X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=88e9a9c004cc4ad3e230f522c239c464718043ff;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=2a9386176050e0941a2eab598a2c8f48ca31ced3;hpb=a3df398bea1970500d44f0e6adc45c9d4bf4a295;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 2a93861..88e9a9c 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,1175 +1,1214 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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.
- *
- * 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 Jalview. If not, see .
- */
-package jalview.datamodel;
-
-import jalview.util.ShiftList;
-
-import java.io.PrintStream;
-import java.util.Enumeration;
-import java.util.Vector;
-
-/**
- * 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 Vector scGroups;
-
- /**
- * 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 Vector seqs;
-
- public SequenceGroup sg;
-
- ScGroup()
- {
- seqs = new Vector();
- }
- }
-
- /**
- * vector of selected seqCigars. This vector is also referenced by each
- * seqCigar contained in it.
- */
- private Vector selected;
-
- /**
- * Construct an alignmentView from a live jalview alignment view. Note -
- * hidden rows will be excluded from alignmentView
- *
- * @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,
- ColumnSelection columnSelection, SequenceGroup selection,
- boolean hasHiddenColumns, boolean selectedRegionOnly,
- boolean recordGroups)
- {
- // refactored from AlignViewport.getAlignmentView(selectedOnly);
- this(new jalview.datamodel.CigarArray(alignment,
- (hasHiddenColumns ? columnSelection : null),
- (selectedRegionOnly ? selection : null)),
- (selectedRegionOnly && selection != null) ? selection
- .getStartRes() : 0);
- // 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)
- {
- Vector sel = selection.getSequences(null);
- this.selected = new Vector();
- selseqs = selection.getSequencesInOrder(alignment, false);
- }
- else
- {
- selseqs = alignment.getSequencesArray();
- }
-
- // get the alignment's group list and make a copy
- Vector grps = new Vector();
- Vector gg = alignment.getGroups();
- Enumeration gge = gg.elements();
- while (gge.hasMoreElements())
- {
- grps.addElement(gge.nextElement());
- }
- ScGroup[] sgrps = null;
- boolean addedgps[] = null;
- if (grps != null)
- {
- SequenceGroup sg;
- 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();
- Vector isg = new Vector();
- Enumeration en = grps.elements();
- while (en.hasMoreElements())
- {
- sg = (SequenceGroup) en.nextElement();
-
- 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.addElement(sg);
- }
- }
- grps = isg;
- }
-
- sgrps = new ScGroup[grps.size()];
- addedgps = new boolean[grps.size()];
- for (int g = 0; g < sgrps.length; g++)
- {
- sg = (SequenceGroup) grps.elementAt(g);
- sgrps[g] = new ScGroup();
- sgrps[g].sg = new SequenceGroup(sg);
- addedgps[g] = false;
- grps.setElementAt(sg.getSequences(null), g);
- }
- // grps 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 && !selectedRegionOnly)
- {
- sequences[csi].setGroupMembership(selected);
- selected.addElement(sequences[csi]);
- }
- if (grps != null)
- {
- for (int sg = 0; sg < sgrps.length; sg++)
- {
- if (((Vector) grps.elementAt(sg)).contains(selseqs[i]))
- {
- sequences[csi].setGroupMembership(sgrps[sg]);
- sgrps[sg].sg.deleteSequence(selseqs[i], false);
- sgrps[sg].seqs.addElement(sequences[csi]);
- if (!addedgps[sg])
- {
- if (scGroups == null)
- {
- scGroups = new Vector();
- }
- addedgps[sg] = true;
- scGroups.addElement(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();
- 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
- *
- * @param sdata
- * @param firstcol
- */
- public AlignmentView(CigarArray sdata, int firstcol)
- {
- this(sdata);
- firstCol = firstcol;
- }
-
- public void setSequences(SeqCigar[] sequences)
- {
- this.sequences = sequences;
- }
-
- public void setContigs(int[] contigs)
- {
- this.contigs = contigs;
- }
-
- public SeqCigar[] getSequences()
- {
- return sequences;
- }
-
- /**
- * @see CigarArray.getDeletedRegions
- * @return int[] { vis_start, sym_start, length }
- */
- public int[] getContigs()
- {
- return contigs;
- }
-
- /**
- * 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();
-
- return new Object[]
- {
- SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
- contigs), colsel };
- }
-
- /**
- * 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 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)
- {
- boolean r = false;
- if (gstart > -1 && gstart <= gend)
- {
- r = true;
- }
-
- SequenceI[] aln = vcal.getSequencesArray();
- {
- /**
- * prune any groups to the visible coordinates of the alignment.
- */
- {
- int nvg = (scGroups != null) ? scGroups.size() : 0;
- if (nvg > 0)
- {
- SequenceGroup[] nsg = new SequenceGroup[nvg];
- for (int g = 0; g < nvg; g++)
- {
- SequenceGroup sg = ((ScGroup) scGroups.elementAt(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.elementAt(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;
- }
- }
- }
- }
- }
-
- /**
- * generate sequence array corresponding to the visible parts of the
- * alignment.
- *
- * @param c
- * @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('-');
- }
- // Remove hidden regions from sequence objects.
