+
+ /**
+ * get the contiguous subalignments in an alignment view.
+ * @param gapCharacter char
+ * @return SequenceI[][]
+ */
+ public SequenceI[][] getVisibleContigs(char gapCharacter)
+ {
+ SequenceI[][] smsa;
+ int njobs = 1;
+ if (sequences == null || width <= 0)
+ {
+ return null;
+ }
+ if (contigs != null && contigs.length > 0)
+ {
+ int start = 0;
+ njobs = 0;
+ int fwidth = width;
+ for (int contig = 0; contig < contigs.length; contig += 3)
+ {
+ if ( (contigs[contig + 1] - start) > 0)
+ {
+ njobs++;
+ }
+ fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+ start = contigs[contig + 1] + contigs[contig + 2];
+ }
+ if (start < fwidth)
+ {
+ njobs++;
+ }
+ smsa = new SequenceI[njobs][];
+ start = 0;
+ int j = 0;
+ for (int contig = 0; contig < contigs.length; contig += 3)
+ {
+ if (contigs[contig + 1] - start > 0)
+ {
+ SequenceI mseq[] = new SequenceI[sequences.length];
+ for (int s = 0; s < mseq.length; s++)
+ {
+ mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+ contigs[contig + 1]);
+ }
+ smsa[j] = mseq;
+ j++;
+ }
+ start = contigs[contig + 1] + contigs[contig + 2];
+ }
+ if (start < fwidth)
+ {
+ SequenceI mseq[] = new SequenceI[sequences.length];
+ for (int s = 0; s < mseq.length; s++)
+ {
+ mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+ fwidth + 1);
+ }
+ smsa[j] = mseq;
+ j++;
+ }
+ }
+ else
+ {
+ smsa = new SequenceI[1][];
+ smsa[0] = new SequenceI[sequences.length];
+ for (int s = 0; s < sequences.length; s++)
+ {
+ smsa[0][s] = sequences[s].getSeq(gapCharacter);
+ }
+ }
+ return smsa;
+ }
+
+ /**
+ * return full msa and hidden regions with visible blocks replaced with new sub alignments
+ * @param nvismsa SequenceI[][]
+ * @param orders AlignmentOrder[] corresponding to each SequenceI[] block.
+ * @return Object[]
+ */
+ public Object[] getUpdatedView(SequenceI[][] nvismsa, AlignmentOrder[] orders,
+ char gapCharacter)
+ {
+ if (sequences == null || width <= 0)
+ {
+ throw new Error("empty view cannot be updated.");
+ }
+ if (nvismsa == null)
+ {
+ throw new Error(
+ "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
+ }
+ if (contigs != null && contigs.length > 0)
+ {
+ SequenceI[] alignment = new SequenceI[sequences.length];
+ ColumnSelection columnselection = new ColumnSelection();
+ if (contigs != null && contigs.length > 0)
+ {
+ int start = 0;
+ int nwidth = 0;
+ int owidth = width;
+ int j = 0;
+ for (int contig = 0; contig < contigs.length; contig += 3)
+ {
+ owidth += contigs[contig + 2]; // recover final column width
+ if (contigs[contig + 1] - start > 0)
+ {
+ int swidth = 0; // subalignment width
+ if (nvismsa[j] != null)
+ {
+ SequenceI mseq[] = nvismsa[j];
+ AlignmentOrder order = (orders == null) ? null : orders[j];
+ j++;
+ if (mseq.length != sequences.length)
+ {
+ throw new Error(
+ "Mismatch between number of sequences in block " + j + " (" +
+ mseq.length + ") and the original view (" +
+ sequences.length + ")");
+ }
+ swidth = mseq[0].getLength(); // JBPNote: could ensure padded here.
+ for (int s = 0; s < mseq.length; s++)
+ {
+ if (alignment[s] == null)
+ {
+ alignment[s] = mseq[s];
+ }
+ else
+ {
+ alignment[s].setSequence(alignment[s].getSequenceAsString() +
+ mseq[s].getSequenceAsString());
+ if (mseq[s].getStart() <= mseq[s].getEnd())
+ {
+ alignment[s].setEnd(mseq[s].getEnd());
+ }
+ if (order != null)
+ {
+ order.updateSequence(mseq[s], alignment[s]);
+ }
+ }
+ }
+ }
+ else
+ {
+ // recover original alignment block or place gaps
+ if (true)
+ {
+ // recover input data
+ for (int s = 0; s < sequences.length; s++)
+ {
+ SequenceI oseq = sequences[s].getSeq(gapCharacter).
