/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.List;
/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
+ * Transient object compactly representing a 'view' of an alignment - with
+ * discontinuities marked. Extended in Jalview 2.7 to optionally record sequence
+ * groups and specific selected regions on the alignment.
*/
public class AlignmentView
{
+ private SeqCigar[] sequences = null;
+
+ private int[] contigs = null;
+
+ private int width = 0;
+
+ private int firstCol = 0;
+
+ /**
+ * one or more ScGroup objects, which are referenced by each seqCigar's group
+ * membership
+ */
+ private List<ScGroup> scGroups = null;
+
+ private boolean isNa = false;
+
+ /**
+ * reference to the complementary CDS/Protein alignment for this alignment, if available
+ */
+ private AlignmentView complementView=null;
+
+ /**
+ * setter for
+ * @param complementView
+ */
+ public void setComplement(AlignmentView complementView)
+ {
+ this.complementView = complementView;
+
+ }
+ /**
+ *
+ * @return true if a complement is available
+ */
+ public boolean hasComplementView()
+ {
+ return complementView!=null;
+ }
+ /**
+ *
+ * @return the complement view or null
+ */
+ public AlignmentView getComplementView()
+ {
+ return complementView;
+ }
+
+ /**
+ * false if the view concerns peptides
+ *
+ * @return
+ */
+ public boolean isNa()
+ {
+ return isNa;
+ }
+
+ /**
+ * Group defined over SeqCigars. Unlike AlignmentI associated groups, each
+ * SequenceGroup hold just the essential properties for the group, but no
+ * references to the sequences involved. SeqCigars hold references to the
+ * seuqenceGroup entities themselves.
+ */
+ private class ScGroup
+ {
+ public List<SeqCigar> seqs;
+
+ public SequenceGroup sg;
+
+ ScGroup()
+ {
+ seqs = new ArrayList<>();
+ }
+
/**
- * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
+ * @param seq
+ * @return true if seq was not a member before and was added to group
*/
- private SeqCigar[] sequences = null;
- private int[] contigs = null;
- private int width=0;
- private int firstCol=0;
+ public boolean add(SeqCigar seq)
+ {
+ if (!seq.isMemberOf(this))
+ {
+ seqs.add(seq);
+ seq.setGroupMembership(this);
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ /**
+ *
+ * @param seq
+ * @return true if seq was a member and was removed from group
+ */
+ public boolean remove(SeqCigar seq)
+ {
+ if (seq.removeGroupMembership(this))
+ {
+ seqs.remove(seq);
+ return true;
+ }
+ return false;
+ }
+
+ public int size()
+ {
+ return seqs.size();
+ }
+ }
+
+ /**
+ * vector of selected seqCigars. This vector is also referenced by each
+ * seqCigar contained in it.
+ */
+ private ScGroup selected;
+
+ /**
+ * Construct an alignmentView from a live jalview alignment view. Note -
+ * hidden rows will be excluded from alignmentView Note: JAL-1179
+ *
+ * @param alignment
+ * - alignment as referenced by an AlignViewport
+ * @param columnSelection
+ * -
+ * @param selection
+ * @param hasHiddenColumns
+ * - mark the hidden columns in columnSelection as hidden in the view
+ * @param selectedRegionOnly
+ * - when set, only include the selected region in the view,
+ * otherwise just mark the selected region on the constructed view.
+ * @param recordGroups
+ * - when set, any groups on the given alignment will be marked on
+ * the view
+ */
+ public AlignmentView(AlignmentI alignment, HiddenColumns hidden,
+ SequenceGroup selection, boolean hasHiddenColumns,
+ boolean selectedRegionOnly, boolean recordGroups)
+ {
+ // refactored from AlignViewport.getAlignmentView(selectedOnly);
+ this(new jalview.datamodel.CigarArray(alignment,
+ (hasHiddenColumns ? hidden : null),
+ (selectedRegionOnly ? selection : null)),
+ (selectedRegionOnly && selection != null)
+ ? selection.getStartRes()
+ : 0);
+ isNa = alignment.isNucleotide();
+ // walk down SeqCigar array and Alignment Array - optionally restricted by
+ // selected region.
