequence_only")); seqAssociated.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent arg0) { - seqAssociated_actionPerformed(arg0); + seqAssociated_actionPerformed(annotations); } }); - this.setLayout(borderLayout1); + this.setLayout(new BorderLayout()); + JPanel jPanel1 = new JPanel(); + JPanel jPanel2 = new JPanel(); jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]")); jPanel1.setBackground(Color.white); jPanel2.setBackground(Color.white); @@ -385,13 +281,13 @@ public class AnnotationColourChooser extends JPanel jPanel1.add(cancel); jPanel2.add(annotations, "grow, wrap"); jPanel2.add(seqAssociated); - jPanel2.add(currentColours); + jPanel2.add(useOriginalColours); JPanel colpanel = new JPanel(new FlowLayout()); colpanel.setBackground(Color.white); colpanel.add(minColour); colpanel.add(maxColour); jPanel2.add(colpanel, "wrap"); - jPanel2.add(threshold); + jPanel2.add(getThreshold()); jPanel2.add(defColours, "skip 1, wrap"); jPanel2.add(thresholdIsMin); jPanel2.add(slider, "grow"); @@ -401,98 +297,83 @@ public class AnnotationColourChooser extends JPanel this.validate(); } - protected void seqAssociated_actionPerformed(ActionEvent arg0) + protected void resetColours_actionPerformed() { - adjusting = true; - String cursel = (String) annotations.getSelectedItem(); - boolean isvalid = false, isseqs = seqAssociated.isSelected(); - this.annotations.removeAllItems(); - for (String anitem : getAnnotationItems(seqAssociated.isSelected())) + setDefaultMinMax(); + updateView(); + } + + private void setDefaultMinMax() + { + minColour.setBackground( + Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange)); + maxColour.setBackground( + Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); + } + + protected void showColourChooser(JPanel colourPanel, String titleKey) + { + String ttl = MessageManager.getString(titleKey); + ColourChooserListener listener = new ColourChooserListener() { - if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem))) + @Override + public void colourSelected(Color c) { - isvalid = true; - cursel = anitem; + colourPanel.setBackground(c); + colourPanel.repaint(); + updateView(); } - this.annotations.addItem(anitem); - } - adjusting = false; - if (isvalid) - { - this.annotations.setSelectedItem(cursel); - } - else + }; + JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl, + colourPanel.getBackground(), listener); + } + + @Override + public void reset() + { + this.ap.alignFrame.changeColour(oldcs); + if (av.getAlignment().getGroups() != null) { - if (annotations.getItemCount() > 0) + + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - annotations.setSelectedIndex(0); + sg.setColourScheme(oldgroupColours.get(sg)); } } } - protected void resetColours_actionPerformed(ActionEvent arg0) - { - setDefaultMinMax(); - changeColour(); - } - - JComboBox annotations; - - int[] annmap; - - JPanel minColour = new JPanel(); - - JPanel maxColour = new JPanel(); - - JButton defColours = new JButton(); - - JButton ok = new JButton(); - - JButton cancel = new JButton(); - - JPanel jPanel1 = new JPanel(); - - JPanel jPanel2 = new JPanel(); - - BorderLayout borderLayout1 = new BorderLayout(); - - JComboBox threshold = new JComboBox(); - - JSlider slider = new JSlider(); - - JTextField thresholdValue = new JTextField(20); - - JCheckBox currentColours = new JCheckBox(); - - JCheckBox thresholdIsMin = new JCheckBox(); - - JCheckBox seqAssociated = new JCheckBox(); - - public void minColour_actionPerformed() + @Override + public void valueChanged(boolean updateAllAnnotation) { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground()); - if (col != null) + if (slider.isEnabled()) { - minColour.setBackground(col); + if (useOriginalColours.isSelected() && !(av + .getGlobalColourScheme() instanceof AnnotationColourGradient)) + { + updateView(); + } + getCurrentAnnotation().threshold.value = getSliderValue(); + propagateSeqAssociatedThreshold(updateAllAnnotation, + getCurrentAnnotation()); + ap.paintAlignment(false, false); } - minColour.repaint(); - changeColour(); } - public void maxColour_actionPerformed() + public void originalColours_actionPerformed() { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground()); - if (col != null) + boolean selected = useOriginalColours.isSelected(); + if (selected) { - maxColour.setBackground(col); + reset(); } - maxColour.repaint(); - changeColour(); + maxColour.setEnabled(!selected); + minColour.setEnabled(!selected); + thresholdIsMin.setEnabled(!selected); + updateView(); } - void changeColour() + @Override + public void updateView() { // Check if combobox is still adjusting if (adjusting) @@ -500,78 +381,77 @@ public class AnnotationColourChooser extends JPanel return; } - currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations - .getSelectedIndex()]]; + int selIndex = annotations.getSelectedIndex(); + int annIndex = annmap[selIndex]; + setCurrentAnnotation( + av.getAlignment().getAlignmentAnnotation()[annIndex]); - int aboveThreshold = -1; - if (threshold.getSelectedIndex() == 1) - { - aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD; - } - else if (threshold.getSelectedIndex() == 2) - { - aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD; - } + int selectedThresholdItem = getSelectedThresholdItem( + getThreshold().getSelectedIndex()); slider.setEnabled(true); thresholdValue.setEnabled(true); - thresholdIsMin.setEnabled(true); + thresholdIsMin.setEnabled(!useOriginalColours.isSelected()); - if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD) + final AlignmentAnnotation currentAnnotation = getCurrentAnnotation(); + if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD) { slider.setEnabled(false); thresholdValue.setEnabled(false); thresholdValue.setText(""); thresholdIsMin.setEnabled(false); } - else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD + else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD && currentAnnotation.threshold == null) { - currentAnnotation - .setThreshold(new jalview.datamodel.GraphLine( - (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f, - "Threshold", Color.black)); + currentAnnotation.setThreshold(new GraphLine( + (currentAnnotation.graphMax - currentAnnotation.graphMin) + / 2f, + "Threshold", Color.black)); } - if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD) + if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD) { adjusting = true; - float range = currentAnnotation.graphMax * 1000 - - currentAnnotation.graphMin * 1000; - - slider.setMinimum((int) (currentAnnotation.graphMin * 1000)); - slider.setMaximum((int) (currentAnnotation.graphMax * 1000)); - slider.setValue((int) (currentAnnotation.threshold.value * 1000)); - thresholdValue.setText(currentAnnotation.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(currentAnnotation, selectedThresholdItem); + + ap.alignmentChanged(); + } + + protected void colorAlignmentContaining(AlignmentAnnotation currentAnn, + int selectedThresholdOption) + { AnnotationColourGradient acg = null; - if (currentColours.isSelected()) + if (useOriginalColours.isSelected()) { - acg = new AnnotationColourGradient(currentAnnotation, - av.getGlobalColourScheme(), aboveThreshold); + acg = new AnnotationColourGradient(currentAnn, + av.getGlobalColourScheme(), selectedThresholdOption); } else { - acg = new AnnotationColourGradient(currentAnnotation, + acg = new AnnotationColourGradient(currentAnn, minColour.getBackground(), maxColour.getBackground(), - aboveThreshold); + selectedThresholdOption); } acg.setSeqAssociated(seqAssociated.isSelected()); - if (currentAnnotation.graphMin == 0f - && currentAnnotation.graphMax == 0f) + if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f) { acg.setPredefinedColours(true); } - acg.thresholdIsMinMax = thresholdIsMin.isSelected(); + acg.setThresholdIsMinMax(thresholdIsMin.isSelected()); - av.setGlobalColourScheme(acg); + this.ap.alignFrame.changeColour(acg); if (av.getAlignment().getGroups() != null) { @@ -582,144 +462,52 @@ public class AnnotationColourChooser extends JPanel { continue; } - - if (currentColours.isSelected()) - { - sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs, - aboveThreshold); - ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated - .isSelected()); - - } - else - { - sg.cs = new AnnotationColourGradient(currentAnnotation, - minColour.getBackground(), maxColour.getBackground(), - aboveThreshold); - ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated - .isSelected()); - } - + sg.setColourScheme(acg.getInstance(av, sg)); } } - ap.alignmentChanged(); - // ensure all associated views (overviews, structures, etc) are notified of - // updated colours. - ap.paintAlignment(true); - } - - public void ok_actionPerformed(ActionEvent e) - { - changeColour(); - try - { - frame.setClosed(true); - } catch (Exception ex) - { - } - } - - public void cancel_actionPerformed(ActionEvent e) - { - reset(); - // ensure all original colouring is propagated to listeners. - ap.paintAlignment(true); - try - { - frame.setClosed(true); - } catch (Exception ex) - { - } - } - - void reset() - { - av.setGlobalColourScheme(oldcs); - if (av.getAlignment().getGroups() != null) - { - - for (SequenceGroup sg : ap.av.getAlignment().getGroups()) - { - sg.cs = (ColourSchemeI) oldgroupColours.get(sg); - } - } - } - - public void thresholdCheck_actionPerformed(ActionEvent e) - { - changeColour(); - } - - public void annotations_actionPerformed(ActionEvent e) - { - changeColour(); } - public void threshold_actionPerformed(ActionEvent e) + @Override + protected void sliderDragReleased() { - changeColour(); + super.sliderDragReleased(); + ap.paintAlignment(true, true); } - public void thresholdValue_actionPerformed(ActionEvent e) - { - try - { - float f = Float.parseFloat(thresholdValue.getText()); - slider.setValue((int) (f * 1000)); - } catch (NumberFormatException ex) - { - } - } - - public void valueChanged(boolean updateAllAnnotation) - { - if (currentColours.isSelected() - && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient)) - { - changeColour(); - } - currentAnnotation.threshold.value = (float) slider.getValue() / 1000f; - propagateSeqAssociatedThreshold(updateAllAnnotation); - ap.paintAlignment(false); - } - - private void propagateSeqAssociatedThreshold(boolean allAnnotation) + /** + * 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) { - if (currentAnnotation.sequenceRef == null - || currentAnnotation.threshold == null) - { - return; + 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); } - // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation - // is false, since we only need to provide a quick visual indicator - - float thr = currentAnnotation.threshold.value; - for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) + for (int i = 0; i < alignmentAnnotation.annotations.length; i++) { - AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i]; - if (aa.label.equals(currentAnnotation.label)) + Annotation ann = alignmentAnnotation.annotations[i]; + if (ann != null && ann.colour != null + && !ann.colour.equals(Color.white)) { - aa.threshold.value = thr; + newCS.setPredefinedColours(true); + break; } } + AnnotationColourChooser achooser = new AnnotationColourChooser(av, ap, + newCS); } - - public void currentColours_actionPerformed(ActionEvent e) - { - if (currentColours.isSelected()) - { - reset(); - } - - maxColour.setEnabled(!currentColours.isSelected()); - minColour.setEnabled(!currentColours.isSelected()); - - changeColour(); - } - - public void thresholdIsMin_actionPerformed(ActionEvent actionEvent) - { - changeColour(); - } - }