import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.Range;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
import jalview.util.Comparison;
import jalview.util.ReverseListIterator;
import jalview.util.StringUtils;
int position, int number, AlignmentI al, boolean performEdit,
AlignmentI[] views)
{
- Edit edit = new Edit(command, seqs, position, number,
- al.getGapCharacter());
- if (al.getHeight() == seqs.length)
- {
- edit.al = al;
- edit.fullAlignmentHeight = true;
- }
-
- addEdit(edit);
-
- if (performEdit)
- {
- performEdit(edit, views);
- }
+ Edit edit = new Edit(command, seqs, position, number, al);
+ appendEdit(edit, al, performEdit, views);
}
/**
// we are redoing an undone cut.
sequence.setDatasetSequence(null);
}
- sequence.deleteChars(command.position,
+ Range cutPositions = sequence.findPositions(command.position + 1,
command.position + command.number);
+ boolean cutIsInternal = cutPositions != null
+ && sequence.getStart() != cutPositions
+ .getBegin() && sequence.getEnd() != cutPositions.getEnd();
+ sequence.deleteChars(command.position, command.position
+ + command.number);
+
if (command.oldds != null && command.oldds[i] != null)
{
// oldds entry contains the cut dataset sequence.
command.oldds = new SequenceI[command.seqs.length];
}
command.oldds[i] = oldds;
- // FIXME JAL-2541 JAL-2526 get correct positions if on a gap
- List<SequenceFeature[]> amendedFeatures = sequence
- .adjustFeatures(command.position, command.position
- + command.number - 1);
- if (command.editedFeatures == null)
+ if (oldds != sequence.getDatasetSequence())
{
- command.editedFeatures = new HashMap<>();
+ oldds.getFeatures().deleteAll();
+ }
+
+ if (cutPositions != null)
+ {
+ cutFeatures(command, sequence, cutPositions.getBegin(),
+ cutPositions.getEnd(), cutIsInternal);
}
- command.editedFeatures.put(sequence, amendedFeatures);
- //
- // adjustFeatures(
- // command,
- // i,
- // sequence.findPosition(command.position),
- // sequence.findPosition(command.position + command.number),
- // false);
}
}
}
*/
static void paste(Edit command, AlignmentI[] views)
{
- StringBuffer tmp;
- boolean newDSNeeded;
- boolean newDSWasNeeded;
- int newstart, newend;
boolean seqWasDeleted = false;
- int start = 0, end = 0;
for (int i = 0; i < command.seqs.length; i++)
{
- newDSNeeded = false;
- newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
+ boolean newDSNeeded = false;
+ boolean newDSWasNeeded = command.oldds != null
+ && command.oldds[i] != null;
SequenceI sequence = command.seqs[i];
if (sequence.getLength() < 1)
{
- // ie this sequence was deleted, we need to
- // readd it to the alignment
+ /*
+ * sequence was deleted; re-add it to the alignment
+ */
if (command.alIndex[i] < command.al.getHeight())
{
List<SequenceI> sequences;
}
seqWasDeleted = true;
}
- newstart = sequence.getStart();
- newend = sequence.getEnd();
+ int newStart = sequence.getStart();
+ int newEnd = sequence.getEnd();
- tmp = new StringBuffer();
+ StringBuilder tmp = new StringBuilder();
tmp.append(sequence.getSequence());
// Undo of a delete does not replace original dataset sequence on to
// alignment sequence.
+ int start = 0;
+ int length = 0;
+
if (command.string != null && command.string[i] != null)
{
if (command.position >= tmp.length())
{
// This occurs if padding is on, and residues
// are removed from end of alignment
- int length = command.position - tmp.length();
- while (length > 0)
+ int len = command.position - tmp.length();
+ while (len > 0)
{
tmp.append(command.gapChar);
- length--;
+ len--;
}
}
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 (!Comparison.isGap(command.string[i][s]))
{
+ length++;
if (!newDSNeeded)
{
newDSNeeded = true;
start = sequence.findPosition(command.position);
- end = sequence.findPosition(command.position
- + command.number);
+ // end = sequence
+ // .findPosition(command.position + command.number);
}
if (sequence.getStart() == start)
{
- newstart--;
+ newStart--;
}
else
{
- newend++;
+ newEnd++;
}
}
}
}
sequence.setSequence(tmp.toString());
- sequence.setStart(newstart);
- sequence.setEnd(newend);
+ sequence.setStart(newStart);
+ sequence.setEnd(newEnd);
+
+ /*
+ * command and Undo share the same dataset sequence if cut was
+ * at start or end of sequence
+ */
+ boolean sameDatasetSequence = false;
if (newDSNeeded)
{
if (sequence.getDatasetSequence() != null)
command.oldds = new SequenceI[command.seqs.length];
}
command.oldds[i] = sequence.getDatasetSequence();
+ sameDatasetSequence = ds == sequence.getDatasetSequence();
+ ds.setSequenceFeatures(sequence.getSequenceFeatures());
sequence.setDatasetSequence(ds);
}
- undoCutFeatures(command, i, start, end);
+ undoCutFeatures(command, command.seqs[i], start, length,
+ sameDatasetSequence);
}
}
adjustAnnotations(command, true, seqWasDeleted, views);
tmp.append(oldstring.substring(end));
command.seqs[i].setSequence(tmp.toString());
command.string[i] = oldstring.substring(start, end).toCharArray();
- String nogapold = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
+ String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
new String(command.string[i]));
if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
{
}
// and then duplicate added annotation on every other alignment
// view
- for (int vnum = 0; views != null
- && vnum < views.length; vnum++)
+ for (int vnum = 0; views != null && vnum < views.length; vnum++)
{
if (views[vnum] != command.al)
{
}
}
- final static void undoCutFeatures(Edit command, int index, final int i,
- final int j)
+ /**
+ * Restores features to the state before a Cut.
