/**
* append a new editCommand
* Note. this shouldn't be called if the edit is an operation affects more alignment objects than the one referenced
- * in al (for example, cut or pasting whole sequences). Use the form with an additional AlignmentI[] views parameter.
+ * in al (for example, cut or pasting whole sequences). Use the form with an additional AlignmentI[] views parameter.
* @param command
* @param seqs
* @param position
final void insertGap(Edit command)
{
+
for (int s = 0; s < command.seqs.length; s++)
{
command.seqs[s].insertCharAt(command.position,
{
command.string[i] = command.seqs[i].getSequence(command.position,
command.position + command.number);
-
- if (command.seqs[i].getDatasetSequence() != null
- || command.seqs[i].getSequenceFeatures() != null)
+ SequenceI oldds = command.seqs[i].getDatasetSequence();
+ if (command.oldds!=null && command.oldds[i]!=null)
{
- for (int s = command.position; s < command.position + command.number;
- s++)
+ // we are redoing an undone cut.
+ command.seqs[i].setDatasetSequence(null);
+ }
+ command.seqs[i].deleteChars(command.position,
+ command.position + command.number);
+ if (command.oldds!=null && command.oldds[i]!=null)
+ {
+ // oldds entry contains the cut dataset sequence.
+ command.seqs[i].setDatasetSequence(command.oldds[i]);
+ command.oldds[i] = oldds;
+ } else {
+ // modify the oldds if necessary
+ if (oldds!=command.seqs[i].getDatasetSequence()
+ || command.seqs[i].getSequenceFeatures() != null)
{
- if (jalview.schemes.ResidueProperties
- .aaIndex[command.seqs[i].getCharAt(s)] != 23)
+ if (command.oldds==null)
{
- adjustFeatures(command, i,
- command.seqs[i].findPosition(command.position),
- command.seqs[i].findPosition(command.position +
- command.number),
- false);
- break;
+ command.oldds = new SequenceI[command.seqs.length];
}
+ command.oldds[i] = oldds;
+ adjustFeatures(command, i,
+ command.seqs[i].findPosition(command.position),
+ command.seqs[i].findPosition(command.position +
+ command.number),
+ false);
}
}
- command.seqs[i].deleteChars(command.position,
- command.position + command.number);
}
if (command.seqs[i].getLength() < 1)
{
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;
if (command.seqs[i].getLength() < 1)
{
// ie this sequence was deleted, we need to
}
seqWasDeleted=true;
}
+ newstart = command.seqs[i].getStart();
+ newend = command.seqs[i].getEnd();
+
tmp = new StringBuffer();
tmp.append(command.seqs[i].getSequence());
-
+ //Undo of a delete does not replace original dataset sequence on to alignment sequence.
+
if (command.string != null && command.string[i] != null)
{
if (command.position >= tmp.length())
}
}
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)
{
- newDSNeeded = true;
- start = command.seqs[i].findPosition(command.position);
- end = command.seqs[i].findPosition(command.position +
+ if (!newDSNeeded)
+ {
+ newDSNeeded = true;
+ start = command.seqs[i].findPosition(command.position);
+ end = command.seqs[i].findPosition(command.position +
command.number);
- break;
+ }
+ if (command.seqs[i].getStart()==start)
+ newstart--;
+ else
+ newend++;
}
}
command.string[i] = null;
}
command.seqs[i].setSequence(tmp.toString());
-
+ command.seqs[i].setStart(newstart);
+ command.seqs[i].setEnd(newend);
if (newDSNeeded)
{
if (command.seqs[i].getDatasetSequence() != null)
- { // use new ds mechanism here
- Sequence ds = new Sequence(command.seqs[i].getName(),
+ {
+ SequenceI ds;
+ if (newDSWasNeeded)
+ {
+ ds = command.oldds[i];
+ } else {
+ // 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());
+ ds.setDescription(command.seqs[i].getDescription());
+ }
+ if (command.oldds==null)
+ {
+ command.oldds = new SequenceI[command.seqs.length];
+ }
+ command.oldds[i]=command.seqs[i].getDatasetSequence();
command.seqs[i].setDatasetSequence(ds);
}
-
adjustFeatures(command, i, start, end, true);
}
}
final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility, AlignmentI[] views)
{
-
AlignmentAnnotation[] annotations = null;
if (modifyVisibility && !insert)
}
command.seqs[s].setAlignmentAnnotation(null);
if (alen!=tmp.length)
- {
+ {
// save the non-null annotation references only
AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
for (int aa=0,aapos=0;aa<tmp.length;aa++)
Annotation[] temp;
for (int a = 0; a < annotations.length; a++)
{
- if (annotations[a].autoCalculated)
+ if (annotations[a].autoCalculated || annotations[a].annotations == null)
{
continue;
}
int tSize = 0;
- if (annotations[a].annotations == null)
- {
- // nothing to edit here ?
- continue;
- }
+
aSize = annotations[a].annotations.length;
if (insert)
{
{
if (command.position < aSize)
{
- if (command.position + command.number > aSize)
+ if (command.position + command.number >= aSize)
{
tSize = aSize;
}
else
{
- tSize = aSize - command.number + command.position;
+ tSize = aSize - command.number;
}
}
else
tSize = aSize;
}
temp = new Annotation[tSize];
-
}
+
if (insert)
{
if (command.position < annotations[a].annotations.length)
class Edit
{
+ public SequenceI[] oldds;
boolean fullAlignmentHeight = false;
Hashtable deletedAnnotationRows;
Hashtable deletedAnnotations;
git://source.jalview.org / jalview.git / blobdiff