+ // test group membership for each sequence in each group, store membership
+ // and record non-empty groups in group list.
+ // record / sub-select selected region on the alignment view
+ SequenceI[] selseqs;
+ if (selection != null && selection.getSize() > 0)
+ {
+ this.selected = new ScGroup();
+ selseqs = selection.getSequencesInOrder(alignment,
+ selectedRegionOnly);
+ }
+ else
+ {
+ selseqs = alignment.getSequencesArray();
+ }
+
+ List<List<SequenceI>> seqsets = new ArrayList<>();
+ // get the alignment's group list and make a copy
+ List<SequenceGroup> grps = new ArrayList<>();
+ List<SequenceGroup> gg = alignment.getGroups();
+ grps.addAll(gg);
+ ScGroup[] sgrps = null;
+ boolean addedgps[] = null;
+ if (grps != null)
+ {
+ if (selection != null && selectedRegionOnly)
+ {
+ // trim annotation to the region being stored.
+ // strip out any groups that do not actually intersect with the
+ // visible and selected region
+ int ssel = selection.getStartRes(), esel = selection.getEndRes();
+ List<SequenceGroup> isg = new ArrayList<>();
+ for (SequenceGroup sg : grps)
+ {
+ if (!(sg.getStartRes() > esel || sg.getEndRes() < ssel))
+ {
+ // adjust bounds of new group, if necessary.
+ if (sg.getStartRes() < ssel)
+ {
+ sg.setStartRes(ssel);
+ }
+ if (sg.getEndRes() > esel)
+ {
+ sg.setEndRes(esel);
+ }
+ sg.setStartRes(sg.getStartRes() - ssel + 1);
+ sg.setEndRes(sg.getEndRes() - ssel + 1);
+
+ isg.add(sg);
+ }
+ }
+ grps = isg;
+ }
+
+ sgrps = new ScGroup[grps.size()];
+ addedgps = new boolean[grps.size()];
+ for (int g = 0; g < sgrps.length; g++)
+ {
+ SequenceGroup sg = grps.get(g);
+ sgrps[g] = new ScGroup();
+ sgrps[g].sg = new SequenceGroup(sg);
+ addedgps[g] = false;
+ // can't set entry 0 in an empty list
+ // seqsets.set(g, sg.getSequences(null));
+ seqsets.add(sg.getSequences());
+ }
+ // seqsets now contains vectors (should be sets) for each group, so we can
+ // track when we've done with the group
+ }
+ int csi = 0;
+ for (int i = 0; i < selseqs.length; i++)
+ {
+ if (selseqs[i] != null)
+ {
+ if (selection != null && selection.getSize() > 0
+ && !selectedRegionOnly)
+ {
+ selected.add(sequences[csi]);
+ }
+ if (seqsets != null)
+ {
+ for (int sg = 0; sg < sgrps.length; sg++)
+ {
+ if ((seqsets.get(sg)).contains(selseqs[i]))
+ {
+ sgrps[sg].sg.deleteSequence(selseqs[i], false);
+ sgrps[sg].add(sequences[csi]);
+ if (!addedgps[sg])
+ {
+ if (scGroups == null)
+ {
+ scGroups = new ArrayList<>();
+ }
+ addedgps[sg] = true;
+ scGroups.add(sgrps[sg]);
+ }
+ }
+ }
+ }
+ csi++;
+ }
+ }
+ // finally, delete the remaining sequences (if any) not selected
+ for (int sg = 0; sg < sgrps.length; sg++)
+ {
+ SequenceI[] sqs = sgrps[sg].sg.getSequencesAsArray(null);
+ for (int si = 0; si < sqs.length; si++)
+ {
+ sgrps[sg].sg.deleteSequence(sqs[si], false);
+ }
+ sgrps[sg] = null;
+ }
+ }
+
+ /**
+ * construct an alignmentView from a SeqCigarArray. Errors are thrown if the
+ * seqcigararray.isSeqCigarArray() flag is not set.