- String seqs[] = getSequenceStrings('-');
- for (int i = 0, j = aln.length; i < j; i++)
- {
- aln[i].setSequence(seqs[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;
- }
-
-
- /**
- * get an array of visible sequence strings for a view on an alignment using
- * the given gap character
- *
- * @param c
- * char
- * @return String[]
- */
- public String[] getSequenceStrings(char c)
- {
- String[] seqs = new String[sequences.length];
- for (int n = 0; n < sequences.length; n++)
- {
- String fullseq = sequences[n].getSequenceString(c);
- if (contigs != null)
- {
- seqs[n] = "";
- int p = 0;
- for (int h = 0; h < contigs.length; h += 3)
- {
- seqs[n] += fullseq.substring(p, contigs[h + 1]);
- p = contigs[h + 1] + contigs[h + 2];
- }
- seqs[n] += fullseq.substring(p);
- }
- else
- {
- seqs[n] = fullseq;
- }
- }
- return seqs;
- }
-
- /**
- *
- * @return visible number of columns in alignment view
- */
- public int getWidth()
- {
- return width;
- }
-
- protected void setWidth(int width)
- {
- this.width = width;
- }
-
- /**
- * 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 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()
- {
- 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 = (ScGroup) view.scGroups.elementAt(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++)
- {
- if (!((SeqCigar) sgr.seqs.elementAt(s)).isMemberOf(sgr))
- {
- os.println("** WARNING: sequence "
- + ((SeqCigar) sgr.seqs.elementAt(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)
- {
- SequenceGroup sg;
- Enumeration en = visal.getGroups().elements();
- int i = 1;
- while (en.hasMoreElements())
- {
- sg = (SequenceGroup) en.nextElement();
- os.println("Group " + (i++) + " begins at column "
- + sg.getStartRes() + " and ends at " + sg.getEndRes());
- }
- }
- }
- }
- }
-
- public static void testSelectionViews(AlignmentI alignment,
- ColumnSelection csel, 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, csel, 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, csel, 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, csel, 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, csel, 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, csel, 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, csel, 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, csel, 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, csel, 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.");
- }
-
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ *
+ * 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 Jalview. If not, see .
+ * 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;
+import java.util.Vector;
+
+/**
+ * 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 scGroups = null;
+
+ private boolean isNa = false;
+
+ /**
+ * 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 Vector seqs;
+
+ public SequenceGroup sg;
+
+ ScGroup()
+ {
+ seqs = new Vector();
+ }
+ }
+
+ /**
+ * vector of selected seqCigars. This vector is also referenced by each
+ * seqCigar contained in it.
+ */
+ private Vector 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,
+ ColumnSelection columnSelection, SequenceGroup selection,
+ boolean hasHiddenColumns, boolean selectedRegionOnly,
+ boolean recordGroups)
+ {
+ // refactored from AlignViewport.getAlignmentView(selectedOnly);
+ this(new jalview.datamodel.CigarArray(alignment,
+ (hasHiddenColumns ? columnSelection : 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)
+ {
+ List sel = selection.getSequences(null);
+ this.selected = new Vector();
+ selseqs = selection
+ .getSequencesInOrder(alignment, selectedRegionOnly);
+ }
+ else
+ {
+ selseqs = alignment.getSequencesArray();
+ }
+
+ List> seqsets = new ArrayList>();
+ // get the alignment's group list and make a copy
+ List grps = new ArrayList();
+ List 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 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)
+ {
+ sequences[csi].setGroupMembership(selected);
+ selected.addElement(sequences[csi]);
+ }
+ if (seqsets != null)
+ {
+ for (int sg = 0; sg < sgrps.length; sg++)
+ {
+ if ((seqsets.get(sg)).contains(selseqs[i]))
+ {
+ sequences[csi].setGroupMembership(sgrps[sg]);
+ sgrps[sg].sg.deleteSequence(selseqs[i], false);
+ sgrps[sg].seqs.addElement(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(
+ MessageManager
+ .getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
+ }
+ // 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
+ *
+ * @param sdata
+ * @param firstcol
+ */
+ public AlignmentView(CigarArray sdata, int firstcol)
+ {
+ this(sdata);
+ firstCol = firstcol;
+ }
+
+ public void setSequences(SeqCigar[] sequences)
+ {
+ this.sequences = sequences;
+ }
+
+ public void setContigs(int[] contigs)
+ {
+ this.contigs = contigs;
+ }
+
+ public SeqCigar[] getSequences()
+ {
+ return sequences;
+ }
+
+ /**
+ * @see CigarArray.getDeletedRegions
+ * @return int[] { vis_start, sym_start, length }
+ */
+ public int[] getContigs()
+ {
+ return contigs;
+ }
+
+ /**
+ * 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();
+
+ return new Object[] {
+ SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
+ contigs), colsel };
+ }
+
+ /**
+ * 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 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)
+ {
+ boolean r = false;
+ if (gstart > -1 && gstart <= gend)
+ {
+ r = true;
+ }
+
+ SequenceI[] aln = vcal.getSequencesArray();
+ {
+ /**
+ * prune any groups to the visible coordinates of the alignment.
+ */
+ {
+ int nvg = (scGroups != null) ? scGroups.size() : 0;
+ if (nvg > 0)
+ {
+ 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;
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * 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()
+ {
+ return width;
+ }
+
+ protected void setWidth(int width)
+ {
+ this.width = width;
+ }
+
+ /**
+ * 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(
+ MessageManager
+ .getString("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(
+ 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)
+ {
+ 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(
+ MessageManager
+ .getString("error.padding_not_yet_implemented"));
+ }
+ }
+ }
+ }
+ }
+ return new Object[] { alignment, columnselection };
+ }
+ 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 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 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()
+ {
+ 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++)
+ {
+ if (!((SeqCigar) sgr.seqs.elementAt(s)).isMemberOf(sgr))
+ {
+ os.println("** WARNING: sequence "
+ + ((SeqCigar) sgr.seqs.elementAt(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,
+ ColumnSelection csel, 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, csel, 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, csel, 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, csel, 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, csel, 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, csel, 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, csel, 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, csel, 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, csel, 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.");
+ }
+
+ }
+}