import jalview.schemes.ColourSchemeI;
import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
import java.util.ArrayList;
+import java.util.Arrays;
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);
}
/**
{
if (consensus.annotations[i] != null)
{
- if (consensus.annotations[i].description.charAt(0) == '[')
+ String desc = consensus.annotations[i].description;
+ if (desc.length() > 1 && desc.charAt(0) == '[')
{
- seqs.append(consensus.annotations[i].description.charAt(1));
+ seqs.append(desc.charAt(1));
}
else
{
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- List<AlignmentAnnotation> aa = new ArrayList<>();
- if (calcId == null)
- {
- return aa;
- }
- for (AlignmentAnnotation a : getAlignmentAnnotation())
- {
- if (calcId.equals(a.getCalcId()))
- {
- aa.add(a);
- }
- }
- return aa;
+ return AlignmentAnnotation.findAnnotation(
+ Arrays.asList(getAlignmentAnnotation()), calcId);
}
@Override
public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
String calcId, String label)
{
- 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))))
- {
- aa.add(ann);
- }
- }
- return aa;
+ return AlignmentAnnotation.findAnnotations(
+ Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
}
/**
*/
public boolean hasAnnotation(String calcId)
{
- if (calcId != null && !"".equals(calcId))
- {
- for (AlignmentAnnotation a : getAlignmentAnnotation())
- {
- if (a.getCalcId() == calcId)
- {
- return true;
- }
- }
- }
- return false;
+ return AlignmentAnnotation
+ .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId);
}
/**
{
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;