/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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 java.awt.event.ItemListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
-import java.util.Hashtable;
+import java.util.HashMap;
+import java.util.Map;
import java.util.Vector;
public class AnnotationColourChooser extends Panel implements
ColourSchemeI oldcs;
- Hashtable oldgroupColours;
+ Map<SequenceGroup, ColourSchemeI> oldgroupColours;
- jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ /*
+ * map from annotation to its menu item display label
+ * - so we know which item to pre-select on restore
+ */
+ private Map<AlignmentAnnotation, String> annotationLabels;
+
+ AlignmentAnnotation currentAnnotation;
boolean adjusting = false;
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable();
+ oldgroupColours = new HashMap<>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs != null)
- {
- oldgroupColours.put(sg, sg.cs);
- }
- else
- {
- oldgroupColours.put(sg, "null");
- }
+ oldgroupColours.put(sg, sg.getColourScheme());
}
}
this.av = av;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setState(acg.isPredefinedColours()
- || acg.getBaseColour() != null);
+ currentColours.setState(
+ acg.isPredefinedColours() || acg.getBaseColour() != null);
if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
// seqAssociated.setState(acg.isSeqAssociated());
}
- Vector<String> list = new Vector<String>();
- int index = 1;
- for (int i = 0; i < anns.length; i++)
- {
- String label = anns[i].label;
- if (anns[i].sequenceRef != null)
- {
- label = label + "_" + anns[i].sequenceRef.getName();
- }
- if (!list.contains(label))
- {
- list.addElement(label);
- }
- else
- {
- list.addElement(label + "_" + (index++));
- }
- }
+ Vector<String> list = getAnnotationItems();
for (int i = 0; i < list.size(); i++)
{
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- annotations.select(acg.getAnnotation());
+ String label = annotationLabels.get(acg.getAnnotation());
+ annotations.select(label);
switch (acg.getAboveThreshold())
{
case AnnotationColourGradient.NO_THRESHOLD:
threshold.select(1);
break;
default:
- throw new Error(
- MessageManager
- .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_dont_know_threshold_annotationcolourgradient"));
}
- thresholdIsMin.setState(acg.thresholdIsMinMax);
+ thresholdIsMin.setState(acg.isThresholdIsMinMax());
thresholdValue.setText("" + acg.getAnnotationThreshold());
}
validate();
}
+ /**
+ * Builds and returns a list of menu items (display text) for choice of
+ * annotation. Also builds a map between annotations and their display labels.
+ *
+ * @return
+ */
+ protected Vector<String> getAnnotationItems()
+ {
+ // TODO remove duplication with gui.AnnotationRowFilter
+ // TODO add 'per sequence only' option / parameter
+
+ annotationLabels = new HashMap<>();
+ Vector<String> list = new Vector<>();
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns == null)
+ {
+ return list;
+ }
+ int index = 1;
+ for (int i = 0; i < anns.length; i++)
+ {
+ String label = anns[i].label;
+ if (anns[i].sequenceRef != null)
+ {
+ /*
+ * be helpful and include sequence id in label for
+ * sequence-associated annotation (JAL-2236)
+ */
+ label = label + "_" + anns[i].sequenceRef.getName();
+ }
+ if (!list.contains(label))
+ {
+ list.addElement(label);
+ annotationLabels.put(anns[i], label);
+ }
+ else
+ {
+ label = label + "_" + (index++);
+ list.addElement(label);
+ annotationLabels.put(anns[i], label);
+ }
+ }
+ return list;
+ }
+
private void setDefaultMinMax()
{
minColour.setBackground(av.applet.getDefaultColourParameter(
"ANNOTATIONCOLOUR_MIN", Color.orange));
- maxColour.setBackground(av.applet.getDefaultColourParameter(
- "ANNOTATIONCOLOUR_MAX", Color.red));
+ maxColour.setBackground(av.applet
+ .getDefaultColourParameter("ANNOTATIONCOLOUR_MAX", Color.red));
}
thresholdValue.setEnabled(false);
thresholdValue.setColumns(5);
currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- currentColours.setLabel(MessageManager
- .getString("label.use_original_colours"));
+ currentColours.setLabel(
+ MessageManager.getString("label.use_original_colours"));
currentColours.addItemListener(this);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel(MessageManager
- .getString("label.threshold_minmax"));
+ thresholdIsMin
+ .setLabel(MessageManager.getString("label.threshold_minmax"));
this.setLayout(borderLayout1);
else if (evt.getSource() == cancel)
{
reset();
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
frame.setVisible(false);
}
if (!adjusting)
{
thresholdValue.setText((slider.getValue() / 1000f) + "");
- if (currentColours.getState()
- && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ if (currentColours.getState() && !(av
+ .getGlobalColourScheme() instanceof AnnotationColourGradient))
{
changeColour();
}
currentAnnotation.threshold.value = slider.getValue() / 1000f;
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
return;
}
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
- .getSelectedIndex()];
+ currentAnnotation = av.getAlignment()
+ .getAlignmentAnnotation()[annotations.getSelectedIndex()];
int aboveThreshold = -1;
if (threshold.getSelectedIndex() == 1)
else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
&& currentAnnotation.threshold == null)
{
- currentAnnotation
- .setThreshold(new jalview.datamodel.GraphLine(
- (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
- "Threshold", Color.black));
+ currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
+ (currentAnnotation.graphMax - currentAnnotation.graphMin)
+ / 2f,
+ "Threshold", Color.black));
}
if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
AnnotationColourGradient acg = null;
if (currentColours.getState())
{
- acg = new AnnotationColourGradient(currentAnnotation,
- av.getGlobalColourScheme(), aboveThreshold);
}
else
{
acg.setPredefinedColours(true);
}
- acg.thresholdIsMinMax = thresholdIsMin.getState();
+ acg.setThresholdIsMinMax(thresholdIsMin.getState());
av.setGlobalColourScheme(acg);
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
-
- if (sg.cs == null)
+ if (sg.getColourScheme() == null)
{
continue;
}
if (currentColours.getState())
{
- sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
- aboveThreshold);
+ sg.setColourScheme(new AnnotationColourGradient(currentAnnotation,
+ sg.getColourScheme(), aboveThreshold));
}
else
{
- sg.cs = new AnnotationColourGradient(currentAnnotation,
+ sg.setColourScheme(new AnnotationColourGradient(currentAnnotation,
minColour.getBackground(), maxColour.getBackground(),
- aboveThreshold);
+ aboveThreshold));
}
-
}
}
// update colours in linked windows
ap.alignmentChanged();
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
void reset()
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- Object cs = oldgroupColours.get(sg);
- if (cs instanceof ColourSchemeI)
- {
- sg.cs = (ColourSchemeI) cs;
- }
- else
- {
- // probably the "null" string we set it to if it was null originally.
- sg.cs = null;
- }
+ sg.setColourScheme(oldgroupColours.get(sg));
}
}
- ap.paintAlignment(true);
-
+ ap.paintAlignment(true, true);
}
@Override
@Override
public void mouseReleased(MouseEvent evt)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
@Override
git://source.jalview.org / jalview.git / blobdiff