}
/**
- * 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();
- }
- // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
-
- }
-
- private void _markRnaHelices()
- {
- int mxval = 0;
- // Figure out number of helices
- // Length of rnasecstr is the number of pairs of positions that base pair
- // with each other in the secondary structure
- for (int x = 0; x < _rnasecstr.length; x++)
- {
-
- /*
- * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
- * this.annotation._rnasecstr[x].getBegin());
- */
- // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
- int val = 0;
- try
- {
- val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
- if (mxval < val)
- {
- mxval = val;
- }
- } catch (NumberFormatException q)
- {
- }
- ;
-
- annotations[_rnasecstr[x].getBegin()].value = val;
- annotations[_rnasecstr[x].getEnd()].value = val;
-
- // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
- // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
- }
- setScore(mxval);
- }
-
- /**
* Checks if annotation labels represent secondary structures
*
*/
}
return null;
}
+
+ /**
+ * 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();
+ }
/**
* checks graphMin and graphMax, secondary structure symbols, sets graphType
}
}
}
+
+ /**
+ * 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.
+ }
/**
* clip the annotation to the columns given by startRes and endRes (inclusive)
{
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,
+ HiddenColumns hidden)
+ {
+ this(alignmentAnnotation);
+ if (annotations == null)
+ {
+ return;
+ }
+ makeVisibleAnnotation(hidden);
+ }
+
public void setPadGaps(boolean padgaps, char gapchar)
{
/**
* machine readable ID string indicating what generated this annotation
*/
- private String calcId = "";
+ protected String calcId = "";
/**
* properties associated with the calcId
Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
String label)
{
- List<AlignmentAnnotation> aa = new ArrayList<>();
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
for (AlignmentAnnotation ann : list)
{
if ((calcId == null || (ann.getCalcId() != null
git://source.jalview.org / jalview.git / commitdiff