/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
*/
package jalview.workers;
-import java.util.List;
-
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+
+import java.util.List;
/**
* Base class for alignment calculation workers
protected AlignmentViewPanel ap;
- protected List<AlignmentAnnotation> ourAnnots = null;
+ protected List<AlignmentAnnotation> ourAnnots;
public AlignCalcWorker(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
}
+ @Override
public boolean involves(AlignmentAnnotation i)
{
return ourAnnots != null && ourAnnots.contains(i);
}
/**
- * permanently remove from the alignment all annotation rows managed by this
+ * Permanently removes from the alignment all annotation rows managed by this
* worker
*/
@Override
- public void removeOurAnnotation()
+ public void removeAnnotation()
{
if (ourAnnots != null && alignViewport != null)
{
alignment.deleteAnnotation(aa, true);
}
}
+ ourAnnots.clear();
}
}
+
// TODO: allow GUI to query workers associated with annotation to add items to
// annotation label panel popup menu
+ @Override
+ public boolean isDeletable()
+ {
+ return false;
+ }
+
+ /**
+ * Calculate min and max values of annotations and set as graphMin, graphMax
+ * on the AlignmentAnnotation. This is needed because otherwise, well, bad
+ * things happen.
+ *
+ * @param ann
+ * @param anns
+ */
+ protected void setGraphMinMax(AlignmentAnnotation ann, Annotation[] anns)
+ {
+ // TODO feels like this belongs inside AlignmentAnnotation!
+ float max = Float.MIN_VALUE;
+ float min = Float.MAX_VALUE;
+ boolean set = false;
+ for (Annotation a : anns)
+ {
+ if (a != null)
+ {
+ set = true;
+ float val = a.value;
+ max = Math.max(max, val);
+ min = Math.min(min, val);
+ }
+ }
+ if (set)
+ {
+ ann.graphMin = min;
+ ann.graphMax = max;
+ }
+ }
+
}