public class Edit
{
-- public SequenceI[] oldds;
++ private SequenceI[] oldds;
- boolean fullAlignmentHeight = false;
+ /**
+ * 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;
- Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
++ private Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
- Map<String, Annotation[]> deletedAnnotations;
- Hashtable<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;
- Hashtable<SequenceI, List<SequenceFeature>> editedFeatures;
+ /*
+ * 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;
-- int position, number;
++ private int position;
-- char gapChar;
++ private int number;
++
++ 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)
{
boolean createNewDs = false;
// TODO: take a (second look) at the dataset creation validation method for
// the very large sequence case
- int eindex = -1, sindex = -1;
- boolean ecalc = false, scalc = false;
++
+ int startIndex = findIndex(start) - 1;
+ int endIndex = findIndex(end) - 1;
+ int startDeleteColumn = -1; // for dataset sequence deletions
+ int deleteCount = 0;
+
- for (int s = i; s < j; s++)
+ for (int s = i; s < j && s < sequence.length; s++)
{
- if (!Comparison.isGap(sequence[s]))
+ if (Comparison.isGap(sequence[s]))
+ {
+ continue;
+ }
+ deleteCount++;
+ if (startDeleteColumn == -1)
+ {
+ startDeleteColumn = findPosition(s) - start;
+ }
+ if (createNewDs)
{
- if (createNewDs)
+ newend--;
+ }
+ else
+ {
+ if (startIndex == s)
{
- newend--;
+ /*
+ * deleting characters from start of sequence; new start is the
+ * sequence position of the next column (position to the right
+ * if the column position is gapped)
+ */
+ newstart = findPosition(j);
+ break;
}
else
{
}
/**
-- * @return The index (zero-based) on this sequence in the MSA. It returns
++ * @return The index (zero-based) of this sequence in the MSA. It returns
* {@code -1} if this information is not available.
*/
@Override
}
/**
-- * Defines the position of this sequence in the MSA. Use the value {@code -1}
-- * if this information is undefined.
++ * Defines the (zero-based) position of this sequence in the MSA. Use the
++ * value {@code -1} if this information is undefined.
*
-- * @param The
-- * position for this sequence. This value is zero-based (zero for
-- * this first sequence)
++ * @param value
*/
@Override
public void setIndex(int value)
/**
* Test a Paste action, where this adds sequences to an alignment.
*/
-- @Test(groups = { "Functional" }, enabled = false)
++ @Test(groups = { "Functional" }, enabled = true)
// TODO fix so it works
public void testPaste_addToAlignment()
{
* and validate the resulting remaining sequence features!
*/
SequenceI[] sqs = new SequenceI[] { seq0 };
+ boolean checkDsSize = true;
- // 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);
+ EditCommand ec = new EditCommand("Cut", Action.CUT, sqs, from, (to
+ - from + 1), alignment);
+ final String msg = String.format("Cut %d-%d ", from + 1, to + 1);
+ boolean newDatasetSequence = copySeq0.getDatasetSequence() != seq0
+ .getDatasetSequence();
- sfs = seq0.getSequenceFeatures();
+ verifyCut(seq0, from, to, msg, start);
/*
- * confirm the number of features has reduced by the
- * number of features within the cut region i.e. by
- * func(length of cut)
+ * verify copy alignment dataset sequence unaffected
*/
- String msg = String.format("Cut %d-%d ", from, to);
- if (to - from == 4)
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
+
+ if (checkDsSize)
{
- // all columns cut
- assertNull(sfs);
+ /*
+ * verify a new dataset sequence has appeared
+ */
+ assertEquals("Wrong Dataset size after cut",
+ newDatasetSequence ? 2 : 1, alignment.getDataset()
+ .getHeight());
}
- else
+ /*
+ * undo and verify all restored
+ */
+ AlignmentI[] views = new AlignmentI[] { alignment };
+ ec.undoCommand(views);
+ sfs = seq0.getSequenceFeatures();
+ assertEquals("After undo of " + msg, func(5), sfs.size());
+ verifyUndo(from, to, sfs);
+
+ /*
+ * verify copy alignment dataset sequence still unaffected
+ */
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
+
+ if (checkDsSize)
{
- assertEquals(msg + "wrong number of features left", func(5)
- - func(to - from + 1), sfs.size());
+ /*
+ * verify dataset sequence has shrunk
+ */
+ assertEquals("Wrong Dataset size after cut", 1,
+ alignment.getDataset().getHeight());
}
+
/*
- * inspect individual features
+ * redo and verify
+ */
+ ec.doCommand(views);
+ verifyCut(seq0, from, to, msg, start);
+
+ /*
+ * verify copy alignment dataset sequence unaffected
*/
- if (sfs != null)
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
+
+ if (checkDsSize)
{
- for (SequenceFeature sf : sfs)
- {
- checkFeatureRelocation(sf, from + 1, to + 1);
- }
+ /*
+ * verify a new dataset sequence has appeared again
+ */
+ assertEquals("Wrong Dataset size after cut",
+ newDatasetSequence ? 2 : 1, alignment.getDataset()
+ .getHeight());
}
++
/*
* undo ready for next cut
*/
git://source.jalview.org / jalview.git / commitdiff