boolean cutIsInternal = cutPositions != null
&& sequence.getStart() != cutPositions
.getBegin() && sequence.getEnd() != cutPositions.getEnd();
+
+ /*
+ * perform the cut; if this results in a new dataset sequence, add
+ * that to the alignment dataset
+ */
+ SequenceI ds = sequence.getDatasetSequence();
sequence.deleteChars(command.position, command.position
+ command.number);
+ SequenceI newDs = sequence.getDatasetSequence();
+ if (newDs != ds && command.al != null
+ && command.al.getDataset() != null
+ && !command.al.getDataset().getSequences().contains(newDs))
+ {
+ command.al.getDataset().addSequence(newDs);
+ }
if (command.oldds != null && command.oldds[i] != null)
{
{
command.oldds = new SequenceI[command.seqs.length];
}
- command.oldds[i] = oldds;
+ command.oldds[i] = oldds;// todo not if !cutIsInternal?
// do we need to edit sequence features for new sequence ?
if (oldds != sequence.getDatasetSequence()
|| (cutIsInternal
&& sequence.getFeatures().hasFeatures()))
+ // todo or just test cutIsInternal && cutPositions != null ?
{
if (cutPositions != null)
{
{
tmp.append(oldstring.substring(end));
}
+ // stash end prior to updating the sequence object so we can save it if
+ // need be.
+ Range oldstartend = new Range(command.seqs[i].getStart(),
+ command.seqs[i].getEnd());
command.seqs[i].setSequence(tmp.toString());
command.string[i] = oldstring
.substring(start, Math.min(end, oldstring.length()))
if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
{
- // probably need a new dataset sequence
- if (newDSWasNeeded)
+ // we may already have dataset and limits stashed...
+ if (newDSWasNeeded || newStartEndWasNeeded)
{
+ if (newDSWasNeeded)
+ {
// then just switch the dataset sequence
SequenceI oldds = command.seqs[i].getDatasetSequence();
command.seqs[i].setDatasetSequence(command.oldds[i]);
command.oldds[i] = oldds;
- }
- else
- if (newStartEndWasNeeded)
- {
- Range newStart = command.oldStartEnd[i];
- command.oldStartEnd[i] = new Range(command.seqs[i].getStart(),
- command.seqs[i].getEnd());
- command.seqs[i].setStart(newStart.getBegin());
- command.seqs[i].setEnd(newStart.getEnd());
+ }
+ if (newStartEndWasNeeded)
+ {
+ Range newStart = command.oldStartEnd[i];
+ command.oldStartEnd[i] = oldstartend;
+ command.seqs[i].setStart(newStart.getBegin());
+ command.seqs[i].setEnd(newStart.getEnd());
+ }
}
else
{
+ // decide if we need a new dataset sequence or modify start/end
// first edit the original dataset sequence string
SequenceI oldds = command.seqs[i].getDatasetSequence();
- String fullseq, osp = oldds.getSequenceAsString();
+ String osp = oldds.getSequenceAsString();
- fullseq = osp.substring(0, ipos) + nogaprep
+ String fullseq = osp.substring(0, ipos) + nogaprep
+ osp.substring(ipos + nogaprep.length());
// and check if new sequence data is different..
{
// modification at end
command.seqs[i].setEnd(
- beforeEditedPositions.getEnd() + nogaprep.length());
+ beforeEditedPositions.getEnd() + nogaprep.length()
+ - nogapold.length());
}
else if (afterEditedPositions != null
&& beforeEditedPositions == null)
public class Edit
{
- public SequenceI[] oldds;
+ private SequenceI[] oldds;
/**
* start and end of sequence prior to edit
*/
- public Range[] oldStartEnd;
+ private Range[] oldStartEnd;
- boolean fullAlignmentHeight = false;
+ private boolean fullAlignmentHeight = false;
- Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
+ private Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
- Map<String, Annotation[]> deletedAnnotations;
+ private Map<String, Annotation[]> deletedAnnotations;
/*
* features deleted by the cut (re-add on Undo)
* (including the original of any shortened features)
*/
- Map<SequenceI, List<SequenceFeature>> deletedFeatures;
+ private Map<SequenceI, List<SequenceFeature>> deletedFeatures;
/*
* shortened features added by the cut (delete on Undo)
*/
- Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
+ private Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
- AlignmentI al;
+ private AlignmentI al;
- Action command;
+ final private Action command;
char[][] string;
SequenceI[] seqs;
- int[] alIndex;
+ private int[] alIndex;
+
+ private int position;
- int position, number;
+ private int number;
- char gapChar;
+ private char gapChar;
public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
char gap)
fullAlignmentHeight = (align.getHeight() == sqs.length);
}
+ /**
+ * Constructor given a REPLACE command and the replacement string
+ *
+ * @param cmd
+ * @param sqs
+ * @param pos
+ * @param count
+ * @param align
+ * @param replace
+ */
Edit(Action cmd, SequenceI[] sqs, int pos, int count,
AlignmentI align, String replace)
{
* <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
+ * <li>the originals of any deleted or shortened features are saved, to re-add
* on Undo</li>
* <li>any added (shortened) features are saved, to delete on Undo</li>
* </ul>
protected static void cutFeatures(Edit command, SequenceI seq,
int fromPosition, int toPosition, boolean cutIsInternal)
{
- /* if the cut is at start or end of sequence
- * then we don't modify the seuqence feature store
+ /*
+ * if the cut is at start or end of sequence
+ * then we don't modify the sequence feature store
*/
if (!cutIsInternal)
{
git://source.jalview.org / jalview.git / blobdiff