*/
package jalview.commands;
+import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import jalview.util.ReverseListIterator;
import jalview.util.StringUtils;
}
command.oldds[i] = oldds;
// FIXME JAL-2541 JAL-2526 get correct positions if on a gap
- adjustFeatures(
- command,
- i,
- sequence.findPosition(command.position),
- sequence.findPosition(command.position + command.number),
- false);
+ List<SequenceFeature[]> amendedFeatures = sequence
+ .adjustFeatures(command.position, command.position
+ + command.number - 1);
+ if (command.editedFeatures == null)
+ {
+ command.editedFeatures = new HashMap<>();
+ }
+ command.editedFeatures.put(sequence, amendedFeatures);
+ //
+ // adjustFeatures(
+ // command,
+ // i,
+ // sequence.findPosition(command.position),
+ // sequence.findPosition(command.position + command.number),
+ // false);
}
}
}
{
newDSNeeded = false;
newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
- if (command.seqs[i].getLength() < 1)
+ SequenceI sequence = command.seqs[i];
+ if (sequence.getLength() < 1)
{
// ie this sequence was deleted, we need to
// readd it to the alignment
{
if (!(command.alIndex[i] < 0))
{
- sequences.add(command.alIndex[i], command.seqs[i]);
+ sequences.add(command.alIndex[i], sequence);
}
}
}
else
{
- command.al.addSequence(command.seqs[i]);
+ command.al.addSequence(sequence);
}
seqWasDeleted = true;
}
- newstart = command.seqs[i].getStart();
- newend = command.seqs[i].getEnd();
+ newstart = sequence.getStart();
+ newend = sequence.getEnd();
tmp = new StringBuffer();
- tmp.append(command.seqs[i].getSequence());
+ tmp.append(sequence.getSequence());
// Undo of a delete does not replace original dataset sequence on to
// alignment sequence.
tmp.insert(command.position, command.string[i]);
for (int s = 0; s < command.string[i].length; s++)
{
- if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
+ // if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]]
+ // != 23)
+ if (!Comparison.isGap(command.string[i][s]))
{
if (!newDSNeeded)
{
newDSNeeded = true;
- start = command.seqs[i].findPosition(command.position);
- end = command.seqs[i]
- .findPosition(command.position + command.number);
+ start = sequence.findPosition(command.position);
+ end = sequence.findPosition(command.position
+ + command.number);
}
- if (command.seqs[i].getStart() == start)
+ if (sequence.getStart() == start)
{
newstart--;
}
command.string[i] = null;
}
- command.seqs[i].setSequence(tmp.toString());
- command.seqs[i].setStart(newstart);
- command.seqs[i].setEnd(newend);
+ sequence.setSequence(tmp.toString());
+ sequence.setStart(newstart);
+ sequence.setEnd(newend);
if (newDSNeeded)
{
- if (command.seqs[i].getDatasetSequence() != null)
+ if (sequence.getDatasetSequence() != null)
{
SequenceI ds;
if (newDSWasNeeded)
{
// make a new DS sequence
// use new ds mechanism here
- ds = new Sequence(command.seqs[i].getName(),
- jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- command.seqs[i].getSequenceAsString()),
- command.seqs[i].getStart(), command.seqs[i].getEnd());
- ds.setDescription(command.seqs[i].getDescription());
+ String ungapped = AlignSeq.extractGaps(Comparison.GapChars,
+ sequence.getSequenceAsString());
+ ds = new Sequence(sequence.getName(), ungapped,
+ sequence.getStart(), sequence.getEnd());
+ ds.setDescription(sequence.getDescription());
}
if (command.oldds == null)
{
command.oldds = new SequenceI[command.seqs.length];
}
- command.oldds[i] = command.seqs[i].getDatasetSequence();
- command.seqs[i].setDatasetSequence(ds);
+ command.oldds[i] = sequence.getDatasetSequence();
+ sequence.setDatasetSequence(ds);
}
- adjustFeatures(command, i, start, end, true);
+ undoCutFeatures(command, i, start, end);
}
}
adjustAnnotations(command, true, seqWasDeleted, views);
}
}
- final static void adjustFeatures(Edit command, int index, final int i,
- final int j, boolean insert)
+ final static void undoCutFeatures(Edit command, int index, final int i,
+ final int j)
{
SequenceI seq = command.seqs[index];
SequenceI sequence = seq.getDatasetSequence();
sequence = seq;
}
- if (insert)
+ /*
+ * insert == true for an Undo of a Cut; restore the original features
+ * and delete the amended ones
+ */
+ if (true)
{
