/**
* Score associated with label and description.
*/
- public float score= Float.NaN;
+ public double score= Double.NaN;
/**
* flag indicating if annotation has a score.
*/
public int graphHeight = 40;
- public boolean padGaps = true;
+ public boolean padGaps = false;
public static final int NO_GRAPH = 0;
/**
* 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)
{
- padGaps = false;
continue;
}
if (annotations[i].secondaryStructure == 'H' ||
}
if(annotations[i].displayCharacter==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;
- }
- else
- padGaps = false;
+ if (annotations[i].displayCharacter.length() > 0)
+ {
+ hasText = true;
}
+ }
if (nonSSLabel)
{
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)
+ {
+ // non-positional
+ return;
+ }
+ 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.
public boolean padAnnotation(int length) {
if (annotations==null)
{
- annotations = new Annotation[length];
- return true;
+ return true; // annotation row is correct - null == not visible and undefined length
}
if (annotations.length<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++)
* 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;
}
/**
/**
* @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;
}
/**
*/
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);
+ }
+ /**
+ * 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)
+ {
+ this.padGaps = padgaps;
+ if(padgaps)
+ {
+ hasText = true;
+ for(int i=0; i<annotations.length; i++)
+ {
+ if(annotations[i]==null)
+ annotations[i] = new Annotation(String.valueOf(gapchar),null,' ',0f);
+ else if(annotations[i].displayCharacter==null ||annotations[i].displayCharacter.equals(" "))
+ annotations[i].displayCharacter=String.valueOf(gapchar);
+ }
+ }
}
}