currentPosition++;
return currentRegion;
}
+
+ @Override
+ public void remove()
+ {
+ localHidden.remove(--currentPosition);
+ }
}
* Hide columns corresponding to the marked bits
*
* @param inserts
- * - columns map to bits starting from zero
+ * - columns mapped to bits starting from zero
*/
public void hideColumns(BitSet inserts)
{
}
/**
+ * Hide columns corresponding to the marked bits, within the range
+ * [start,end]. Entries in tohide which are outside [start,end] are ignored.
+ *
+ * @param tohide
+ * columns mapped to bits starting from zero
+ * @param start
+ * start of range to hide columns within
+ * @param end
+ * end of range to hide columns within
+ */
+ public void hideColumns(BitSet tohide, int start, int end)
+ {
+ clearHiddenColumnsInRange(start, end);
+
+ // make sure only bits between start and end are set
+ tohide.clear(0, start - 1);
+ tohide.clear(Math.min(end + 1, tohide.length() - 1),
+ tohide.length() - 1);
+
+ hideColumns(tohide);
+ }
+
+ /**
+ * Make all columns in the range [start,end] visible
+ *
+ * @param start
+ * start of range to show columns
+ * @param end
+ * end of range to show columns
+ */
+ private void clearHiddenColumnsInRange(int start, int end)
+ {
+ try
+ {
+ LOCK.writeLock().lock();
+
+ HiddenCursorPosition pos = cursor.findRegionForColumn(start);
+ int index = pos.getRegionIndex();
+ int startindex = index; // first index in hiddenColumns to remove
+
+ if (index != -1 && index != hiddenColumns.size())
+ {
+ // regionIndex is the region which either contains start
+ // or lies to the right of start
+ int[] region = hiddenColumns.get(index);
+ if (region[0] < start && region[1] >= start)
+ {
+ // region contains start, truncate so that it ends just before start
+ region[1] = start - 1;
+ startindex++;
+ }
+ }
+
+ pos = cursor.findRegionForColumn(end);
+ index = pos.getRegionIndex();
+ int endindex = index - 1; // last index in hiddenColumns to remove
+
+ if (index != -1 && index != hiddenColumns.size())
+ {
+ // regionIndex is the region which either contains end
+ // or lies to the right of end
+ int[] region = hiddenColumns.get(index);
+ if (region[0] <= end && region[1] > end)
+ {
+ // region contains end, truncate so that it starts just after end
+ region[0] = end + 1;
+ }
+ }
+
+ hiddenColumns.subList(startindex, endindex + 1).clear();
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
+ }
+
+ /**
*
* @param inserts
* BitSet where hidden columns will be marked
protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
{
-
- HiddenColumns hidden = new HiddenColumns();
- BitSet inserts = new BitSet(), mask = new BitSet();
-
- // set mask to preserve existing hidden columns outside selected group
- if (ap.av.hasHiddenColumns())
- {
- ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
- }
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+ BitSet inserts = new BitSet();
boolean markedPopup = false;
// mark inserts in current selection
{
// mark just the columns in the selection group to be hidden
inserts.set(ap.av.getSelectionGroup().getStartRes(),
- ap.av.getSelectionGroup().getEndRes() + 1);
-
- // and clear that part of the mask
- mask.andNot(inserts);
+ ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
// now clear columns without gaps
for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
}
inserts.and(sq.getInsertionsAsBits());
}
- }
- else
- {
- // initially, mark all columns to be hidden
- inserts.set(0, ap.av.getAlignment().getWidth());
-
- // and clear out old hidden regions completely
- mask.clear();
+ hidden.hideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes());
}
// now mark for sequence under popup if we haven't already done it
- if (!markedPopup && sequence != null)
+ else if (!markedPopup && sequence != null)
{
- inserts.and(sequence.getInsertionsAsBits());
- }
+ inserts.or(sequence.getInsertionsAsBits());
- // finally, preserve hidden regions outside selection
- inserts.or(mask);
-
- // and set hidden columns accordingly
- hidden.hideColumns(inserts);
-
- ap.av.getAlignment().setHiddenColumns(hidden);
+ // and set hidden columns accordingly
+ hidden.hideColumns(inserts);
+ }
refresh();
}
// get sequences from the alignment
List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
- // get the Popup Menu for first sequence - no insertions
- testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), null);
- testee.hideInsertions_actionPerformed(null);
-
- HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
- Iterator<int[]> it = hidden.iterator();
- assertFalse(it.hasNext());
-
+ // add our own seqs to avoid problems with changes to existing sequences
+ // (gap at end of sequences varies depending on how tests are run!)
Sequence seqGap1 = new Sequence("GappySeq",
"AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
seqGap1.createDatasetSequence();
"AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
seqGap2.createDatasetSequence();
seqs.add(seqGap2);
- Sequence seqGap3 = new Sequence("OneGapSeq",
+ Sequence seqGap3 = new Sequence("AnotherGapSeq",
"AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
seqGap3.createDatasetSequence();
seqs.add(seqGap3);
+ Sequence seqGap4 = new Sequence("NoGaps",
+ "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
+ seqGap4.createDatasetSequence();
+ seqs.add(seqGap4);
+
+ ColumnSelection sel = new ColumnSelection();
+ parentPanel.av.getAlignment().getHiddenColumns()
+ .revealAllHiddenColumns(sel);
+
+ // get the Popup Menu for 7th sequence - no insertions
+ testee = new PopupMenu(parentPanel, (Sequence) seqs.get(7), null);
+ testee.hideInsertions_actionPerformed(null);
+
+ HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
+ Iterator<int[]> it = hidden.iterator();
+ assertFalse(it.hasNext());
// get the Popup Menu for GappySeq - this time we have insertions
testee = new PopupMenu(parentPanel, (Sequence) seqs.get(4), null);
assertFalse(it.hasNext());
- ColumnSelection sel = new ColumnSelection();
+ sel = new ColumnSelection();
hidden.revealAllHiddenColumns(sel);
// make a sequence group and hide insertions within the group
git://source.jalview.org / jalview.git / commitdiff