+ */
public AlignmentView(CigarArray seqcigararray)
{
if (!seqcigararray.isSeqCigarArray())
- throw new Error("Implementation Error - can only make an alignment view from a CigarArray of sequences.");
- //contigs = seqcigararray.applyDeletions();
+ {
+ throw new Error(
+ "Implementation Error - can only make an alignment view from a CigarArray of sequences.");
+ }
+ // contigs = seqcigararray.applyDeletions();
contigs = seqcigararray.getDeletedRegions();
sequences = seqcigararray.getSeqCigarArray();
width = seqcigararray.getWidth(); // visible width
}
+
/**
- * Create an alignmentView where the first column corresponds with the 'firstcol' column of some reference alignment
+ * Create an alignmentView where the first column corresponds with the
+ * 'firstcol' column of some reference alignment
+ *
* @param sdata
* @param firstcol
*/
- public AlignmentView(CigarArray sdata, int firstcol) {
+ public AlignmentView(CigarArray sdata, int firstcol)
+ {
this(sdata);
- firstCol=firstcol;
+ firstCol = firstcol;
}
public void setSequences(SeqCigar[] sequences)
{
return sequences;
}
+
/**
* @see CigarArray.getDeletedRegions
* @return int[] { vis_start, sym_start, length }
{
return contigs;
}
+
/**
- * get the full alignment and a columnselection object marking the hidden regions
- * @param gapCharacter char
+ * get the full alignment and a columnselection object marking the hidden
+ * regions
+ *
+ * @param gapCharacter
+ * char
* @return Object[] { SequenceI[], ColumnSelection}
*/
- public Object[] getAlignmentAndColumnSelection(char gapCharacter) {
- ColumnSelection colsel = new ColumnSelection();
+ public Object[] getAlignmentAndHiddenColumns(char gapCharacter)
+ {
+ HiddenColumns hidden = new HiddenColumns();
- return new Object[] { SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel, contigs), colsel};
+ return new Object[] { SeqCigar.createAlignmentSequences(sequences,
+ gapCharacter, hidden, contigs),
+ hidden };
}
+
/**
- * getSequenceStrings
- *
- * @param c char
- * @return String[]
+ * return the visible alignment corresponding to this view. Sequences in this
+ * alignment are edited versions of the parent sequences - where hidden
+ * regions have been removed. NOTE: the sequence data in this alignment is not
+ * complete!
+ *
+ * @param c
+ * @return
*/
- public String[] getSequenceStrings(char c)
+ public AlignmentI getVisibleAlignment(char c)
+ {
+ SequenceI[] aln = getVisibleSeqs(c);
+
+ AlignmentI vcal = new Alignment(aln);
+ addPrunedGroupsInOrder(vcal, -1, -1, true);
+ return vcal;
+ }
+
+ /**
+ * add groups from view to the given alignment
+ *
+ * @param vcal
+ * @param gstart
+ * -1 or 0 to width-1
+ * @param gend
+ * -1 or gstart to width-1
+ * @param viscontigs
+ * - true if vcal is alignment of the visible regions of the view
+ * (e.g. as returned from getVisibleAlignment)
+ */
+ private void addPrunedGroupsInOrder(AlignmentI vcal, int gstart, int gend,
+ boolean viscontigs)
{
- String[] seqs=new String[sequences.length];
- for (int n=0; n<sequences.length; n++) {
- String fullseq = sequences[n].getSequenceString(c);
- if (contigs != null)
+ boolean r = false;
+ if (gstart > -1 && gstart <= gend)
+ {
+ r = true;
+ }
+
+ SequenceI[] aln = vcal.getSequencesArray();
+ {
+ /**
+ * prune any groups to the visible coordinates of the alignment.
+ */
{
- seqs[n] = "";
- int p = 0;
- for (int h = 0; h < contigs.length; h += 3)
+ int nvg = (scGroups != null) ? scGroups.size() : 0;
+ if (nvg > 0)
{
- seqs[n] += fullseq.substring(p, contigs[h + 1]);
- p = contigs[h + 1] + contigs[h + 2];
+ SequenceGroup[] nsg = new SequenceGroup[nvg];
+ for (int g = 0; g < nvg; g++)
+ {
+ SequenceGroup sg = scGroups.get(g).sg;
+ if (r)
+ {
+ if (sg.getStartRes() > gend || sg.getEndRes() < gstart)
+ {
+ // Skip this group
+ nsg[g] = null;
+ continue;
+ }
+ }
+
+ // clone group properties
+ nsg[g] = new SequenceGroup(sg);
+
+ // may need to shift/trim start and end ?
