X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=48ebb7a0ff767d48b3496153f4a7945ea0eda871;hb=refs%2Fheads%2FJAL-3437_load_project;hp=6c08cdc50c53bb79a116f605ef1a8c89ec005f9d;hpb=3a1126a2e5ed6c1515f7c16acbc830e530811cdc;p=jalview.git diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java index 6c08cdc..48ebb7a 100644 --- a/src/jalview/datamodel/HiddenColumns.java +++ b/src/jalview/datamodel/HiddenColumns.java @@ -86,6 +86,27 @@ public class HiddenColumns */ private List hiddenColumns = new ArrayList<>(); + private BitSet hiddenBitSet; + + /** + * Returns a BitSet with a set bit for each hidden column (0, 1, ...). This is + * valid at the time of calling, but will not reflect any changes made + * afterwards. + * + * @return + */ + public BitSet getBitset() + { + if (hiddenBitSet == null) + { + hiddenBitSet = new BitSet(); + for (int[] range : hiddenColumns) + { + hiddenBitSet.set(range[0], range[1] + 1); + } + } + return hiddenBitSet; + } /** * Constructor */ @@ -213,6 +234,7 @@ public class HiddenColumns prevHiddenCount); } finally { + hiddenBitSet = null; LOCK.writeLock().unlock(); } } @@ -264,6 +286,7 @@ public class HiddenColumns insertRangeAtOverlap(i, start, end, region); added = true; } + hiddenBitSet = null; return added; } @@ -310,6 +333,7 @@ public class HiddenColumns } numColumns += region[1] - oldend; hiddenColumns.subList(i + 1, endi + 1).clear(); + hiddenBitSet = null; } /** @@ -330,6 +354,7 @@ public class HiddenColumns } finally { + hiddenBitSet = null; LOCK.writeLock().unlock(); } } @@ -356,6 +381,7 @@ public class HiddenColumns } finally { + hiddenBitSet = null; LOCK.writeLock().unlock(); } } @@ -394,13 +420,12 @@ public class HiddenColumns int colsToRemove = region[1] - region[0] + 1; hiddenColumns.remove(regionIndex); numColumns -= colsToRemove; - - cursor.updateForDeletedRegion(hiddenColumns); } } } } finally { + hiddenBitSet = null; LOCK.writeLock().unlock(); } } @@ -471,6 +496,10 @@ public class HiddenColumns } } + /** + * Answers true if obj is an instance of HiddenColumns, and holds the same + * array of start-end column ranges as this, else answers false + */ @Override public boolean equals(Object obj) { @@ -618,6 +647,7 @@ public class HiddenColumns } finally { + hiddenBitSet = null; LOCK.readLock().unlock(); } } @@ -684,16 +714,19 @@ public class HiddenColumns { LOCK.readLock().lock(); - int regionindex = cursor.findRegionForColumn(column, false) - .getRegionIndex(); - if (regionindex > -1 && regionindex < hiddenColumns.size()) + if (!hiddenColumns.isEmpty()) { - int[] region = hiddenColumns.get(regionindex); - // already know that column <= region[1] as cursor returns containing - // region or region to right - if (column >= region[0]) + int regionindex = cursor.findRegionForColumn(column, false) + .getRegionIndex(); + if (regionindex > -1 && regionindex < hiddenColumns.size()) { - return false; + int[] region = hiddenColumns.get(regionindex); + // already know that column <= region[1] as cursor returns containing + // region or region to right + if (column >= region[0]) + { + return false; + } } } return true; @@ -771,19 +804,44 @@ public class HiddenColumns */ public void hideColumns(BitSet inserts) { + hideColumns(inserts, 0, inserts.length() - 1); + } + + /** + * 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 + */ + private void hideColumns(BitSet tohide, int start, int end) + { try { LOCK.writeLock().lock(); - for (int firstSet = inserts - .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts - .nextSetBit(lastSet)) + for (int firstSet = tohide + .nextSetBit(start), lastSet = start; firstSet >= start + && lastSet <= end; firstSet = tohide + .nextSetBit(lastSet)) { - lastSet = inserts.nextClearBit(firstSet); - hideColumns(firstSet, lastSet - 1); + lastSet = tohide.nextClearBit(firstSet); + if (lastSet <= end) + { + hideColumns(firstSet, lastSet - 1); + } + else if (firstSet <= end) + { + hideColumns(firstSet, end); + } } cursor = new HiddenColumnsCursor(hiddenColumns); } finally { + hiddenBitSet = null; LOCK.writeLock().unlock(); } } @@ -791,6 +849,7 @@ public class HiddenColumns /** * Hide columns corresponding to the marked bits, within the range * [start,end]. Entries in tohide which are outside [start,end] are ignored. + * NB Existing entries in [start,end] are cleared. * * @param tohide * columns mapped to bits starting from zero @@ -799,19 +858,10 @@ public class HiddenColumns * @param end * end of range to hide columns within */ - public void hideColumns(BitSet tohide, int start, int end) + public void clearAndHideColumns(BitSet tohide, int start, int end) { clearHiddenColumnsInRange(start, end); - - // make sure only bits between start and end are set - if (!tohide.isEmpty()) - { - tohide.clear(0, start); - tohide.clear(Math.min(end + 1, tohide.length() + 1), - tohide.length() + 1); - } - - hideColumns(tohide); + hideColumns(tohide, start, end); } /** @@ -873,6 +923,7 @@ public class HiddenColumns } } finally { + hiddenBitSet = null; LOCK.writeLock().unlock(); } } @@ -888,16 +939,12 @@ public class HiddenColumns { LOCK.writeLock().lock(); - BitSet hiddenBitSet = new BitSet(); - for (int[] range : hiddenColumns) - { - hiddenBitSet.set(range[0], range[1] + 1); - } - hiddenBitSet.andNot(updates); + getBitset().andNot(updates); hiddenColumns.clear(); hideColumns(hiddenBitSet); } finally { + hiddenBitSet = null; LOCK.writeLock().unlock(); } } @@ -991,7 +1038,7 @@ public class HiddenColumns try { LOCK.readLock().lock(); - return new HiddenColsIterator(hiddenColumns); + return new RangeIterator(hiddenColumns); } finally { LOCK.readLock().unlock(); @@ -1012,7 +1059,7 @@ public class HiddenColumns try { LOCK.readLock().lock(); - return new HiddenColsIterator(start, end, hiddenColumns); + return new RangeIterator(start, end, hiddenColumns); } finally { LOCK.readLock().unlock(); @@ -1028,7 +1075,7 @@ public class HiddenColumns * @param end * position to end at (inclusive, visible column position) */ - public Iterator getBoundedStartIterator(int start, int end) + public Iterator getStartRegionIterator(int start, int end) { try { @@ -1045,7 +1092,7 @@ public class HiddenColumns HiddenCursorPosition pos = cursor .findRegionForColumn(absoluteStart - 1, false); - return new BoundedStartRegionIterator(pos, start, end, + return new StartRegionIterator(pos, start, end, hiddenColumns); } finally { @@ -1067,7 +1114,8 @@ public class HiddenColumns try { LOCK.readLock().lock(); - return new VisibleColsIterator(start, end, hiddenColumns); + return new RangeElementsIterator( + new VisibleContigsIterator(start, end + 1, hiddenColumns)); } finally { LOCK.readLock().unlock();