import jalview.schemes.ColourSchemeI;
import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
*/
public class SequenceGroup implements AnnotatedCollectionI
{
+ // TODO ideally this event notification functionality should be separated into
+ // a
+ // subclass of ViewportProperties similarly to ViewportRanges. Done here as
+ // quick fix for JAL-2665
+ public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
+
+ protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
+ public void addPropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ public void removePropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+ // end of event notification functionality initialisation
+
String groupName;
String description;
if (s != null && !sequences.contains(s))
{
sequences.add(s);
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+ sequences.size() - 1, sequences.size());
}
if (recalc)
conservation.description = "Conservation for group " + getName()
+ " less than " + consPercGaps + "% gaps";
// preserve width if already set
- int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
- : endRes + 1)
+ int aWidth = (conservation.annotations != null)
+ ? (endRes < conservation.annotations.length
+ ? conservation.annotations.length
+ : endRes + 1)
: endRes + 1;
conservation.annotations = null;
conservation.annotations = new Annotation[aWidth]; // should be alignment
consensus.description = "Percent Identity";
consensusData = cnsns;
// preserve width if already set
- int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
- : endRes + 1)
+ int aWidth = (consensus.annotations != null)
+ ? (endRes < consensus.annotations.length
+ ? consensus.annotations.length
+ : endRes + 1)
: endRes + 1;
consensus.annotations = null;
consensus.annotations = new Annotation[aWidth]; // should be alignment width
synchronized (sequences)
{
sequences.remove(s);
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+ sequences.size() + 1, sequences.size());
if (recalc)
{
*/
public void setStartRes(int i)
{
+ int before = startRes;
startRes = i;
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
}
/**
*/
public void setEndRes(int i)
{
+ int before = endRes;
endRes = i;
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes);
}
/**
ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
for (AlignmentAnnotation ann : getAlignmentAnnotation())
{
- if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
- .equals(calcId)))
- && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
- && (label == null || (ann.label != null && ann.label
- .equals(label))))
+ if ((calcId == null || (ann.getCalcId() != null
+ && ann.getCalcId().equals(calcId)))
+ && (seq == null || (ann.sequenceRef != null
+ && ann.sequenceRef == seq))
+ && (label == null
+ || (ann.label != null && ann.label.equals(label))))
{
aa.add(ann);
}
{
synchronized (sequences)
{
+ int before = sequences.size();
sequences.clear();
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
+ sequences.size());
}
}
@Override
public boolean isNucleotide()
{
- if (context != null) {
+ if (context != null)
+ {
return context.isNucleotide();
}
return false;