/**
* Score associated with label and description.
*/
- public float score;
+ public double score= Double.NaN;
/**
* flag indicating if annotation has a score.
*/
public boolean hasScore=false;
-
+
public GraphLine threshold;
// Graphical hints and tips
public static final int LINE_GRAPH = 2;
+ public boolean belowAlignment = true;
+
public static int getGraphValueFromString(String string)
{
*
* @param label DOCUMENT ME!
* @param description DOCUMENT ME!
- * @param annotations DOCUMENT ME!
+ * @param annotations DOCUMENT ME!about:blank
+Loading...
*/
public AlignmentAnnotation(String label, String description,
Annotation[] annotations)
}
if(annotations[i].displayCharacter==null)
+ {
+ padGaps = false;
continue;
-
+ }
if (annotations[i].displayCharacter.length() == 1
&& !annotations[i].displayCharacter.equals("H")
* if appropriate.
*/
private void validateRangeAndDisplay() {
+
if (annotations==null)
{
visible=false; // try to prevent renderer from displaying.
return; // this is a non-annotation row annotation - ie a sequence score.
}
+
int graphType = graph;
float min = graphMin;
float max = graphMax;
this.height = annotation.height;
this.label = annotation.label;
this.padGaps = annotation.padGaps;
+ this.visible = annotation.visible;
+ if (this.hasScore = annotation.hasScore)
+ {
+ this.score = annotation.score;
+ }
if (threshold!=null) {
threshold = new GraphLine(annotation.threshold);
}
*/
public void restrict(int startRes, int endRes)
{
+ if (annotations==null)
+ return;
Annotation[] temp = new Annotation[endRes-startRes+1];
if (startRes<annotations.length)
{
{
return;
}
+ sequenceRef=seqRef;
if (annotations==null)
{
return;
}
sequenceMapping = new java.util.Hashtable();
- sequenceRef = seqRef;
int seqPos;
for (int i = 0; i < annotations.length; i++)
/**
* @return the score
*/
- public float getScore()
+ public double getScore()
{
return score;
}
/**
* @param score the score to set
*/
- public void setScore(float score)
+ public void setScore(double score)
{
+ hasScore=true;
this.score = score;
}
/**
- *
+ *
* @return true if annotation has an associated score
*/
public boolean hasScore()
{
- return hasScore;
+ return hasScore || !Double.isNaN(score);
+ }
+ /**
+ * Score only annotation
+ * @param label
+ * @param description
+ * @param score
+ */
+ public AlignmentAnnotation(String label, String description, double score)
+ {
+ this(label, description, null);
+ setScore(score);
}
}