+ if (r && !viscontigs)
+ {
+ // Not fully tested code - routine not yet called with
+ // viscontigs==false
+ if (nsg[g].getStartRes() < gstart)
+ {
+ nsg[g].setStartRes(0);
+ }
+ else
+ {
+ nsg[g].setStartRes(nsg[g].getStartRes() - gstart);
+ nsg[g].setEndRes(nsg[g].getEndRes() - gstart);
+ }
+ if (nsg[g].getEndRes() > (gend - gstart))
+ {
+ nsg[g].setEndRes(gend - gstart);
+ }
+ }
+ }
+ if (viscontigs)
+ {
+ // prune groups to cover just the visible positions between
+ // gstart/gend.
+ if (contigs != null)
+ {
+ int p = 0;
+ ShiftList prune = new ShiftList();
+ if (r)
+ {
+ // adjust for start of alignment within visible window.
+ prune.addShift(gstart, -gstart); //
+ }
+ for (int h = 0; h < contigs.length; h += 3)
+ {
+ {
+ prune.addShift(p + contigs[h + 1],
+ contigs[h + 2] - contigs[h + 1]);
+ }
+ p = contigs[h + 1] + contigs[h + 2];
+ }
+ for (int g = 0; g < nsg.length; g++)
+ {
+ if (nsg[g] != null)
+ {
+ int s = nsg[g].getStartRes(), t = nsg[g].getEndRes();
+ int w = 1 + t - s;
+ if (r)
+ {
+ if (s < gstart)
+ {
+ s = gstart;
+ }
+ if (t > gend)
+ {
+ t = gend;
+ }
+ }
+ s = prune.shift(s);
+ t = prune.shift(t);
+ nsg[g].setStartRes(s);
+ nsg[g].setEndRes(t);
+ }
+ }
+ }
+ }
+
+ for (int nsq = 0; nsq < aln.length; nsq++)
+ {
+ for (int g = 0; g < nvg; g++)
+ {
+ if (nsg[g] != null
+ && sequences[nsq].isMemberOf(scGroups.get(g)))
+ {
+ nsg[g].addSequence(aln[nsq], false);
+ }
+ }
+ }
+ for (int g = 0; g < nvg; g++)
+ {
+ if (nsg[g] != null && nsg[g].getSize() > 0)
+ {
+ vcal.addGroup(nsg[g]);
+ }
+ nsg[g] = null;
+ }
}
- seqs[n] += fullseq.substring(p);
- } else
- seqs[n] = fullseq;
+ }
+ }
+ }
+
+ /**
+ * generate sequence array corresponding to the visible parts of the
+ * alignment.
