/**
* Creates a new AlignmentAnnotation object.
*
- * @param label DOCUMENT ME!
- * @param description DOCUMENT ME!
- * @param annotations DOCUMENT ME!about:blank
-Loading...
+ * @param label short label shown under sequence labels
+ * @param description text displayed on mouseover
+ * @param annotations set of positional annotation elements
*/
public AlignmentAnnotation(String label, String description,
Annotation[] annotations)
void areLabelsSecondaryStructure()
{
boolean nonSSLabel = false;
+ char firstChar=0;
for (int i = 0; i < annotations.length; i++)
{
if (annotations[i] == null)
{
continue;
}
-
- if (annotations[i].displayCharacter.length() == 1
- && !annotations[i].displayCharacter.equals("H")
- && !annotations[i].displayCharacter.equals("E")
- && !annotations[i].displayCharacter.equals("-")
- && !annotations[i].displayCharacter.equals("."))
+ if (annotations[i].displayCharacter.length() == 1)
+ {
+ firstChar = annotations[i].displayCharacter.charAt(0);
+ // check to see if it looks like a sequence or is secondary structure labelling.
+ if (
+ // Uncomment to only catch case where displayCharacter==secondary Structure
+ // to correctly redisplay SS annotation imported from Stockholm, exported to JalviewXML and read back in again.
+ // && annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
+ firstChar!='H'
+ && firstChar!='E'
+ && firstChar!='-'
+ && firstChar!='-' && firstChar<jalview.schemes.ResidueProperties.aaIndex.length)
{
if (jalview.schemes.ResidueProperties.aaIndex
- [annotations[i].displayCharacter.charAt(0)] < 23)
+ [firstChar] < 23)
{
nonSSLabel = true;
}
}
+ }
- if (annotations[i].displayCharacter.length() > 0)
- {
- hasText = true;
- }
+ if (annotations[i].displayCharacter.length() > 0)
+ {
+ hasText = true;
}
+ }
if (nonSSLabel)
{
*/
public void restrict(int startRes, int endRes)
{
+ if (annotations==null)
+ {
+ // non-positional
+ return;
+ }
if (startRes<0)
startRes=0;
if (startRes>=annotations.length)
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)
{