- return LINE_GRAPH;
- }
- else
- {
- return NO_GRAPH;
- }
- }
-
- /**
- * Creates a new AlignmentAnnotation object.
- *
- * @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)
- {
- setAnnotationId();
- // always editable?
- editable = true;
- this.label = label;
- this.description = description;
- this.annotations = annotations;
-
- validateRangeAndDisplay();
- }
-
- /**
- * Copy constructor creates a new independent annotation row with the same
- * associated sequenceRef
- *
- * @param annotation
- */
- public AlignmentAnnotation(AlignmentAnnotation annotation)
- {
- setAnnotationId();
- this.label = new String(annotation.label);
- if (annotation.description != null)
- {
- this.description = new String(annotation.description);
- }
- this.graphMin = annotation.graphMin;
- this.graphMax = annotation.graphMax;
- this.graph = annotation.graph;
- this.graphHeight = annotation.graphHeight;
- this.graphGroup = annotation.graphGroup;
- this.groupRef = annotation.groupRef;
- this.editable = annotation.editable;
- this.autoCalculated = annotation.autoCalculated;
- this.hasIcons = annotation.hasIcons;
- this.hasText = annotation.hasText;
- this.height = annotation.height;
- this.label = annotation.label;
- this.padGaps = annotation.padGaps;
- this.visible = annotation.visible;
- this.centreColLabels = annotation.centreColLabels;
- this.scaleColLabel = annotation.scaleColLabel;
- this.showAllColLabels = annotation.showAllColLabels;
- this.calcId = annotation.calcId;
- if (annotation.properties != null)
- {
- properties = new HashMap<>();
- for (Map.Entry<String, String> val : annotation.properties.entrySet())
- {
- properties.put(val.getKey(), val.getValue());
- }
- }
- if (this.hasScore = annotation.hasScore)
- {
- this.score = annotation.score;
- }
- if (annotation.threshold != null)
- {
- threshold = new GraphLine(annotation.threshold);
- }
- Annotation[] ann = annotation.annotations;
- if (annotation.annotations != null)
- {
- this.annotations = new Annotation[ann.length];
- for (int i = 0; i < ann.length; i++)
- {
- if (ann[i] != null)
- {
- annotations[i] = new Annotation(ann[i]);
- if (_linecolour != null)
- {
- _linecolour = annotations[i].colour;
- }
- }
- }
- }
- if (annotation.sequenceRef != null)
- {
- this.sequenceRef = annotation.sequenceRef;
- if (annotation.sequenceMapping != null)
- {
- Integer p = null;
- sequenceMapping = new HashMap<>();
- Iterator<Integer> pos = annotation.sequenceMapping.keySet()
- .iterator();
- while (pos.hasNext())
- {
- // could optimise this!
- p = pos.next();
- Annotation a = annotation.sequenceMapping.get(p);
- if (a == null)
- {
- continue;
- }
- if (ann != null)
- {
- for (int i = 0; i < ann.length; i++)
- {
- if (ann[i] == a)
- {
- sequenceMapping.put(p, annotations[i]);
- }
- }
- }
- }
- }
- else
- {
- this.sequenceMapping = null;
- }
- }
- // TODO: check if we need to do this: JAL-952
- // if (this.isrna=annotation.isrna)
- {
- // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
- }
- validateRangeAndDisplay(); // construct hashcodes, etc.
- }
-
- /**
- * copy constructor with edit based on the hidden columns marked in colSel
- *
- * @param alignmentAnnotation
- * @param colSel
- */
- public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
- HiddenColumns hidden)
- {
- this(alignmentAnnotation);
- if (annotations == null)
- {
- return;
- }
- makeVisibleAnnotation(hidden);
- }
-
- /**
- * Creates a new AlignmentAnnotation object.
- *
- * @param label
- * DOCUMENT ME!
- * @param description
- * DOCUMENT ME!
- * @param annotations
- * DOCUMENT ME!
- * @param min
- * DOCUMENT ME!
- * @param max
- * DOCUMENT ME!
- * @param winLength
- * DOCUMENT ME!
- */
- public AlignmentAnnotation(String label, String description,
- Annotation[] annotations, float min, float max, int graphType)
- {
- setAnnotationId();
- // graphs are not editable
- editable = graphType == 0;
-
- this.label = label;
- this.description = description;
- this.annotations = annotations;
- graph = graphType;
- graphMin = min;
- graphMax = max;
- validateRangeAndDisplay();
- }
-
- /**
- * Score only annotation
- *
- * @param label
- * @param description
- * @param score
- */
- public AlignmentAnnotation(String label, String description, double score)
- {
- this(label, description, null);
- setScore(score);
- }
-
- /**
- * Updates the _rnasecstr field Determines the positions that base pair and
- * the positions of helices based on secondary structure from a Stockholm file
- *
- * @param rnaAnnotation
- */
- private void _updateRnaSecStr(CharSequence rnaAnnotation)
- {
- try
- {
- _rnasecstr = Rna.getHelixMap(rnaAnnotation);
- invalidrnastruc = -1;
- } catch (WUSSParseException px)
- {
- // DEBUG System.out.println(px);
- invalidrnastruc = px.getProblemPos();
- }
- if (invalidrnastruc > -1)
- {
- return;
- }
-
- if (_rnasecstr != null && _rnasecstr.length > 0)
- {
- // show all the RNA secondary structure annotation symbols.
- isrna = true;
- showAllColLabels = true;
- scaleColLabel = true;
- _markRnaHelices();