+ *
+ * @param c
+ * gap character to use to recreate the alignment
+ * @return
+ */
+ private SequenceI[] getVisibleSeqs(char c)
+ {
+ SequenceI[] aln = new SequenceI[sequences.length];
+ for (int i = 0, j = sequences.length; i < j; i++)
+ {
+ aln[i] = sequences[i].getSeq(c);
+ // Remove hidden regions from sequence
+ aln[i].setSequence(getASequenceString(c, i));
+ }
+ return aln;
+ }
+
+ /**
+ * creates new alignment objects for all contiguous visible segments
+ *
+ * @param c
+ * @param start
+ * @param end
+ * @param regionOfInterest
+ * specify which sequences to include (or null to include all
+ * sequences)
+ * @return AlignmentI[] - all alignments where each sequence is a subsequence
+ * constructed from visible contig regions of view
+ */
+ public AlignmentI[] getVisibleContigAlignments(char c)
+ {
+ int nvc = 0;
+ int[] vcontigs = getVisibleContigs();
+ SequenceI[][] contigviews = getVisibleContigs(c);
+ AlignmentI[] vcals = new AlignmentI[contigviews.length];
+ for (nvc = 0; nvc < contigviews.length; nvc++)
+ {
+ vcals[nvc] = new Alignment(contigviews[nvc]);
+ if (scGroups != null && scGroups.size() > 0)
+ {
+ addPrunedGroupsInOrder(vcals[nvc], vcontigs[nvc * 2],
+ vcontigs[nvc * 2 + 1], true);
+ }
+ }
+ return vcals;
+ }
+
+ /**
+ * build a string excluding hidden regions from a particular sequence in the
+ * view
+ *
+ * @param c
+ * @param n
+ * @return
+ */
+ private String getASequenceString(char c, int n)
+ {
+ String sqn;
+ String fullseq = sequences[n].getSequenceString(c);
+ if (contigs != null)
+ {
+ sqn = "";
+ int p = 0;
+ for (int h = 0; h < contigs.length; h += 3)
+ {
+ sqn += fullseq.substring(p, contigs[h + 1]);
+ p = contigs[h + 1] + contigs[h + 2];
+ }
+ sqn += fullseq.substring(p);
+ }
+ else
+ {
+ sqn = fullseq;
+ }
+ return sqn;
+ }
+
+ /**
+ * get an array of visible sequence strings for a view on an alignment using
+ * the given gap character uses getASequenceString
+ *
+ * @param c
+ * char
+ * @return String[]
+ */
+ public String[] getSequenceStrings(char c)
+ {
+ String[] seqs = new String[sequences.length];
+ for (int n = 0; n < sequences.length; n++)
+ {
+ seqs[n] = getASequenceString(c, n);
}
return seqs;
}
+
/**
- *
+ *
* @return visible number of columns in alignment view
*/
- public int getWidth() {
+ public int getWidth()
+ {
return width;
}
- protected void setWidth(int width) {
+ protected void setWidth(int width)
+ {
this.width = width;
}
+
/**
* get the contiguous subalignments in an alignment view.
- * @param gapCharacter char
+ *
+ * @param gapCharacter
+ * char
* @return SequenceI[][]
*/
- public SequenceI[][] getVisibleContigs(char gapCharacter) {
+ public SequenceI[][] getVisibleContigs(char gapCharacter)
+ {
SequenceI[][] smsa;
int njobs = 1;
- if (sequences==null || width<=0)
+ if (sequences == null || width <= 0)
+ {
return null;
+ }
if (contigs != null && contigs.length > 0)
{
int start = 0;
int fwidth = width;
for (int contig = 0; contig < contigs.length; contig += 3)
{
- if ( (contigs[contig + 1] - start) > 0)
+ if ((contigs[contig + 1] - start) > 0)
{
njobs++;
}
- fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+ fwidth += contigs[contig + 2]; // end up with full region width
+ // (including hidden regions)
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,
- contigs[contig + 1]);
+ mseq[s] = sequences[s].getSeq(gapCharacter)
+ .getSubSequence(start, contigs[contig + 1]);
}
smsa[j] = mseq;
j++;
for (int s = 0; s < mseq.length; s++)
{
mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
- fwidth + 1);
+ fwidth + 1);
}
smsa[j] = mseq;
j++;
}
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 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) {
+ public Object[] getUpdatedView(SequenceI[][] nvismsa,
+ AlignmentOrder[] orders, char gapCharacter)
+ {
if (sequences == null || width <= 0)
{
- throw new Error("empty view cannot be updated.");
+ throw new Error(MessageManager
+ .getString("error.empty_view_cannot_be_updated"));
}
if (nvismsa == null)
+ {
throw new Error(
- "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
+ "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
+ }
if (contigs != null && contigs.length > 0)
{
SequenceI[] alignment = new SequenceI[sequences.length];
- ColumnSelection columnselection = new ColumnSelection();
+ // ColumnSelection columnselection = new ColumnSelection();
+ HiddenColumns hidden = new HiddenColumns();
if (contigs != null && contigs.length > 0)
{
int start = 0;
if (nvismsa[j] != null)
{
SequenceI mseq[] = nvismsa[j];
- AlignmentOrder order=(orders==null) ? null : orders[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.