+ // TODO shift right features that lie to the right of the restored cut
+ // (add a start position parameter to SequenceFeatures.shift)
+
if (command.editedFeatures != null
&& command.editedFeatures.containsKey(seq))
{
- sequence.setSequenceFeatures(command.editedFeatures.get(seq));
+ for (SequenceFeature[] toRestore : command.editedFeatures.get(seq))
+ {
+ sequence.addSequenceFeature(toRestore[0]);
+ if (toRestore[1] != null)
+ {
+ sequence.deleteFeature(toRestore[1]);
+ }
+ }
}
-
return;
}
- List<SequenceFeature> sf = sequence.getFeatures()
- .getPositionalFeatures();
-
- if (sf.isEmpty())
- {
- return;
- }
-
- List<SequenceFeature> oldsf = new ArrayList<SequenceFeature>();
-
- int cSize = j - i;
-
- for (SequenceFeature feature : sf)
- {
- SequenceFeature copy = new SequenceFeature(feature);
-
- oldsf.add(copy);
-
- if (feature.getEnd() < i)
- {
- continue;
- }
-
- if (feature.getBegin() > j)
- {
- int newBegin = copy.getBegin() - cSize;
- int newEnd = copy.getEnd() - cSize;
- SequenceFeature newSf = new SequenceFeature(feature, newBegin,
- newEnd, feature.getFeatureGroup(), feature.getScore());
- sequence.deleteFeature(feature);
- sequence.addSequenceFeature(newSf);
- // feature.setBegin(newBegin);
- // feature.setEnd(newEnd);
- continue;
- }
-
- int newBegin = feature.getBegin();
- int newEnd = feature.getEnd();
- if (newBegin >= i)
- {
- newBegin = i;
- // feature.setBegin(i);
- }
-
- if (newEnd < j)
- {
- newEnd = j - 1;
- // feature.setEnd(j - 1);
- }
- newEnd = newEnd - cSize;
- // feature.setEnd(feature.getEnd() - (cSize));
-
- sequence.deleteFeature(feature);
- if (newEnd >= newBegin)
- {
- sequence.addSequenceFeature(new SequenceFeature(feature, newBegin,
- newEnd, feature.getFeatureGroup(), feature.getScore()));
- }
- // if (feature.getBegin() > feature.getEnd())
- // {
- // sequence.deleteFeature(feature);
- // }
- }
-
- if (command.editedFeatures == null)
- {
- command.editedFeatures = new Hashtable<SequenceI, List<SequenceFeature>>();
- }
-
- command.editedFeatures.put(seq, oldsf);
+ // List<SequenceFeature> sf = sequence.getFeatures()
+ // .getPositionalFeatures();
+ //
+ // if (sf.isEmpty())
+ // {
+ // return;
+ // }
+ //
+ // List<SequenceFeature> oldsf = new ArrayList<SequenceFeature>();
+ //
+ // int cSize = j - i;
+ //
+ // for (SequenceFeature feature : sf)
+ // {
+ // SequenceFeature copy = new SequenceFeature(feature);
+ //
+ // oldsf.add(copy);
+ //
+ // if (feature.getEnd() < i)
+ // {
+ // continue;
+ // }
+ //
+ // if (feature.getBegin() > j)
+ // {
+ // int newBegin = copy.getBegin() - cSize;
+ // int newEnd = copy.getEnd() - cSize;
+ // SequenceFeature newSf = new SequenceFeature(feature, newBegin,
+ // newEnd, feature.getFeatureGroup(), feature.getScore());
+ // sequence.deleteFeature(feature);
+ // sequence.addSequenceFeature(newSf);
+ // // feature.setBegin(newBegin);
+ // // feature.setEnd(newEnd);
+ // continue;
+ // }
+ //
+ // int newBegin = feature.getBegin();
+ // int newEnd = feature.getEnd();
+ // if (newBegin >= i)
+ // {
+ // newBegin = i;
+ // // feature.setBegin(i);
+ // }
+ //
+ // if (newEnd < j)
+ // {
+ // newEnd = j - 1;
+ // // feature.setEnd(j - 1);
+ // }
+ // newEnd = newEnd - cSize;
+ // // feature.setEnd(feature.getEnd() - (cSize));
+ //
+ // sequence.deleteFeature(feature);
+ // if (newEnd >= newBegin)
+ // {
+ // sequence.addSequenceFeature(new SequenceFeature(feature, newBegin,
+ // newEnd, feature.getFeatureGroup(), feature.getScore()));
+ // }
+ // // if (feature.getBegin() > feature.getEnd())
+ // // {
+ // // sequence.deleteFeature(feature);
+ // // }
+ // }
+ //
+ // if (command.editedFeatures == null)
+ // {
+ // command.editedFeatures = new Hashtable<SequenceI,
+ // List<SequenceFeature>>();
+ // }
+ //
+ // command.editedFeatures.put(seq, oldsf);
}
boolean fullAlignmentHeight = false;
- Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
+ Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
- Hashtable<String, Annotation[]> deletedAnnotations;
+ Map<String, Annotation[]> deletedAnnotations;
- Hashtable<SequenceI, List<SequenceFeature>> editedFeatures;
+ Map<SequenceI, List<SequenceFeature[]>> editedFeatures;
AlignmentI al;
git://source.jalview.org / jalview.git / blobdiff