+ return changed;
+ }
+
+ @Override
+ public void setupJPredAlignment()
+ {
+ SequenceI repseq = getSequenceAt(0);
+ setSeqrep(repseq);
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideList(repseq.getInsertions());
+ setHiddenColumns(cs);
+ }
+
+ @Override
+ public HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input)
+ {
+ int profsqpos = 0;
+
+ char gc = getGapCharacter();
+ Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+ HiddenColumns nview = (HiddenColumns) alandhidden[1];
+ SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+ return propagateInsertions(profileseq, origseq, nview);
+ }
+
+ /**
+ *
+ * @param profileseq
+ * sequence in al which corresponds to origseq
+ * @param al
+ * alignment which is to have gaps inserted into it
+ * @param origseq
+ * sequence corresponding to profileseq which defines gap map for
+ * modifying al
+ */
+ private HiddenColumns propagateInsertions(SequenceI profileseq,
+ SequenceI origseq, HiddenColumns hc)
+ {
+ // take the set of hidden columns, and the set of gaps in origseq,
+ // and remove all the hidden gaps from hiddenColumns
+
+ // first get the gaps as a Bitset
+ // then calculate hidden ^ not(gap)
+ BitSet gaps = origseq.gapBitset();
+ hc.andNot(gaps);
+
+ // for each sequence in the alignment, except the profile sequence,
+ // insert gaps corresponding to each hidden region but where each hidden
+ // column region is shifted backwards by the number of preceding visible
+ // gaps update hidden columns at the same time
+ HiddenColumns newhidden = new HiddenColumns();
+
+ int numGapsBefore = 0;
+ int gapPosition = 0;
+ Iterator<int[]> it = hc.iterator();
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+
+ // get region coordinates accounting for gaps
+ // we can rely on gaps not being *in* hidden regions because we already
+ // removed those
+ while (gapPosition < region[0])
+ {
+ gapPosition++;
+ if (gaps.get(gapPosition))
+ {
+ numGapsBefore++;
+ }
+ }
+
+ int left = region[0] - numGapsBefore;
+ int right = region[1] - numGapsBefore;
+
+ newhidden.hideColumns(left, right);
+ padGaps(left, right, profileseq);
+ }
+ return newhidden;
+ }
+
+ /**
+ * Pad gaps in all sequences in alignment except profileseq
+ *
+ * @param left
+ * position of first gap to insert
+ * @param right
+ * position of last gap to insert
+ * @param profileseq
+ * sequence not to pad
+ */
+ private void padGaps(int left, int right, SequenceI profileseq)
+ {
+ char gc = getGapCharacter();
+
+ // make a string with number of gaps = length of hidden region
+ StringBuilder sb = new StringBuilder();
+ for (int g = 0; g < right - left + 1; g++)
+ {
+ sb.append(gc);
+ }
+
+ // loop over the sequences and pad with gaps where required
+ for (int s = 0, ns = getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = getSequenceAt(s);
+ if ((sqobj != profileseq) && (sqobj.getLength() >= left))
+ {
+ String sq = sqobj.getSequenceAsString();
+ sqobj.setSequence(
+ sq.substring(0, left) + sb.toString() + sq.substring(left));
+ }
+ }
+ }
+
+ ////
+ //// Contact Matrix Holder Boilerplate
+ ////
+ ContactMapHolder cmholder = new ContactMapHolder();
+
+ @Override
+ public Collection<ContactMatrixI> getContactMaps()
+ {
+ return cmholder.getContactMaps();
+ }
+
+ @Override
+ public ContactMatrixI getContactMatrixFor(AlignmentAnnotation _aa)
+ {
+ ContactMatrixI cm = cmholder.getContactMatrixFor(_aa);
+ if (cm == null && _aa.groupRef != null)
+ {
+ cm = _aa.groupRef.getContactMatrixFor(_aa);
+ }
+ if (cm == null && _aa.sequenceRef != null)
+ {
+ cm = _aa.sequenceRef.getContactMatrixFor(_aa);
+ if (cm == null && _aa.sequenceRef.getDatasetSequence() != null)
+ {
+ // TODO fix up this logic and unify with getContactListFor
+ cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
+ }
+ }
+ return cm;
+ }
+
+ @Override
+ public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+ {
+ if (_aa.annotations == null || column >= _aa.annotations.length
+ || column < 0)
+ {
+ return null;
+ }
+ ContactListI cl = cmholder.getContactListFor(_aa, column);
+ if (cl == null && _aa.groupRef != null)
+ {
+ cl = _aa.groupRef.getContactListFor(_aa, column);
+ }
+ if (cl == null && _aa.sequenceRef != null)
+ {
+ if (_aa.annotations[column] != null)
+ {
+ // sequence associated
+ cl = _aa.sequenceRef.getContactListFor(_aa, column);
+ if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
+ {
+ int spos = _aa.sequenceRef.findPosition(column);
+ if (spos >= _aa.sequenceRef.getStart()
+ && spos <= 1 + _aa.sequenceRef.getEnd())
+ {
+ cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
+ spos - _aa.sequenceRef.getStart());
+ }
+ }
+ }
+ }
+ return cl;
+ }
+
+ @Override
+ public AlignmentAnnotation addContactList(ContactMatrixI cm)
+ {
+ AlignmentAnnotation aa = cmholder.addContactList(cm);
+
+ Annotation _aa[] = new Annotation[getWidth()];
+ for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
+ {
+ ;
+ }
+ aa.annotations = _aa;
+ addAnnotation(aa);
+ return aa;
+ }
+
+ @Override
+ public void addContactListFor(AlignmentAnnotation annotation,
+ ContactMatrixI cm)
+ {
+ cmholder.addContactListFor(annotation, cm);
+