+ if (mseq.length != sequences.length)
+ {
+ throw new Error(MessageManager.formatMessage(
+ "error.mismatch_between_number_of_sequences_in_block",
+ new String[]
+ { Integer.valueOf(j).toString(),
+ Integer.valueOf(mseq.length).toString(),
+ Integer.valueOf(sequences.length)
+ .toString() }));
+ }
+ swidth = mseq[0].getLength(); // JBPNote: could ensure padded
+ // here.
for (int s = 0; s < mseq.length; s++)
{
if (alignment[s] == null)
}
else
{
- alignment[s].setSequence(alignment[s].getSequenceAsString() +
- mseq[s].getSequenceAsString());
+ 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) {
+ if (order != null)
+ {
order.updateSequence(mseq[s], alignment[s]);
}
}
// recover input data
for (int s = 0; s < sequences.length; s++)
{
- SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
- contigs[contig + 1]);
+ SequenceI oseq = sequences[s].getSeq(gapCharacter)
+ .getSubSequence(start, contigs[contig + 1]);
if (swidth < oseq.getLength())
{
swidth = oseq.getLength();
}
else
{
- alignment[s].setSequence(alignment[s].getSequenceAsString() +
- oseq.getSequenceAsString());
+ alignment[s]
+ .setSequence(alignment[s].getSequenceAsString()
+ + oseq.getSequenceAsString());
if (oseq.getEnd() >= oseq.getStart())
{
alignment[s].setEnd(oseq.getEnd());
// 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);
+ 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());
+ 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);
+ hidden.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);
nwidth += contigs[contig + 2];
}
// Do final segment - if it exists
if (nvismsa[j] != null)
{
SequenceI mseq[] = nvismsa[j];
- AlignmentOrder order = (orders!=null) ? orders[j] : null;
+ AlignmentOrder order = (orders != null) ? orders[j] : null;
swidth = mseq[0].getLength();
for (int s = 0; s < mseq.length; s++)
{
}
else
{
- alignment[s].setSequence(alignment[s].getSequenceAsString() +
- mseq[s].getSequenceAsString());
+ 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) {
+ if (order != null)
+ {
order.updateSequence(mseq[s], alignment[s]);
}
}
// recover input data
for (int s = 0; s < sequences.length; s++)
{
- SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
- owidth + 1);
+ SequenceI oseq = sequences[s].getSeq(gapCharacter)
+ .getSubSequence(start, owidth + 1);
if (swidth < oseq.getLength())
{
swidth = oseq.getLength();
}
else
{
- alignment[s].setSequence(alignment[s].getSequenceAsString() +
- oseq.getSequenceAsString());
+ alignment[s]
+ .setSequence(alignment[s].getSequenceAsString()
+ + oseq.getSequenceAsString());
if (oseq.getEnd() >= oseq.getStart())
{
alignment[s].setEnd(oseq.getEnd());
else
{
// place gaps.
- throw new Error("Padding not yet implemented.");
+ throw new Error(MessageManager
+ .getString("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()};
+ return new Object[] { alignment, hidden };
+ }
+ else
+ {
+ if (nvismsa.length != 1)
+ {
+ throw new Error(MessageManager.formatMessage(
+ "error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view",
+ new String[]
+ { Integer.valueOf(nvismsa.length).toString() }));
+ }
+ if (nvismsa[0] != null)
+ {
+ return new Object[] { nvismsa[0], new HiddenColumns() };
+ }
else
- return getAlignmentAndColumnSelection(gapCharacter);
+ {
+ return getAlignmentAndHiddenColumns(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.
