/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * 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.Enumeration;
+import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
/**
* Transient object compactly representing a 'view' of an alignment - with
* one or more ScGroup objects, which are referenced by each seqCigar's group
* membership
*/
- private Vector scGroups;
+ private List<ScGroup> scGroups = null;
- private boolean isNa=false;
+ 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()
*/
private class ScGroup
{
- public Vector seqs;
+ public List<SeqCigar> seqs;
public SequenceGroup sg;
ScGroup()
{
- seqs = new Vector();
+ seqs = new ArrayList<>();
+ }
+
+ /**
+ * @param seq
+ * @return true if seq was not a member before and was added to group
+ */
+ 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 Vector selected;
+ private ScGroup selected;
/**
* Construct an alignmentView from a live jalview alignment view. Note -
* - 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)
+ 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 ? columnSelection : null),
+ (hasHiddenColumns ? hidden : null),
(selectedRegionOnly ? selection : null)),
- (selectedRegionOnly && selection != null) ? selection
- .getStartRes() : 0);
+ (selectedRegionOnly && selection != null)
+ ? selection.getStartRes()
+ : 0);
isNa = alignment.isNucleotide();
// walk down SeqCigar array and Alignment Array - optionally restricted by
// selected region.
SequenceI[] selseqs;
if (selection != null && selection.getSize() > 0)
{
- List<SequenceI> sel = selection.getSequences(null);
- this.selected = new Vector();
- selseqs = selection
- .getSequencesInOrder(alignment, selectedRegionOnly);
+ 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
- Vector grps = new Vector();
+ List<SequenceGroup> grps = new ArrayList<>();
List<SequenceGroup> gg = alignment.getGroups();
grps.addAll(gg);
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())
+ List<SequenceGroup> isg = new ArrayList<>();
+ for (SequenceGroup sg : grps)
{
- sg = (SequenceGroup) en.nextElement();
-
if (!(sg.getStartRes() > esel || sg.getEndRes() < ssel))
{
// adjust bounds of new group, if necessary.
sg.setStartRes(sg.getStartRes() - ssel + 1);
sg.setEndRes(sg.getEndRes() - ssel + 1);
- isg.addElement(sg);
+ isg.add(sg);
}
}
grps = isg;
addedgps = new boolean[grps.size()];
for (int g = 0; g < sgrps.length; g++)
{
- sg = (SequenceGroup) grps.elementAt(g);
+ SequenceGroup sg = grps.get(g);
sgrps[g] = new ScGroup();
sgrps[g].sg = new SequenceGroup(sg);
addedgps[g] = false;
- grps.setElementAt(sg.getSequences(null), g);
+ // can't set entry 0 in an empty list
+ // seqsets.set(g, sg.getSequences(null));
+ seqsets.add(sg.getSequences());
}
- // grps now contains vectors (should be sets) for each group, so we can
+ // seqsets now contains vectors (should be sets) for each group, so we can
// track when we've done with the group
}
int csi = 0;
if (selection != null && selection.getSize() > 0
&& !selectedRegionOnly)
{
- sequences[csi].setGroupMembership(selected);
- selected.addElement(sequences[csi]);
+ selected.add(sequences[csi]);
}
- if (grps != null)
+ if (seqsets != null)
{
for (int sg = 0; sg < sgrps.length; sg++)
{
- if (((Vector) grps.elementAt(sg)).contains(selseqs[i]))
+ 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]);
+ sgrps[sg].add(sequences[csi]);
if (!addedgps[sg])
{
if (scGroups == null)
{
- scGroups = new Vector();
+ scGroups = new ArrayList<>();
}
addedgps[sg] = true;
- scGroups.addElement(sgrps[sg]);
+ scGroups.add(sgrps[sg]);
}
}
}
* char
* @return Object[] { SequenceI[], ColumnSelection}
*/
- public Object[] getAlignmentAndColumnSelection(char gapCharacter)
+ public Object[] getAlignmentAndHiddenColumns(char gapCharacter)
{
- ColumnSelection colsel = new ColumnSelection();
+ HiddenColumns hidden = new HiddenColumns();
- return new Object[]
- {
- SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
- contigs), colsel };
+ return new Object[] { SeqCigar.createAlignmentSequences(sequences,
+ gapCharacter, hidden, contigs),
+ hidden };
}
/**
* - 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)
+ private void addPrunedGroupsInOrder(AlignmentI vcal, int gstart, int gend,
+ boolean viscontigs)
