X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=4d69fa4ef3ea1355c83ca89ffe2454d9c4ed20d2;hb=536a4a9c407a4c07b71e86e75135eaa2ba5e8850;hp=97955701204e99265fb89dde14d7149077bf2fa1;hpb=dd85e0fbce881a3c71ad20026311a28a10eb12de;p=jalview.git diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index 9795570..4d69fa4 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -28,31 +28,67 @@ import java.util.ArrayList; import java.util.BitSet; import java.util.Collections; import java.util.List; -import java.util.Vector; /** - * NOTE: Columns are zero based. + * Data class holding the selected columns and hidden column ranges for a view. + * Ranges are base 1. */ public class ColumnSelection { + /** + * A class to hold an efficient representation of selected columns + */ private class IntList { /* * list of selected columns (ordered by selection order, not column order) */ - private List order = new ArrayList(); + private List order; + + /* + * an unmodifiable view of the selected columns list + */ + private List _uorder; /** * bitfield for column selection - allows quick lookup */ - private BitSet selected = new BitSet(); + private BitSet selected; + + /** + * Constructor + */ + IntList() + { + order = new ArrayList(); + _uorder = Collections.unmodifiableList(order); + selected = new BitSet(); + } + + /** + * Copy constructor + * + * @param other + */ + IntList(IntList other) + { + this(); + if (other != null) + { + int j = other.size(); + for (int i = 0; i < j; i++) + { + add(other.elementAt(i)); + } + } + } /** * adds a new column i to the selection - only if i is not already selected * * @param i */ - public void add(int i) + void add(int i) { if (!selected.get(i)) { @@ -61,13 +97,13 @@ public class ColumnSelection } } - public void clear() + void clear() { order.clear(); selected.clear(); } - public void remove(int col) + void remove(int col) { Integer colInt = new Integer(col); @@ -82,22 +118,27 @@ public class ColumnSelection } } - public boolean contains(Integer colInt) + boolean contains(Integer colInt) { return selected.get(colInt); } - public boolean isEmpty() + boolean isEmpty() { return order.isEmpty(); } - public List getList() + /** + * Returns a read-only view of the selected columns list + * + * @return + */ + List getList() { - return order; + return _uorder; } - public int size() + int size() { return order.size(); } @@ -108,7 +149,7 @@ public class ColumnSelection * @param i * @return */ - public int elementAt(int i) + int elementAt(int i) { return order.get(i); } @@ -151,7 +192,7 @@ public class ColumnSelection * @param change * - delta for shift */ - public void compensateForEdits(int start, int change) + void compensateForEdits(int start, int change) { BitSet mask = new BitSet(); for (int i = 0; i < order.size(); i++) @@ -169,14 +210,63 @@ public class ColumnSelection // lastly update the bitfield all at once selected.or(mask); } + + boolean isSelected(int column) + { + return selected.get(column); + } + + int getMaxColumn() + { + return selected.length() - 1; + } + + int getMinColumn() + { + return selected.get(0) ? 0 : selected.nextSetBit(0); + } + + /** + * @return a series of selection intervals along the range + */ + List getRanges() + { + List rlist = new ArrayList(); + if (selected.isEmpty()) + { + return rlist; + } + int next = selected.nextSetBit(0), clear = -1; + while (next != -1) + { + clear = selected.nextClearBit(next); + rlist.add(new int[] { next, clear - 1 }); + next = selected.nextSetBit(clear); + } + return rlist; + } + + @Override + public int hashCode() + { + // TODO Auto-generated method stub + return selected.hashCode(); + } + + @Override + public boolean equals(Object obj) + { + if (obj instanceof IntList) + { + return ((IntList) obj).selected.equals(selected); + } + return false; + } } - IntList selected = new IntList(); - /* - * list of hidden column [start, end] ranges; the list is maintained in - * ascending start column order - */ - Vector hiddenColumns; + IntList selection = new IntList(); + + HiddenColumns hiddenColumns = new HiddenColumns(); /** * Add a column to the selection @@ -186,7 +276,7 @@ public class ColumnSelection */ public void addElement(int col) { - selected.add(col); + selection.add(col); } /** @@ -194,7 +284,7 @@ public class ColumnSelection */ public void clear() { - selected.clear(); + selection.clear(); } /** @@ -205,7 +295,7 @@ public class ColumnSelection */ public void removeElement(int col) { - selected.remove(col); + selection.remove(col); } /** @@ -222,20 +312,35 @@ public class ColumnSelection for (int i = start; i < end; i++) { colInt = new Integer(i); - if (selected.contains(colInt)) + if (selection.contains(colInt)) { - selected.remove(colInt); + selection.remove(colInt); } } } /** - * Returns a list of selected columns. The list contains no duplicates but is - * not necessarily ordered. + * Returns a read-only view of the (possibly empty) list of selected columns + *

+ * The list contains no duplicates but is not necessarily ordered. It also may + * include columns hidden from the current view. To modify (for example sort) + * the list, you should first make a copy. + *

+ * The list is not thread-safe: iterating over it could result in + * ConcurrentModificationException if it is modified by another thread. */ public List getSelected() { - return selected.getList(); + return selection.getList(); + } + + /** + * @return list of int arrays containing start and end column position for + * runs of selected columns ordered from right to left. + */ + public List getSelectedRanges() + { + return selection.getRanges(); } /** @@ -243,11 +348,11 @@ public class ColumnSelection * @param col * index to search for in column selection * - * @return true if Integer(col) is in selection. + * @return true if col is selected */ public boolean contains(int col) { - return selected.contains(new Integer(col)); + return (col > -1) ? selection.isSelected(col) : false; } /** @@ -255,7 +360,7 @@ public class ColumnSelection */ public boolean isEmpty() { - return selected == null || selected.isEmpty(); + return selection == null || selection.isEmpty(); } /** @@ -265,17 +370,11 @@ public class ColumnSelection */ public int getMax() { - int max = -1; - - for (int sel : getSelected()) + if (selection.isEmpty()) { - if (sel > max) - { - max = sel; - } + return -1; } - - return max; + return selection.getMaxColumn(); } /** @@ -285,17 +384,11 @@ public class ColumnSelection */ public int getMin() { - int min = 1000000000; - - for (int sel : getSelected()) + if (selection.isEmpty()) { - if (sel < min) - { - min = sel; - } + return 1000000000; } - - return min; + return selection.getMinColumn(); } /** @@ -306,47 +399,12 @@ public class ColumnSelection * @param left * shift in edit (+ve for removal, or -ve for inserts) */ - public List compensateForEdit(int start, int change) - { - List deletedHiddenColumns = null; - selected.compensateForEdits(start, change); - - if (hiddenColumns != null) + /* public List compensateForEdit(int start, int change) { - deletedHiddenColumns = new ArrayList(); - int hSize = hiddenColumns.size(); - for (int i = 0; i < hSize; i++) - { - int[] region = hiddenColumns.elementAt(i); - if (region[0] > start && start + change > region[1]) - { - deletedHiddenColumns.add(region); - - hiddenColumns.removeElementAt(i); - i--; - hSize--; - continue; - } - - if (region[0] > start) - { - region[0] -= change; - region[1] -= change; - } - - if (region[0] < 0) - { - region[0] = 0; - } - - } - - this.revealHiddenColumns(0); + selection.compensateForEdits(start, change); + return hiddenColumns.compensateForEdit(start, change, this); } - - return deletedHiddenColumns; - } - + */ /** * propagate shift in alignment columns to column selection special version of * compensateForEdit - allowing for edits within hidden regions @@ -358,37 +416,8 @@ public class ColumnSelection */ private void compensateForDelEdits(int start, int change) { - - selected.compensateForEdits(start, change); - - if (hiddenColumns != null) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - if (region[0] >= start) - { - region[0] -= change; - } - if (region[1] >= start) - { - region[1] -= change; - } - if (region[1] < region[0]) - { - hiddenColumns.removeElementAt(i--); - } - - if (region[0] < 0) - { - region[0] = 0; - } - if (region[1] < 0) - { - region[1] = 0; - } - } - } + selection.compensateForEdits(start, change); + hiddenColumns.compensateForDelEdits(start, change); } /** @@ -398,7 +427,7 @@ public class ColumnSelection * @param shiftrecord * @return */ - public ShiftList compensateForEdits(ShiftList shiftrecord) + private ShiftList compensateForEdits(ShiftList shiftrecord) { if (shiftrecord != null) { @@ -409,7 +438,6 @@ public class ColumnSelection for (int i = 0, j = shifts.size(); i < j; i++) { int[] sh = shifts.get(i); - // compensateForEdit(shifted+sh[0], sh[1]); compensateForDelEdits(shifted + sh[0], sh[1]); shifted -= sh[1]; } @@ -419,100 +447,6 @@ public class ColumnSelection return null; } - /** - * removes intersection of position,length ranges in deletions from the - * start,end regions marked in intervals. - * - * @param shifts - * @param intervals - * @return - */ - private boolean pruneIntervalVector(final List shifts, - Vector intervals) - { - boolean pruned = false; - int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1; - int hr[] = intervals.elementAt(i); - int sr[] = shifts.get(s); - while (i <= j && s <= t) - { - boolean trailinghn = hr[1] >= sr[0]; - if (!trailinghn) - { - if (i < j) - { - hr = intervals.elementAt(++i); - } - else - { - i++; - } - continue; - } - int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert - if (endshift < hr[0] || endshift < sr[0]) - { // leadinghc disjoint or not a deletion - if (s < t) - { - sr = shifts.get(++s); - } - else - { - s++; - } - continue; - } - boolean leadinghn = hr[0] >= sr[0]; - boolean leadinghc = hr[0] < endshift; - boolean trailinghc = hr[1] < endshift; - if (leadinghn) - { - if (trailinghc) - { // deleted hidden region. - intervals.removeElementAt(i); - pruned = true; - j--; - if (i <= j) - { - hr = intervals.elementAt(i); - } - continue; - } - if (leadinghc) - { - hr[0] = endshift; // clip c terminal region - leadinghn = !leadinghn; - pruned = true; - } - } - if (!leadinghn) - { - if (trailinghc) - { - if (trailinghn) - { - hr[1] = sr[0] - 1; - pruned = true; - } - } - else - { - // sr contained in hr - if (s < t) - { - sr = shifts.get(++s); - } - else - { - s++; - } - continue; - } - } - } - return pruned; // true if any interval was removed or modified by - // operations. - } /** * remove any hiddenColumns or selected columns and shift remaining based on a @@ -520,28 +454,21 @@ public class ColumnSelection * * @param deletions */ - public void pruneDeletions(ShiftList deletions) + private void pruneDeletions(ShiftList deletions) { if (deletions != null) { final List shifts = deletions.getShifts(); if (shifts != null && shifts.size() > 0) { - // delete any intervals intersecting. - if (hiddenColumns != null) - { - pruneIntervalVector(shifts, hiddenColumns); - if (hiddenColumns != null && hiddenColumns.size() == 0) - { - hiddenColumns = null; - } - } - if (selected != null && selected.size() > 0) + hiddenColumns.pruneDeletions(shifts); + + if (selection != null && selection.size() > 0) { - selected.pruneColumnList(shifts); - if (selected != null && selected.size() == 0) + selection.pruneColumnList(shifts); + if (selection != null && selection.size() == 0) { - selected = null; + selection = null; } } // and shift the rest. @@ -550,225 +477,20 @@ public class ColumnSelection } } - /** - * This Method is used to return all the HiddenColumn regions - * - * @return empty list or List of hidden column intervals - */ - public List getHiddenColumns() - { - return hiddenColumns == null ? Collections. emptyList() - : hiddenColumns; - } - /** - * Return absolute column index for a visible column index - * - * @param column - * int column index in alignment view - * @return alignment column index for column - */ - public int adjustForHiddenColumns(int column) + public void hideSelectedColumns(AlignmentI al) { - int result = column; - if (hiddenColumns != null) + synchronized (selection) { - for (int i = 0; i < hiddenColumns.size(); i++) + for (int[] selregions : selection.getRanges()) { - int[] region = hiddenColumns.elementAt(i); - if (result >= region[0]) - { - result += region[1] - region[0] + 1; - } + al.getHiddenColumns().hideColumns(selregions[0], selregions[1]); } + selection.clear(); } - return result; - } - /** - * Use this method to find out where a column will appear in the visible - * alignment when hidden columns exist. If the column is not visible, then the - * left-most visible column will always be returned. - * - * @param hiddenColumn - * int - * @return int - */ - public int findColumnPosition(int hiddenColumn) - { - int result = hiddenColumn; - if (hiddenColumns != null) - { - int index = 0; - int[] region; - do - { - region = hiddenColumns.elementAt(index++); - if (hiddenColumn > region[1]) - { - result -= region[1] + 1 - region[0]; - } - } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size())); - if (hiddenColumn > region[0] && hiddenColumn < region[1]) - { - return region[0] + hiddenColumn - result; - } - } - return result; // return the shifted position after removing hidden columns. } - /** - * Use this method to determine where the next hiddenRegion starts - */ - public int findHiddenRegionPosition(int hiddenRegion) - { - int result = 0; - if (hiddenColumns != null) - { - int index = 0; - int gaps = 0; - do - { - int[] region = hiddenColumns.elementAt(index); - if (hiddenRegion == 0) - { - return region[0]; - } - - gaps += region[1] + 1 - region[0]; - result = region[1] + 1; - index++; - } while (index < hiddenRegion + 1); - - result -= gaps; - } - - return result; - } - - /** - * THis method returns the rightmost limit of a region of an alignment with - * hidden columns. In otherwords, the next hidden column. - * - * @param index - * int - */ - public int getHiddenBoundaryRight(int alPos) - { - if (hiddenColumns != null) - { - int index = 0; - do - { - int[] region = hiddenColumns.elementAt(index); - if (alPos < region[0]) - { - return region[0]; - } - - index++; - } while (index < hiddenColumns.size()); - } - - return alPos; - - } - - /** - * This method returns the leftmost limit of a region of an alignment with - * hidden columns. In otherwords, the previous hidden column. - * - * @param index - * int - */ - public int getHiddenBoundaryLeft(int alPos) - { - if (hiddenColumns != null) - { - int index = hiddenColumns.size() - 1; - do - { - int[] region = hiddenColumns.elementAt(index); - if (alPos > region[1]) - { - return region[1]; - } - - index--; - } while (index > -1); - } - - return alPos; - - } - - public void hideSelectedColumns() - { - while (!selected.isEmpty()) - { - int column = selected.elementAt(0); - hideColumns(column); - } - - } - - /** - * Adds the specified column range to the hidden columns - * - * @param start - * @param end - */ - public void hideColumns(int start, int end) - { - if (hiddenColumns == null) - { - hiddenColumns = new Vector(); - } - - /* - * traverse existing hidden ranges and insert / amend / append as - * appropriate - */ - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - - if (end < region[0] - 1) - { - /* - * insert discontiguous preceding range - */ - hiddenColumns.insertElementAt(new int[] { start, end }, i); - return; - } - - if (end <= region[1]) - { - /* - * new range overlaps existing, or is contiguous preceding it - adjust - * start column - */ - region[0] = Math.min(region[0], start); - return; - } - - if (start <= region[1] + 1) - { - /* - * new range overlaps existing, or is contiguous following it - adjust - * start and end columns - */ - region[0] = Math.min(region[0], start); - region[1] = Math.max(region[1], end); - return; - } - } - - /* - * remaining case is that the new range follows everything else - */ - hiddenColumns.addElement(new int[] { start, end }); - } /** * Hides the specified column and any adjacent selected columns @@ -776,7 +498,7 @@ public class ColumnSelection * @param res * int */ - public void hideColumns(int col) + public void hideSelectedColumns(int col, HiddenColumns hidden) { /* * deselect column (whether selected or not!) @@ -809,72 +531,12 @@ public class ColumnSelection min = max; } - hideColumns(min, max); + hidden.hideColumns(min, max); } - /** - * Unhides, and adds to the selection list, all hidden columns - */ - public void revealAllHiddenColumns() - { - if (hiddenColumns != null) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - for (int j = region[0]; j < region[1] + 1; j++) - { - addElement(j); - } - } - } - hiddenColumns = null; - } - /** - * Reveals, and marks as selected, the hidden column range with