+ * 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() {
+ public int[] getVisibleContigs()
+ {
if (contigs != null && contigs.length > 0)
{
int start = 0;
int fwidth = width;
for (int contig = 0; contig < contigs.length; contig += 3)
{
- if ( (contigs[contig + 1] - start) > 0)
+ if ((contigs[contig + 1] - start) > 0)
{
nvis++;
}
- fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+ 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)
+ 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;
+ viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive
+ nvis += 2;
}
start = contigs[contig + 1] + contigs[contig + 2];
}
- if (start<fwidth) {
+ if (start < fwidth)
+ {
viscontigs[nvis] = start;
- viscontigs[nvis+1]=fwidth; // end is inclusive
- nvis+=2;
+ viscontigs[nvis + 1] = fwidth - 1; // end is inclusive
+ nvis += 2;
}
return viscontigs;
- } else {
- return new int[] { 0, width};
+ }
+ else
+ {
+ return new int[] { 0, width - 1 };
}
}
+
/**
- *
- * @return position of first visible column of AlignmentView within its parent's alignment reference frame
+ *
+ * @return position of first visible column of AlignmentView within its
+ * parent's alignment reference frame
*/
- public int getAlignmentOrigin() {
- // TODO Auto-generated method stub
+ public int getAlignmentOrigin()
+ {
return firstCol;
}
+
+ /**
+ * compute a deletion map for the current view according to the given
+ * gap/match map
+ *
+ * @param gapMap
+ * (as returned from SequenceI.gapMap())
+ * @return int[] {intersection of visible regions with gapMap)
+ */
+ public int[] getVisibleContigMapFor(int[] gapMap)
+ {
+ int[] delMap = null;
+ int[] viscontigs = getVisibleContigs();
+ int spos = 0;
+ int i = 0;
+ if (viscontigs != null)
+ {
+ // viscontigs maps from a subset of the gapMap to the gapMap, so it will
+ // always be equal to or shorter than gapMap
+ delMap = new int[gapMap.length];
+ for (int contig = 0; contig < viscontigs.length; contig += 2)
+ {
+
+ while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])
+ {
+ spos++;
+ }
+ while (spos < gapMap.length
+ && gapMap[spos] <= viscontigs[contig + 1])
+ {
+ delMap[i++] = spos++;
+ }
+ }
+ int tmap[] = new int[i];
+ System.arraycopy(delMap, 0, tmap, 0, i);
+ delMap = tmap;
+ }
+ return delMap;
+ }
+
+ /**
+ * apply the getSeq(gc) method to each sequence cigar, and return the array of
+ * edited sequences, optionally with hidden regions removed.
+ *
+ * @param gc
+ * gap character to use for insertions
+ * @param delete
+ * remove hidden regions from sequences. Note: currently implemented
+ * in a memory inefficient way - space needed is 2*result set for
+ * deletion
+ *
+ * @return SequenceI[]
+ */
+ public SequenceI[] getEditedSequences(char gc, boolean delete)
+ {
+ SeqCigar[] msf = getSequences();
+ SequenceI[] aln = new SequenceI[msf.length];
+ for (int i = 0, j = msf.length; i < j; i++)
+ {
+ aln[i] = msf[i].getSeq(gc);
+ }
+ if (delete)
+ {
+ String[] sqs = getSequenceStrings(gc);
+ for (int i = 0; i < sqs.length; i++)
+ {
+ aln[i].setSequence(sqs[i]);
+ sqs[i] = null;
+ }
+ }
+ return aln;
+ }
+
+ public static void summariseAlignmentView(AlignmentView view,
+ PrintStream os)
+ {
+ os.print("View has " + view.sequences.length + " of which ");
+ if (view.selected == null)
+ {
+ os.print("None");
+ }
+ else
+ {
+ os.print(" " + view.selected.size());
+ }
+ os.println(" are selected.");
+ os.print("View is " + view.getWidth() + " columns wide");
+ int viswid = 0;
+ int[] contigs = view.getContigs();
+ if (contigs != null)
+ {
+ viswid = view.width;
+ for (int i = 0; i < contigs.length; i += 3)
+ {
+ viswid += contigs[i + 2];
+ }
+ os.println("with " + viswid + " visible columns spread over "
+ + contigs.length / 3 + " regions.");
+ }
+ else
+ {
+ viswid = view.width;
+ os.println(".");
+ }
+ if (view.scGroups != null)
+ {
+ os.println("There are " + view.scGroups.size()
+ + " groups defined on the view.");
+ for (int g = 0; g < view.scGroups.size(); g++)
+ {
+ ScGroup sgr = view.scGroups.get(g);
+ os.println("Group " + g + ": Name = " + sgr.sg.getName()
+ + " Contains " + sgr.seqs.size() + " Seqs.");
+ os.println("This group runs from " + sgr.sg.getStartRes() + " to "
