{
}
- public EditCommand(String description)
+ public EditCommand(String desc)
{
- this.description = description;
+ this.description = desc;
}
- public EditCommand(String description, Action command, SequenceI[] seqs,
+ public EditCommand(String desc, Action command, SequenceI[] seqs,
int position, int number, AlignmentI al)
{
- this.description = description;
+ this.description = desc;
if (command == Action.CUT || command == Action.PASTE)
{
setEdit(new Edit(command, seqs, position, number, al));
performEdit(0, null);
}
- public EditCommand(String description, Action command, String replace,
+ public EditCommand(String desc, Action command, String replace,
SequenceI[] seqs, int position, int number, AlignmentI al)
{
- this.description = description;
+ this.description = desc;
if (command == Action.REPLACE)
{
setEdit(new Edit(command, seqs, position, number, al, replace));
{
// modify the oldds if necessary
if (oldds != sequence.getDatasetSequence()
- || sequence.getSequenceFeatures() != null)
+ || sequence.getFeatures().hasFeatures())
{
if (command.oldds == null)
{
command.oldds = new SequenceI[command.seqs.length];
}
command.oldds[i] = oldds;
- adjustFeatures(command, i,
+ // 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),
+ sequence.findPosition(command.position + command.number),
false);
}
}
AlignmentAnnotation[] tmp;
for (int s = 0; s < command.seqs.length; s++)
{
+ command.seqs[s].sequenceChanged();
+
if (modifyVisibility)
{
// Rows are only removed or added to sequence object.
}
}
- final static void adjustFeatures(Edit command, int index, int i, int j,
- boolean insert)
+ final static void adjustFeatures(Edit command, int index, final int i,
+ final int j, boolean insert)
{
SequenceI seq = command.seqs[index];
SequenceI sequence = seq.getDatasetSequence();
return;
}
- SequenceFeature[] sf = sequence.getSequenceFeatures();
+ List<SequenceFeature> sf = sequence.getFeatures()
+ .getPositionalFeatures();
- if (sf == null)
+ if (sf.isEmpty())
{
return;
}
- SequenceFeature[] oldsf = new SequenceFeature[sf.length];
+ List<SequenceFeature> oldsf = new ArrayList<SequenceFeature>();
int cSize = j - i;
- for (int s = 0; s < sf.length; s++)
+ for (SequenceFeature feature : sf)
{
- SequenceFeature copy = new SequenceFeature(sf[s]);
+ SequenceFeature copy = new SequenceFeature(feature);
- oldsf[s] = copy;
+ oldsf.add(copy);
- if (sf[s].getEnd() < i)
+ if (feature.getEnd() < i)
{
continue;
}
- if (sf[s].getBegin() > j)
+ if (feature.getBegin() > j)
{
- sf[s].setBegin(copy.getBegin() - cSize);
- sf[s].setEnd(copy.getEnd() - cSize);
+ 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;
}
- if (sf[s].getBegin() >= i)
+ int newBegin = feature.getBegin();
+ int newEnd = feature.getEnd();
+ if (newBegin >= i)
{
- sf[s].setBegin(i);
+ newBegin = i;
+ // feature.setBegin(i);
}
- if (sf[s].getEnd() < j)
+ if (newEnd < j)
{
- sf[s].setEnd(j - 1);
+ newEnd = j - 1;
+ // feature.setEnd(j - 1);
}
+ newEnd = newEnd - cSize;
+ // feature.setEnd(feature.getEnd() - (cSize));
- sf[s].setEnd(sf[s].getEnd() - (cSize));
-
- if (sf[s].getBegin() > sf[s].getEnd())
+ sequence.deleteFeature(feature);
+ if (newEnd >= newBegin)
{
- sequence.deleteFeature(sf[s]);
+ 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, SequenceFeature[]>();
+ command.editedFeatures = new Hashtable<SequenceI, List<SequenceFeature>>();
}
command.editedFeatures.put(seq, oldsf);
Hashtable<String, Annotation[]> deletedAnnotations;
- Hashtable<SequenceI, SequenceFeature[]> editedFeatures;
+ Hashtable<SequenceI, List<SequenceFeature>> editedFeatures;
AlignmentI al;
char gapChar;
- public Edit(Action command, SequenceI[] seqs, int position, int number,
- char gapChar)
+ public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
+ char gap)
{
- this.command = command;
- this.seqs = seqs;
- this.position = position;
- this.number = number;
- this.gapChar = gapChar;
+ this.command = cmd;
+ this.seqs = sqs;
+ this.position = pos;
+ this.number = count;
+ this.gapChar = gap;
}
- Edit(Action command, SequenceI[] seqs, int position, int number,
- AlignmentI al)
+ Edit(Action cmd, SequenceI[] sqs, int pos, int count,
+ AlignmentI align)
{
- this.gapChar = al.getGapCharacter();
- this.command = command;
- this.seqs = seqs;
- this.position = position;
- this.number = number;
- this.al = al;
-
- alIndex = new int[seqs.length];
- for (int i = 0; i < seqs.length; i++)
+ this.gapChar = align.getGapCharacter();
+ this.command = cmd;
+ this.seqs = sqs;
+ this.position = pos;
+ this.number = count;
+ this.al = align;
+
+ alIndex = new int[sqs.length];
+ for (int i = 0; i < sqs.length; i++)
{
- alIndex[i] = al.findIndex(seqs[i]);
+ alIndex[i] = align.findIndex(sqs[i]);
}
- fullAlignmentHeight = (al.getHeight() == seqs.length);
+ fullAlignmentHeight = (align.getHeight() == sqs.length);
}
- Edit(Action command, SequenceI[] seqs, int position, int number,
- AlignmentI al, String replace)
+ Edit(Action cmd, SequenceI[] sqs, int pos, int count,
+ AlignmentI align, String replace)
{
- this.command = command;
- this.seqs = seqs;
- this.position = position;
- this.number = number;
- this.al = al;
- this.gapChar = al.getGapCharacter();
- string = new char[seqs.length][];
- for (int i = 0; i < seqs.length; i++)
+ this.command = cmd;
+ this.seqs = sqs;
+ this.position = pos;
+ this.number = count;
+ this.al = align;
+ this.gapChar = align.getGapCharacter();
+ string = new char[sqs.length][];
+ for (int i = 0; i < sqs.length; i++)
{
string[i] = replace.toCharArray();
}
- fullAlignmentHeight = (al.getHeight() == seqs.length);
+ fullAlignmentHeight = (align.getHeight() == sqs.length);
}
public SequenceI[] getSequences()
git://source.jalview.org / jalview.git / blobdiff