/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
*
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 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 javax.swing.JSlider;
-import javax.swing.JTextField;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
import net.miginfocom.swing.MigLayout;
-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<SequenceGroup, ColourSchemeI> oldgroupColours;
- ColourSchemeI oldcs;
+ private JCheckBox useOriginalColours = new JCheckBox();
- Hashtable oldgroupColours;
+ JPanel minColour = new JPanel();
+
+ JPanel maxColour = new JPanel();
- jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ private JCheckBox thresholdIsMin = new JCheckBox();
- boolean adjusting = false;
+ protected static final int MIN_WIDTH = 500;
- /**
- * enabled if the user is dragging the slider - try to keep updates to a
- * minimun
- */
- boolean sliderDragging = false;
+ protected static final int MIN_HEIGHT = 240;
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
+ 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.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
MessageManager.getString("label.colour_by_annotation"), 520,
215);
-
- slider.addChangeListener(new ChangeListener()
- {
- @Override
- public void stateChanged(ChangeEvent evt)
- {
- if (!adjusting)
- {
- thresholdValue.setText((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);
- }
-
- @Override
- 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)
{
if (oldcs instanceof AnnotationColourGradient)
{
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());
seqAssociated.setSelected(acg.isSeqAssociated());
}
- annotations = new JComboBox(
- getAnnotationItems(seqAssociated.isSelected()));
+ Vector<String> 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)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- annotations.setSelectedItem(acg.getAnnotation());
+ String label = getAnnotationMenuLabel(acg.getAnnotation());
+ 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"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_dont_know_about_threshold_setting"));
}
- thresholdIsMin.setSelected(acg.thresholdIsMinMax);
- thresholdValue.setText("" + acg.getAnnotationThreshold());
- }
-
- try
- {
- jbInit();
- } catch (Exception ex)
- {
+ thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
+ thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold()));
}
+ jbInit();
adjusting = false;
- changeColour();
+ updateView();
frame.invalidate();
frame.pack();
-
- }
-
- private Vector<String> getAnnotationItems(boolean isSeqAssociated)
- {
- Vector<String> list = new Vector<String>();
- 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.add(label);
-
- }
- else
- {
- if (!isSeqAssociated)
- {
- anmap[list.size()] = i;
- list.add(label + "_" + (index++));
- }
- }
- }
- seqAssociated.setEnabled(enableSeqAss);
- this.annmap = new int[list.size()];
- System.arraycopy(anmap, 0, this.annmap, 0, this.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));
- }
-
- public AnnotationColourChooser()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ super.jbInit();
- private void jbInit() throws Exception
- {
minColour.setFont(JvSwingUtils.getLabelFont());
minColour.setBorder(BorderFactory.createEtchedBorder());
minColour.setPreferredSize(new Dimension(40, 20));
{
if (minColour.isEnabled())
{
- minColour_actionPerformed();
+ showColourChooser(minColour, "label.select_colour_minimum_value");
}
}
});
{
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()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed(e);
- }
- });
- cancel.setOpaque(false);
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed(e);
- }
- });
+
+ defColours = new JButton();
defColours.setOpaque(false);
defColours.setText(MessageManager.getString("action.set_defaults"));
defColours.setToolTipText(MessageManager
@Override
public void actionPerformed(ActionEvent arg0)
{
- resetColours_actionPerformed(arg0);
+ resetColours_actionPerformed();
}
});
- annotations.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
- threshold.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- threshold_actionPerformed(e);
- }
- });
- thresholdValue.addActionListener(new ActionListener()
- {
- @Override
- 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);
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");
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)
return;
}
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
- .getSelectedIndex()]];
+ setCurrentAnnotation(
+ av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+ .getSelectedIndex()]]);
- 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)
{
{
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)
+ @Override
+ protected void sliderDragReleased()
{
- reset();
- // ensure all original colouring is propagated to listeners.
- ap.paintAlignment(true);
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
- {
- }
+ super.sliderDragReleased();
+ ap.paintAlignment(true, true);
}
-
- 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)
- {
- changeColour();
- }
-
- 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 = slider.getValue() / 1000f;
- propagateSeqAssociatedThreshold(updateAllAnnotation);
- ap.paintAlignment(false);
- }
-
- private void propagateSeqAssociatedThreshold(boolean allAnnotation)
- {
- if (currentAnnotation.sequenceRef == null
- || currentAnnotation.threshold == null)
- {
- return;
- }
- // 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++)
- {
- AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
- if (aa.label.equals(currentAnnotation.label)
- && (currentAnnotation.getCalcId() == null ? aa.getCalcId() == null
- : currentAnnotation.getCalcId()
- .equals(aa.getCalcId())))
- {
- if (aa.threshold == null)
- {
- aa.threshold = new GraphLine(currentAnnotation.threshold);
- }
- else
- {
- aa.threshold.value = thr;
- }
- }
- }
- }
-
- 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();
- }
-
}
git://source.jalview.org / jalview.git / blobdiff