+ + sgr.sg.getEndRes());
+ for (int s = 0; s < sgr.seqs.size(); s++)
+ {
+ // JBPnote this should be a unit test for ScGroup
+ if (!sgr.seqs.get(s).isMemberOf(sgr))
+ {
+ os.println("** WARNING: sequence " + sgr.seqs.get(s).toString()
+ + " is not marked as member of group.");
+ }
+ }
+ }
+ AlignmentI visal = view.getVisibleAlignment('-');
+ if (visal != null)
+ {
+ os.println("Vis. alignment is " + visal.getWidth()
+ + " wide and has " + visal.getHeight() + " seqs.");
+ if (visal.getGroups() != null && visal.getGroups().size() > 0)
+ {
+
+ int i = 1;
+ for (SequenceGroup sg : visal.getGroups())
+ {
+ os.println("Group " + (i++) + " begins at column "
+ + sg.getStartRes() + " and ends at " + sg.getEndRes());
+ }
+ }
+ }
+ }
+ }
+
+ public static void testSelectionViews(AlignmentI alignment,
+ HiddenColumns hidden, SequenceGroup selection)
+ {
+ System.out.println("Testing standard view creation:\n");
+ AlignmentView view = null;
+ try
+ {
+ System.out.println(
+ "View with no hidden columns, no limit to selection, no groups to be collected:");
+ view = new AlignmentView(alignment, hidden, selection, false, false,
+ false);
+ summariseAlignmentView(view, System.out);
+
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.err.println(
+ "Failed to generate alignment with selection but no groups marked.");
+ }
+ try
+ {
+ System.out.println(
+ "View with no hidden columns, no limit to selection, and all groups to be collected:");
+ view = new AlignmentView(alignment, hidden, selection, false, false,
+ true);
+ summariseAlignmentView(view, System.out);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.err.println(
+ "Failed to generate alignment with selection marked but no groups marked.");
+ }
+ try
+ {
+ System.out.println(
+ "View with no hidden columns, limited to selection and no groups to be collected:");
+ view = new AlignmentView(alignment, hidden, selection, false, true,
+ false);
+ summariseAlignmentView(view, System.out);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.err.println(
+ "Failed to generate alignment with selection restricted but no groups marked.");
+ }
+ try
+ {
+ System.out.println(
+ "View with no hidden columns, limited to selection, and all groups to be collected:");
+ view = new AlignmentView(alignment, hidden, selection, false, true,
+ true);
+ summariseAlignmentView(view, System.out);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.err.println(
+ "Failed to generate alignment with selection restricted and groups marked.");
+ }
+ try
+ {
+ System.out.println(
+ "View *with* hidden columns, no limit to selection, no groups to be collected:");
+ view = new AlignmentView(alignment, hidden, selection, true, false,
+ false);
+ summariseAlignmentView(view, System.out);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.err.println(
+ "Failed to generate alignment with selection but no groups marked.");
+ }
+ try
+ {
+ System.out.println(
+ "View *with* hidden columns, no limit to selection, and all groups to be collected:");
+ view = new AlignmentView(alignment, hidden, selection, true, false,
+ true);
+ summariseAlignmentView(view, System.out);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.err.println(
+ "Failed to generate alignment with selection marked but no groups marked.");
+ }
+ try
+ {
+ System.out.println(
+ "View *with* hidden columns, limited to selection and no groups to be collected:");
+ view = new AlignmentView(alignment, hidden, selection, true, true,
+ false);
+ summariseAlignmentView(view, System.out);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.err.println(
+ "Failed to generate alignment with selection restricted but no groups marked.");
+ }
+ try
+ {
+ System.out.println(
+ "View *with* hidden columns, limited to selection, and all groups to be collected:");
+ view = new AlignmentView(alignment, hidden, selection, true, true,
+ true);
+ summariseAlignmentView(view, System.out);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.err.println(
+ "Failed to generate alignment with selection restricted and groups marked.");
+ }
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff