+
+ /**
+ * Update any mappings to 'virtual' sequences to compatible real ones, if
+ * present in the added sequences. Returns a count of mappings updated.
+ *
+ * @param seqs
+ * @return
+ */
+ @Override
+ public int realiseMappings(List<SequenceI> seqs)
+ {
+ int count = 0;
+ for (SequenceI seq : seqs)
+ {
+ for (AlignedCodonFrame mapping : getCodonFrames())
+ {
+ count += mapping.realiseWith(seq);
+ }
+ }
+ return count;
+ }
+
+ /**
+ * Returns the first AlignedCodonFrame that has a mapping between the given
+ * dataset sequences
+ *
+ * @param mapFrom
+ * @param mapTo
+ * @return
+ */
+ @Override
+ public AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo)
+ {
+ for (AlignedCodonFrame acf : getCodonFrames())
+ {
+ if (acf.getAaForDnaSeq(mapFrom) == mapTo)
+ {
+ return acf;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
+ {
+ int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
+ int startPos = alignmentStartEnd[0];
+ int endPos = alignmentStartEnd[1];
+
+ int[] lowestRange = new int[] { -1, -1 };
+ int[] higestRange = new int[] { -1, -1 };
+
+ for (int[] hiddenCol : hiddenCols)
+ {
+ lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+ higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+ }
+
+ if (lowestRange[0] == -1 && lowestRange[1] == -1)
+ {
+ startPos = alignmentStartEnd[0];
+ }
+ else
+ {
+ startPos = lowestRange[1] + 1;
+ }
+
+ if (higestRange[0] == -1 && higestRange[1] == -1)
+ {
+ endPos = alignmentStartEnd[1];
+ }
+ else
+ {
+ endPos = higestRange[0] - 1;
+ }
+ return new int[] { startPos, endPos };
+ }
+ @Override
+ public void setHiddenColumns(HiddenColumns cols)
+ {
+ hiddenCols = cols;
+ }
+
+ Map<Object, ContactMatrixI> contactmaps = new HashMap<Object, ContactMatrixI>();
+ @Override
+ public
+ ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+ {
+ ContactMatrixI cm = contactmaps.get(_aa.annotationId);
+ if (cm == null)
+ {
+ return null;
+ }
+ return cm.getContactList(column);
+ }
+
+ @Override
+ public AlignmentAnnotation addContactList(ContactMatrixI cm)
+ {
+ Annotation _aa[] = new Annotation[getWidth()];
+ Annotation dummy = new Annotation(0.0f);
+ for (int i = 0; i < _aa.length; _aa[i++] = dummy)
+ {
+ ;
+ }
+ AlignmentAnnotation aa = new AlignmentAnnotation("Contact Matrix",
+ "Contact Matrix", _aa);
+ aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
+ aa.graphMin = cm.getMin();
+ aa.graphMax = cm.getMax();
+ aa.editable = false;
+ // aa.autoCalculated = true;
+ contactmaps.put(aa.annotationId, cm);
+ addAnnotation(aa);
+ return aa;
+ }