{
boolean r = false;
if (gstart > -1 && gstart <= gend)
SequenceGroup[] nsg = new SequenceGroup[nvg];
for (int g = 0; g < nvg; g++)
{
- SequenceGroup sg = ((ScGroup) scGroups.elementAt(g)).sg;
+ SequenceGroup sg = scGroups.get(g).sg;
if (r)
{
if (sg.getStartRes() > gend || sg.getEndRes() < gstart)
for (int h = 0; h < contigs.length; h += 3)
{
{
- prune.addShift(p + contigs[h + 1], contigs[h + 2]
- - contigs[h + 1]);
+ prune.addShift(p + contigs[h + 1],
+ contigs[h + 2] - contigs[h + 1]);
}
p = contigs[h + 1] + contigs[h + 2];
}
for (int g = 0; g < nvg; g++)
{
if (nsg[g] != null
- && sequences[nsq].isMemberOf(scGroups.elementAt(g)))
+ && sequences[nsq].isMemberOf(scGroups.get(g)))
{
nsg[g].addSequence(aln[nsq], false);
}
* 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('-');
- }
- // Remove hidden regions from sequence objects.
- String seqs[] = getSequenceStrings('-');
- for (int i = 0, j = aln.length; i < j; i++)
- {
- aln[i].setSequence(seqs[i]);
+ aln[i] = sequences[i].getSeq(c);
+ // Remove hidden regions from sequence
+ aln[i].setSequence(getASequenceString(c, i));
}
return aln;
}
}
/**
+ * 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
+ * the given gap character uses getASequenceString
*
* @param c
* char
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;
- }
+ seqs[n] = getASequenceString(c, n);
}
return seqs;
}
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++;
{
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)
{
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;
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 + ")");
+ 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.
}
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());
}
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());
}
}
// 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
}
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 };
+ return new Object[] { alignment, hidden };
}
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);
+ 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() };
+ return new Object[] { nvismsa[0], new HiddenColumns() };
}
else
{
- return getAlignmentAndColumnSelection(gapCharacter);
+ return getAlignmentAndHiddenColumns(gapCharacter);
}
}
}
if (start < fwidth)
{
viscontigs[nvis] = start;
- viscontigs[nvis + 1] = fwidth; // end is inclusive
+ viscontigs[nvis + 1] = fwidth - 1; // end is inclusive
nvis += 2;
}
return viscontigs;
}
else
{
- return new int[]
- { 0, width };
+ return new int[] { 0, width - 1 };
}
}
+ " groups defined on the view.");
for (int g = 0; g < view.scGroups.size(); g++)
{
- ScGroup sgr = (ScGroup) view.scGroups.elementAt(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))
+ // JBPnote this should be a unit test for ScGroup
+ if (!sgr.seqs.get(s).isMemberOf(sgr))
{
- os.println("** WARNING: sequence "
- + ((SeqCigar) sgr.seqs.elementAt(s)).toString()
+ os.println("** WARNING: sequence " + sgr.seqs.get(s).toString()
+ " is not marked as member of group.");
}
}
}
public static void testSelectionViews(AlignmentI alignment,
- ColumnSelection csel, SequenceGroup selection)
+ 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, csel, selection, false, false,
+ 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.");
+ 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,
+ 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.");
+ 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,
+ 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.");
+ 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,
+ 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.");
+ 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,
+ 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.");
+ 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,
+ 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.");
+ 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,
+ 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.");
+ 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);
+ 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.");
+ System.err.println(
+ "Failed to generate alignment with selection restricted and groups marked.");
}
}
git://source.jalview.org / jalview.git / blobdiff