*/
public void restrict(int startRes, int endRes)
{
+ if (startRes<0)
+ startRes=0;
+ if (startRes>=annotations.length)
+ startRes = annotations.length-1;
+ if (endRes>=annotations.length)
+ endRes = annotations.length-1;
if (annotations==null)
return;
Annotation[] temp = new Annotation[endRes-startRes+1];
if (startRes<annotations.length)
{
- System.arraycopy(annotations, startRes, temp, 0, Math.min(endRes, annotations.length-1)-startRes+1);
+ System.arraycopy(annotations, startRes, temp, 0, endRes-startRes+1);
}
if (sequenceRef!=null) {
// Clip the mapping, if it exists.
* number of non-null annotation elements.
* @return
*/
- private int compactAnnotationArray() {
- int j=0;
- for (int i=0;i<annotations.length; i++) {
- if (annotations[i]!=null && j!=i) {
- annotations[j++] = annotations[i];
+ public int compactAnnotationArray() {
+ int i=0,iSize=annotations.length;
+ while (i<iSize)
+ {
+ if (annotations[i]==null) {
+ if (i+1<iSize)
+ System.arraycopy(annotations, i+1, annotations, i, iSize-i-1);
+ iSize--;
+ } else {
+ i++;
}
}
Annotation[] ann = annotations;
- annotations = new Annotation[j];
- System.arraycopy(ann, 0, annotations, 0, j);
+ annotations = new Annotation[i];
+ System.arraycopy(ann, 0, annotations, 0, i);
ann = null;
- return j;
+ return iSize;
}
/**
this(label, description, null);
setScore(score);
}
+ /**
+ * copy constructor with edit based on the hidden columns marked in colSel
+ * @param alignmentAnnotation
+ * @param colSel
+ */
+ public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
+ ColumnSelection colSel)
+ {
+ this(alignmentAnnotation);
+ if (annotations==null)
+ {
+ return;
+ }
+ colSel.makeVisibleAnnotation(this);
+ }
public void setPadGaps(boolean padgaps, char gapchar)
{