/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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;
* 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;
+
+ /**
+ * false if the view concerns peptides
+ *
+ * @return
+ */
+ public boolean isNa()
+ {
+ return isNa;
+ }
/**
* Group defined over SeqCigars. Unlike AlignmentI associated groups, each
(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
selseqs = alignment.getSequencesArray();
}
+ List<List<SequenceI>> seqsets=new ArrayList<List<SequenceI>>();
// get the alignment's group list and make a copy
- Vector grps = new Vector();
+ List<SequenceGroup> grps = new ArrayList<SequenceGroup>();
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<SequenceGroup>();
+ 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);
+ seqsets.set(g, sg.getSequences(null));
}
- // 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;
sequences[csi].setGroupMembership(selected);
selected.addElement(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);
{
if (scGroups == null)
{
- scGroups = new Vector();
+ scGroups = new ArrayList<ScGroup>();
}
addedgps[sg] = true;
- scGroups.addElement(sgrps[sg]);
+ scGroups.add(sgrps[sg]);
}
}
}
{
if (!seqcigararray.isSeqCigarArray())
{
- throw new Error(
- "Implementation Error - can only make an alignment view from a CigarArray of sequences.");
+ throw new Error(MessageManager.getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
}
// contigs = seqcigararray.applyDeletions();
contigs = seqcigararray.getDeletedRegions();
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 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);
}
{
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)
{
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
{
// place gaps.
- throw new Error("Padding not yet implemented.");
+ throw new Error(MessageManager.getString("error.padding_not_yet_implemented"));
}
}
}
{
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)
{
+ " 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 "
git://source.jalview.org / jalview.git / blobdiff