+ getSubSequence(start,
+ contigs[contig + 1]);
+ if (swidth < oseq.getLength())
+ {
+ swidth = oseq.getLength();
+ }
+ if (alignment[s] == null)
+ {
+ alignment[s] = oseq;
+ }
+ else
+ {
+ alignment[s].setSequence(alignment[s].getSequenceAsString() +
+ oseq.getSequenceAsString());
+ if (oseq.getEnd() >= oseq.getStart())
+ {
+ alignment[s].setEnd(oseq.getEnd());
+ }
+ }
+ }
+
+ }
+ j++;
+ }
+ nwidth += swidth;
+ }
+ // advance to begining of visible region
+ start = contigs[contig + 1] + contigs[contig + 2];
+ // add hidden segment to right of next region
+ for (int s = 0; s < sequences.length; s++)
+ {
+ SequenceI hseq = sequences[s].getSeq(gapCharacter).getSubSequence(
+ contigs[contig +
+ 1], start);
+ if (alignment[s] == null)
+ {
+ alignment[s] = hseq;
+ }
+ else
+ {
+ alignment[s].setSequence(alignment[s].getSequenceAsString() +
+ hseq.getSequenceAsString());
+ if (hseq.getEnd() >= hseq.getStart())
+ {
+ alignment[s].setEnd(hseq.getEnd());
+ }
+ }
+ }
+ // mark hidden segment as hidden in the new alignment
+ columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);
+ nwidth += contigs[contig + 2];
+ }
+ // Do final segment - if it exists
+ if (j < nvismsa.length)
+ {
+ int swidth = 0;
+ if (nvismsa[j] != null)
+ {
+ SequenceI mseq[] = nvismsa[j];
+ AlignmentOrder order = (orders != null) ? orders[j] : null;
+ swidth = mseq[0].getLength();
+ for (int s = 0; s < mseq.length; s++)
+ {
+ if (alignment[s] == null)
+ {
+ alignment[s] = mseq[s];
+ }
+ else
+ {
+ alignment[s].setSequence(alignment[s].getSequenceAsString() +
+ mseq[s].getSequenceAsString());
+ if (mseq[s].getEnd() >= mseq[s].getStart())
+ {
+ alignment[s].setEnd(mseq[s].getEnd());
+ }
+ if (order != null)
+ {
+ order.updateSequence(mseq[s], alignment[s]);
+ }
+ }
+ }
+ }
+ else
+ {
+ if (start < owidth)
+ {
+ // recover input data or place gaps
+ if (true)
+ {
+ // recover input data
+ for (int s = 0; s < sequences.length; s++)
+ {
+ SequenceI oseq = sequences[s].getSeq(gapCharacter).
+ getSubSequence(start,
+ owidth + 1);
+ if (swidth < oseq.getLength())
+ {
+ swidth = oseq.getLength();
+ }
+ if (alignment[s] == null)
+ {
+ alignment[s] = oseq;
+ }
+ else
+ {
+ alignment[s].setSequence(alignment[s].getSequenceAsString() +
+ oseq.getSequenceAsString());
+ if (oseq.getEnd() >= oseq.getStart())
+ {
+ alignment[s].setEnd(oseq.getEnd());
+ }
+ }
+ }
+ nwidth += swidth;
+ }
+ else
+ {
+ // place gaps.
+ throw new Error("Padding not yet implemented.");
+ }
+ }
+ }
+ }
+ }
+ return new Object[]
+ {
+ alignment, columnselection};
+ }
+ else
+ {
+ if (nvismsa.length != 1)
+ {
+ throw new Error("Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks=" +
+ nvismsa.length);
+ }
+ if (nvismsa[0] != null)
+ {
+ return new Object[]
+ {
+ nvismsa[0], new ColumnSelection()};
+ }
+ else
+ {
+ return getAlignmentAndColumnSelection(gapCharacter);
+ }
+ }
+ }
+
+ /**
+ * returns simple array of start end positions of visible range on alignment.
+ * vis_start and vis_end are inclusive - use SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence from underlying alignment.
+ * @return int[] { start_i, end_i } for 1<i<n visible regions.
+ */
+ public int[] getVisibleContigs()
+ {
+ if (contigs != null && contigs.length > 0)
+ {
+ int start = 0;
+ int nvis = 0;
+ int fwidth = width;
+ for (int contig = 0; contig < contigs.length; contig += 3)
+ {
+ if ( (contigs[contig + 1] - start) > 0)
+ {
+ nvis++;
+ }
+ fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+ start = contigs[contig + 1] + contigs[contig + 2];
+ }
+ if (start < fwidth)
+ {
+ nvis++;
+ }
+ int viscontigs[] = new int[nvis * 2];
+ nvis = 0;
+ start = 0;
+ for (int contig = 0; contig < contigs.length; contig += 3)
+ {
+ if ( (contigs[contig + 1] - start) > 0)
+ {
+ viscontigs[nvis] = start;
+ viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive
+ nvis += 2;
+ }
+ start = contigs[contig + 1] + contigs[contig + 2];
+ }
+ if (start < fwidth)
+ {
+ viscontigs[nvis] = start;
+ viscontigs[nvis + 1] = fwidth; // end is inclusive
+ nvis += 2;
+ }
+ return viscontigs;
+ }
+ else
+ {
+ return new int[]
+ {
+ 0, width};
+ }
+ }
+
+ /**
+ *
+ * @return position of first visible column of AlignmentView within its parent's alignment reference frame
+ */
+ public int getAlignmentOrigin()
+ {
+ // TODO Auto-generated method stub
+ return firstCol;
+ }