*/
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
+ 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;
/**
*
- * Implements the SequenceI interface for a char[] based sequence object.
- *
- * @author $author$
- * @version $Revision$
+ * Implements the SequenceI interface for a char[] based sequence object
*/
public class Sequence extends ASequence implements SequenceI
{
return count;
}
+
+ @Override
+ public List<SequenceFeature[]> adjustFeatures(int fromColumn, int toColumn)
+ {
+ List<SequenceFeature[]> amended = new ArrayList<>();
+
+ if (toColumn < fromColumn)
+ {
+ return amended;
+ }
+
+ synchronized (sequenceFeatureStore)
+ {
+ /*
+ * get features that overlap or span the cut region
+ */
+ List<SequenceFeature> overlaps = findFeatures(fromColumn, toColumn);
+ int cutWidth = toColumn - fromColumn + 1;
+
+ /*
+ * get features that strictly follow the cut region,
+ * and shift them left by the width of the cut
+ */
+ List<SequenceFeature> follow = findFeatures(toColumn + 1,
+ Integer.MAX_VALUE);
+ follow.removeAll(overlaps);
+ for (SequenceFeature sf : follow)
+ {
+ SequenceFeature copy = new SequenceFeature(sf, sf.getBegin()
+ - cutWidth, sf.getEnd() - cutWidth, sf.getFeatureGroup(),
+ sf.getScore());
+ deleteFeature(sf);
+ addSequenceFeature(copy);
+ }
+
+ /*
+ * adjust start-end of overlapping features, and delete if enclosed by
+ * the cut, or a partially overlapping contact feature
+ */
+ for (SequenceFeature sf : overlaps)
+ {
+ // TODO recode to compute newBegin, newEnd, isDelete
+ // then perform the action
+ int sfBegin = sf.getBegin();
+ int sfEnd = sf.getEnd();
+ int startCol = findIndex(sfBegin);
+ int endCol = findIndex(sfEnd);
+ if (startCol >= fromColumn && endCol <= toColumn)
+ {
+ // within cut region - delete feature
+ deleteFeature(sf);
+ amended.add(new SequenceFeature[] { sf, null });
+ continue;
+ }
+ if (startCol < fromColumn && endCol > toColumn)
+ {
+ // feature spans cut region - shift end left
+ SequenceFeature copy = new SequenceFeature(sf, sf.getBegin(),
+ sf.getEnd() - cutWidth, sf.getFeatureGroup(),
+ sf.getScore());
+ deleteFeature(sf);
+ addSequenceFeature(copy);
+ amended.add(new SequenceFeature[] { sf, copy });
+ continue;
+ }
+ // todo partial overlap - delete if contact feature
+ }
+ }
+
+ return amended;
+ }
}
* @param c1
* @param c2
*/
- public int replace(char c1, char c2);
+ int replace(char c1, char c2);
+
+ /**
+ * Adjusts position and extent of features to allow for cut of the specified
+ * (inclusive) column range. Returns a list of {originalFeature,
+ * amendedFeature} for
+ * <ul>
+ * <li>features that have been deleted (as within the cut) - amendedFeature is
+ * null</li>
+ * <li>truncated features (as overlapping or spanning the cut)</li>
+ * </ul>
+ * Contact features that overlap the cut region are deleted. Contact features
+ * that enclose the cut region are shortened.
+ *
+ * @param fromColumn
+ * @param toColumn
+ * @return
+ */
+ List<SequenceFeature[]> adjustFeatures(int fromColumn, int toColumn);
}
}
/**
- * Adds the shift value to the start and end of all positional features.
- * Returns true if at least one feature was updated, else false.
+ * Adds the shift amount to the start and end of all positional features whose
+ * start position is at or after fromPosition. Returns true if at least one
+ * feature was shifted, else false.
*
- * @param shift
+ * @param fromPosition
+ * @param shiftBy
* @return
*/
- public synchronized boolean shiftFeatures(int shift)
+ public synchronized boolean shiftFeatures(int fromPosition, int shiftBy)
{
/*
* Because begin and end are final fields (to ensure the data store's
boolean modified = false;
for (SequenceFeature sf : getPositionalFeatures())
{
- modified = true;
- int newBegin = sf.getBegin() + shift;
- int newEnd = sf.getEnd() + shift;
-
- /*
- * sanity check: don't shift left of the first residue
- */
- if (newEnd > 0)
+ if (sf.getBegin() >= fromPosition)
{
- newBegin = Math.max(1, newBegin);
- SequenceFeature sf2 = new SequenceFeature(sf, newBegin, newEnd,
- sf.getFeatureGroup(), sf.getScore());
- addFeature(sf2);
+ modified = true;
+ int newBegin = sf.getBegin() + shiftBy;
+ int newEnd = sf.getEnd() + shiftBy;
+
+ /*
+ * sanity check: don't shift left of the first residue
+ */
+ if (newEnd > 0)
+ {
+ newBegin = Math.max(1, newBegin);
+ SequenceFeature sf2 = new SequenceFeature(sf, newBegin, newEnd,
+ sf.getFeatureGroup(), sf.getScore());
+ addFeature(sf2);
+ }
+ delete(sf);
}
- delete(sf);
}
return modified;
}
* {@inheritDoc}
*/
@Override
- public boolean shiftFeatures(int shift)
+ public boolean shiftFeatures(int fromPosition, int shiftBy)
{
boolean modified = false;
for (FeatureStore fs : featureStore.values())
{
- modified |= fs.shiftFeatures(shift);
+ modified |= fs.shiftFeatures(fromPosition, shiftBy);
}
return modified;
}
float getMaximumScore(String type, boolean positional);
/**
- * Adds the shift amount to the start and end of all positional features,
- * returning true if at least one feature was shifted, else false
+ * Adds the shift amount to the start and end of all positional features whose
+ * start position is at or after fromPosition. Returns true if at least one
+ * feature was shifted, else false.