the given - * start column - * - * @param start - */ - public void revealHiddenColumns(int start) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - if (start == region[0]) - { - for (int j = region[0]; j < region[1] + 1; j++) - { - addElement(j); - } - - hiddenColumns.removeElement(region); - break; - } - } - if (hiddenColumns.size() == 0) - { - hiddenColumns = null; - } - } - - public boolean isVisible(int column) - { - if (hiddenColumns != null) - { - for (int[] region : hiddenColumns) - { - if (column >= region[0] && column <= region[1]) - { - return false; - } - } - } - return true; - } /** * Copy constructor @@ -885,29 +547,7 @@ public class ColumnSelection { if (copy != null) { - if (copy.selected != null) - { - selected = new IntList(); - for (int i = 0, j = copy.selected.size(); i < j; i++) - { - selected.add(copy.selected.elementAt(i)); - } - } - if (copy.hiddenColumns != null) - { - hiddenColumns = new Vector(copy.hiddenColumns.size()); - for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++) - { - int[] rh, cp; - rh = copy.hiddenColumns.elementAt(i); - if (rh != null) - { - cp = new int[rh.length]; - System.arraycopy(rh, 0, cp, 0, rh.length); - hiddenColumns.addElement(cp); - } - } - } + selection = new IntList(copy.selection); } } @@ -918,234 +558,10 @@ public class ColumnSelection { } - public String[] getVisibleSequenceStrings(int start, int end, - SequenceI[] seqs) - { - int i, iSize = seqs.length; - String selection[] = new String[iSize]; - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - for (i = 0; i < iSize; i++) - { - StringBuffer visibleSeq = new StringBuffer(); - List regions = getHiddenColumns(); - - int blockStart = start, blockEnd = end; - int[] region; - int hideStart, hideEnd; - - for (int j = 0; j < regions.size(); j++) - { - region = regions.get(j); - hideStart = region[0]; - hideEnd = region[1]; - - if (hideStart < start) - { - continue; - } - - blockStart = Math.min(blockStart, hideEnd + 1); - blockEnd = Math.min(blockEnd, hideStart); - - if (blockStart > blockEnd) - { - break; - } - - visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd)); - - blockStart = hideEnd + 1; - blockEnd = end; - } - - if (end > blockStart) - { - visibleSeq.append(seqs[i].getSequence(blockStart, end)); - } - - selection[i] = visibleSeq.toString(); - } - } - else - { - for (i = 0; i < iSize; i++) - { - selection[i] = seqs[i].getSequenceAsString(start, end); - } - } - - return selection; - } - - /** - * return all visible segments between the given start and end boundaries - * - * @param start - * (first column inclusive from 0) - * @param end - * (last column - not inclusive) - * @return int[] {i_start, i_end, ..} where intervals lie in - * start<=i_start<=i_end 0) - { - List visiblecontigs = new ArrayList(); - List regions = getHiddenColumns(); - int vstart = start; - int[] region; - int hideStart, hideEnd; - for (int j = 0; vstart < end && j < regions.size(); j++) - { - region = regions.get(j); - hideStart = region[0]; - hideEnd = region[1]; - if (hideEnd < vstart) - { - continue; - } - if (hideStart > vstart) - { - visiblecontigs.add(new int[] { vstart, hideStart - 1 }); - } - vstart = hideEnd + 1; - } - - if (vstart < end) - { - visiblecontigs.add(new int[] { vstart, end - 1 }); - } - int[] vcontigs = new int[visiblecontigs.size() * 2]; - for (int i = 0, j = visiblecontigs.size(); i < j; i++) - { - int[] vc = visiblecontigs.get(i); - visiblecontigs.set(i, null); - vcontigs[i * 2] = vc[0]; - vcontigs[i * 2 + 1] = vc[1]; - } - visiblecontigs.clear(); - return vcontigs; - } - else - { - return new int[] { start, end - 1 }; - } - } - /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). - * - * @param alignmentAnnotation - */ - public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation) - { - makeVisibleAnnotation(-1, -1, alignmentAnnotation); - } - - /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). - * - * @param start - * remove any annotation to the right of this column - * @param end - * remove any annotation to the left of this column - * @param alignmentAnnotation - * the annotation to operate on - */ - public void makeVisibleAnnotation(int start, int end, - AlignmentAnnotation