+ * <ul>
+ * <li>re-add any features deleted by the cut</li>
+ * <li>remove any truncated features created by the cut</li>
+ * <li>shift right any features to the right of the cut</li>
+ * </ul>
+ *
+ * @param command
+ * the Cut command
+ * @param seq
+ * the sequence the Cut applied to
+ * @param start
+ * the start residue position of the cut
+ * @param length
+ * the number of residues cut
+ * @param sameDatasetSequence
+ * true if dataset sequence and frame of reference were left
+ * unchanged by the Cut
+ */
+ final static void undoCutFeatures(Edit command, SequenceI seq,
+ final int start, final int length, boolean sameDatasetSequence)
{
- SequenceI seq = command.seqs[index];
SequenceI sequence = seq.getDatasetSequence();
if (sequence == null)
{
}
/*
- * insert == true for an Undo of a Cut; restore the original features
- * and delete the amended ones
+ * shift right features that lie to the right of the restored cut (but not
+ * if dataset sequence unchanged - so coordinates were changed by Cut)
*/
- if (true)
+ if (!sameDatasetSequence)
{
- // TODO shift right features that lie to the right of the restored cut
- // (add a start position parameter to SequenceFeatures.shift)
+ /*
+ * shift right all features right of and not
+ * contiguous with the cut position
+ */
+ seq.getFeatures().shiftFeatures(start + 1, length);
- if (command.editedFeatures != null
- && command.editedFeatures.containsKey(seq))
+ /*
+ * shift right any features that start at the cut position,
+ * unless they were truncated
+ */
+ List<SequenceFeature> sfs = seq.findFeatures(start, start);
+ for (SequenceFeature sf : sfs)
{
- for (SequenceFeature[] toRestore : command.editedFeatures.get(seq))
+ if (sf.getBegin() == start)
{
- sequence.addSequenceFeature(toRestore[0]);
- if (toRestore[1] != null)
+ if (!command.truncatedFeatures.containsKey(seq)
+ || !command.truncatedFeatures.get(seq).contains(sf))
{
- sequence.deleteFeature(toRestore[1]);
+ /*
+ * feature was shifted left to cut position (not truncated),
+ * so shift it back right
+ */
+ SequenceFeature shifted = new SequenceFeature(sf, sf.getBegin()
+ + length, sf.getEnd() + length, sf.getFeatureGroup(),
+ sf.getScore());
+ seq.addSequenceFeature(shifted);
+ seq.deleteFeature(sf);
}
}
}
- 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);
+ /*
+ * restore any features that were deleted or truncated
+ */
+ if (command.deletedFeatures != null
+ && command.deletedFeatures.containsKey(seq))
+ {
+ for (SequenceFeature deleted : command.deletedFeatures.get(seq))
+ {
+ sequence.addSequenceFeature(deleted);
+ }
+ }
+ /*
+ * delete any truncated features
+ */
+ if (command.truncatedFeatures != null
+ && command.truncatedFeatures.containsKey(seq))
+ {
+ for (SequenceFeature amended : command.truncatedFeatures.get(seq))
+ {
+ sequence.deleteFeature(amended);
+ }
+ }
}
/**
Map<String, Annotation[]> deletedAnnotations;
- Map<SequenceI, List<SequenceFeature[]>> editedFeatures;
+ /*
+ * features deleted by the cut (re-add on Undo)
+ * (including the original of any shortened features)
+ */
+ Map<SequenceI, List<SequenceFeature>> deletedFeatures;
+
+ /*
+ * shortened features added by the cut (delete on Undo)
+ */
+ Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
AlignmentI al;
Edit(Action cmd, SequenceI[] sqs, int pos, int count,
AlignmentI align)
{
- this.gapChar = align.getGapCharacter();
- this.command = cmd;
- this.seqs = sqs;
- this.position = pos;
- this.number = count;
+ this(cmd, sqs, pos, count, align.getGapCharacter());
+
this.al = align;
alIndex = new int[sqs.length];
Edit(Action cmd, SequenceI[] sqs, int pos, int count,
AlignmentI align, String replace)
{
- this.command = cmd;
- this.seqs = sqs;
- this.position = pos;
- this.number = count;
- this.al = align;
- this.gapChar = align.getGapCharacter();
+ this(cmd, sqs, pos, count, align);
+
string = new char[sqs.length][];