*
- * @param shift
+ * @param fromPosition
+ * @param shiftBy
*/
- abstract boolean shiftFeatures(int shift);
+ boolean shiftFeatures(int fromPosition, int shiftBy);
}
\ No newline at end of file
int startShift = absStart - sequenceStart + 1;
if (startShift != 0)
{
- modified |= sequence.getFeatures().shiftFeatures(startShift);
+ modified |= sequence.getFeatures().shiftFeatures(1,
+ startShift);
}
}
}
*/
SequenceI[] sqs = new SequenceI[] { seq0 };
- // goal is to have this passing for all from/to values!!
- // for (int from = 0; from < seq0.getLength(); from++)
- // {
- // for (int to = from; to < seq0.getLength(); to++)
- for (int from = 1; from < 3; from++)
+ for (int from = 0; from < seq0.getLength(); from++)
{
- for (int to = 2; to < 3; to++)
+ for (int to = from; to < seq0.getLength(); to++)
{
testee.appendEdit(Action.CUT, sqs, from, (to - from + 1),
alignment, true);
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
import jalview.datamodel.SequenceFeature;
public void testShiftFeatures()
{
FeatureStore fs = new FeatureStore();
- assertFalse(fs.shiftFeatures(1));
+ assertFalse(fs.shiftFeatures(0, 1)); // nothing to do
SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
fs.addFeature(sf1);
fs.addFeature(sf4);
/*
- * shift features right by 5
+ * shift all features right by 5
*/
- assertTrue(fs.shiftFeatures(5));
+ assertTrue(fs.shiftFeatures(0, 5));
// non-positional features untouched:
List<SequenceFeature> nonPos = fs.getNonPositionalFeatures();
* feature at [7-10] should be removed
* feature at [13-19] should become [1-4]
*/
- assertTrue(fs.shiftFeatures(-15));
+ assertTrue(fs.shiftFeatures(0, -15));
pos = fs.getPositionalFeatures();
assertEquals(pos.size(), 2);
SequenceFeatures.sortFeatures(pos, true);
assertEquals(pos.get(0).getEnd(), 4);
assertEquals(pos.get(1).getBegin(), 13);
assertEquals(pos.get(1).getEnd(), 22);
+
+ /*
+ * shift right by 4 from position 2 onwards
+ * feature at [1-4] unchanged, feature at [13-22] shifts
+ */
+ assertTrue(fs.shiftFeatures(2, 4));
+ pos = fs.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertEquals(pos.get(0).getBegin(), 1);
+ assertEquals(pos.get(0).getEnd(), 4);
+ assertEquals(pos.get(1).getBegin(), 17);
+ assertEquals(pos.get(1).getEnd(), 26);
+
+ /*
+ * shift right by 4 from position 18 onwards
+ * should be no change
+ */
+ SequenceFeature f1 = pos.get(0);
+ SequenceFeature f2 = pos.get(1);
+ assertFalse(fs.shiftFeatures(18, 4)); // no update
+ pos = fs.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertSame(pos.get(0), f1);
+ assertSame(pos.get(1), f2);
}
}
public void testShiftFeatures()
{
SequenceFeatures store = new SequenceFeatures();
- assertFalse(store.shiftFeatures(1));
+ assertFalse(store.shiftFeatures(0, 1));
SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
store.add(sf1);
/*
* shift features right by 5
*/
- assertTrue(store.shiftFeatures(5));
+ assertTrue(store.shiftFeatures(0, 5));
// non-positional features untouched:
List<SequenceFeature> nonPos = store.getNonPositionalFeatures();
* feature at [7-10] should be removed
* feature at [13-19] should become [1-4]
*/
- assertTrue(store.shiftFeatures(-15));
+ assertTrue(store.shiftFeatures(0, -15));
pos = store.getPositionalFeatures();
assertEquals(pos.size(), 2);
SequenceFeatures.sortFeatures(pos, true);
assertEquals(pos.get(1).getBegin(), 13);
assertEquals(pos.get(1).getEnd(), 22);
assertEquals(pos.get(1).getType(), "Disulfide bond");
+
+ /*
+ * shift right by 4 from column 2
+ * feature at [1-4] should be unchanged
+ * feature at [13-22] should become [17-26]
+ */
+ assertTrue(store.shiftFeatures(2, 4));
+ pos = store.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertEquals(pos.get(0).getBegin(), 1);
+ assertEquals(pos.get(0).getEnd(), 4);
+ assertEquals(pos.get(0).getType(), "Metal");
+ assertEquals(pos.get(1).getBegin(), 17);
+ assertEquals(pos.get(1).getEnd(), 26);
+ assertEquals(pos.get(1).getType(), "Disulfide bond");
+
+ /*
+ * shift right from column 18
+ * should be no updates
+ */
+ SequenceFeature f1 = pos.get(0);
+ SequenceFeature f2 = pos.get(1);
+ assertFalse(store.shiftFeatures(18, 6));
+ pos = store.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertSame(pos.get(0), f1);
+ assertSame(pos.get(1), f2);
}
@Test(groups = "Functional")
git://source.jalview.org / jalview.git / commitdiff