for (int i = 0; i < sqs.length; i++)
{
string[i] = replace.toCharArray();
}
-
- fullAlignmentHeight = (align.getHeight() == sqs.length);
}
public SequenceI[] getSequences()
return new ReverseListIterator<Edit>(getEdits());
}
}
+
+ /**
+ * Adjusts features for Cut, and saves details of changes made to allow Undo
+ * <ul>
+ * <li>features left of the cut are unchanged</li>
+ * <li>features right of the cut are shifted left</li>
+ * <li>features internal to the cut region are deleted</li>
+ * <li>features that overlap or span the cut are shortened</li>
+ * <li>the originals of any deleted or shorted features are saved, to re-add
+ * on Undo</li>
+ * <li>any added (shortened) features are saved, to delete on Undo</li>
+ * </ul>
+ *
+ * @param command
+ * @param seq
+ * @param fromPosition
+ * @param toPosition
+ * @param cutIsInternal
+ */
+ protected static void cutFeatures(Edit command, SequenceI seq,
+ int fromPosition, int toPosition, boolean cutIsInternal)
+ {
+ if (!cutIsInternal)
+ {
+ return;
+ }
+ List<SequenceFeature> added = new ArrayList<>();
+ List<SequenceFeature> removed = new ArrayList<>();
+
+ SequenceFeaturesI featureStore = seq.getFeatures();
+ if (toPosition < fromPosition || featureStore == null)
+ {
+ return;
+ }
+
+ int cutStartPos = fromPosition;
+ int cutEndPos = toPosition;
+ int cutWidth = cutEndPos - cutStartPos + 1;
+
+ synchronized (featureStore)
+ {
+ /*
+ * get features that overlap the cut region
+ */
+ List<SequenceFeature> toAmend = featureStore.findFeatures(
+ cutStartPos, cutEndPos);
+
+ /*
+ * add any contact features that span the cut region
+ * (not returned by findFeatures)
+ */
+ for (SequenceFeature contact : featureStore.getContactFeatures())
+ {
+ if (contact.getBegin() < cutStartPos
+ && contact.getEnd() > cutEndPos)
+ {
+ toAmend.add(contact);
+ }
+ }
+
+ /*
+ * adjust start-end of overlapping features;
+ * delete features enclosed by the cut;
+ * delete partially overlapping contact features
+ */
+ for (SequenceFeature sf : toAmend)
+ {
+ int sfBegin = sf.getBegin();
+ int sfEnd = sf.getEnd();
+ int newBegin = sfBegin;
+ int newEnd = sfEnd;
+ boolean toDelete = false;
+ boolean follows = false;
+
+ if (sfBegin >= cutStartPos && sfEnd <= cutEndPos)
+ {
+ /*
+ * feature lies within cut region - delete it
+ */
+ toDelete = true;
+ }
+ else if (sfBegin < cutStartPos && sfEnd > cutEndPos)
+ {
+ /*
+ * feature spans cut region - left-shift the end
+ */
+ newEnd -= cutWidth;
+ }
+ else if (sfEnd <= cutEndPos)
+ {
+ /*
+ * feature overlaps left of cut region - truncate right
+ */
+ newEnd = cutStartPos - 1;
+ if (sf.isContactFeature())
+ {
+ toDelete = true;
+ }
+ }
+ else if (sfBegin >= cutStartPos)
+ {
+ /*
+ * remaining case - feature overlaps right
+ * truncate left, adjust end of feature
+ */
+ newBegin = cutIsInternal ? cutStartPos : cutEndPos + 1;
+ newEnd = newBegin + sfEnd - cutEndPos - 1;
+ if (sf.isContactFeature())
+ {
+ toDelete = true;
+ }
+ }
+
+ seq.deleteFeature(sf);
+ if (!follows)
+ {
+ removed.add(sf);
+ }
+ if (!toDelete)
+ {
+ SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
+ sf.getFeatureGroup(), sf.getScore());
+ seq.addSequenceFeature(copy);
+ if (!follows)
+ {
+ added.add(copy);
+ }
+ }
+ }
+
+ /*
+ * and left shift any features lying to the right of the cut region
+ * (but not if the cut is at start or end of sequence)
+ */
+ if (cutIsInternal)
+ {
+ featureStore.shiftFeatures(cutEndPos + 1, -cutWidth);
+ }
+ }
+
+ /*
+ * save deleted and amended features, so that Undo can
+ * re-add or delete them respectively
+ */
+ if (command.deletedFeatures == null)
+ {
+ command.deletedFeatures = new HashMap<>();
+ }
+ if (command.truncatedFeatures == null)
+ {
+ command.truncatedFeatures = new HashMap<>();
+ }
+ command.deletedFeatures.put(seq, removed);
+ command.truncatedFeatures.put(seq, added);
+ }
}
git://source.jalview.org / jalview.git / blobdiff