alignmentAnnotation) - { - if (alignmentAnnotation.annotations == null) - { - return; - } - if (start == end && end == -1) - { - start = 0; - end = alignmentAnnotation.annotations.length; - } - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - // then mangle the alignmentAnnotation annotation array - Vector annels = new Vector(); - Annotation[] els = null; - List regions = getHiddenColumns(); - int blockStart = start, blockEnd = end; - int[] region; - int hideStart, hideEnd, w = 0; - - for (int j = 0; j < regions.size(); j++) - { - region = regions.get(j); - hideStart = region[0]; - hideEnd = region[1]; - - if (hideStart < start) - { - continue; - } - - blockStart = Math.min(blockStart, hideEnd + 1); - blockEnd = Math.min(blockEnd, hideStart); - - if (blockStart > blockEnd) - { - break; - } - - annels.addElement(els = new Annotation[blockEnd - blockStart]); - System.arraycopy(alignmentAnnotation.annotations, blockStart, els, - 0, els.length); - w += els.length; - blockStart = hideEnd + 1; - blockEnd = end; - } - - if (end > blockStart) - { - annels.addElement(els = new Annotation[end - blockStart + 1]); - if ((els.length + blockStart) <= alignmentAnnotation.annotations.length) - { - // copy just the visible segment of the annotation row - System.arraycopy(alignmentAnnotation.annotations, blockStart, - els, 0, els.length); - } - else - { - // copy to the end of the annotation row - System.arraycopy(alignmentAnnotation.annotations, blockStart, - els, 0, - (alignmentAnnotation.annotations.length - blockStart)); - } - w += els.length; - } - if (w == 0) - { - return; - } - - alignmentAnnotation.annotations = new Annotation[w]; - w = 0; - - for (Annotation[] chnk : annels) - { - System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, - chnk.length); - w += chnk.length; - } - } - else - { - alignmentAnnotation.restrict(start, end); - } - } /** * Invert the column selection from first to end-1. leaves hiddenColumns @@ -1154,9 +570,9 @@ public class ColumnSelection * @param first * @param end */ - public void invertColumnSelection(int first, int width) + public void invertColumnSelection(int first, int width, AlignmentI al) { - boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0; + boolean hasHidden = al.getHiddenColumns().hasHidden(); for (int i = first; i < width; i++) { if (contains(i)) @@ -1165,7 +581,7 @@ public class ColumnSelection } else { - if (!hasHidden || isVisible(i)) + if (!hasHidden || al.getHiddenColumns().isVisible(i)) { addElement(i); } @@ -1185,9 +601,10 @@ public class ColumnSelection { for (Integer col : colsel.getSelected()) { - if (hiddenColumns != null && isVisible(col.intValue())) + if (hiddenColumns != null + && hiddenColumns.isVisible(col.intValue())) { - selected.add(col); + selection.add(col); } } } @@ -1201,10 +618,10 @@ public class ColumnSelection */ public void setElementsFrom(ColumnSelection colsel) { - selected = new IntList(); - if (colsel.selected != null && colsel.selected.size() > 0) + selection = new IntList(); + if (colsel.selection != null && colsel.selection.size() > 0) { - if (hiddenColumns != null && hiddenColumns.size() > 0) + if (hiddenColumns.hasHidden()) { // only select visible columns in this columns selection addElementsFrom(colsel); @@ -1240,7 +657,7 @@ public class ColumnSelection // return propagateInsertions(profileseq, al, ) char gc = al.getGapCharacter(); - Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc); + Object[] alandcolsel = input.getAlignmentAndHiddenColumns(gc); ColumnSelection nview = (ColumnSelection) alandcolsel[1]; SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos]; nview.propagateInsertions(profileseq, al, origseq); @@ -1257,18 +674,18 @@ public class ColumnSelection * - sequence corresponding to profileseq which defines gap map for * modifying al */ - public void propagateInsertions(SequenceI profileseq, AlignmentI al, + private void propagateInsertions(SequenceI profileseq, AlignmentI al, SequenceI origseq) { char gc = al.getGapCharacter(); // recover mapping between sequence's non-gap positions and positions // mapping to view. pruneDeletions(ShiftList.parseMap(origseq.gapMap())); - int[] viscontigs = getVisibleContigs(0, profileseq.getLength()); + int[] viscontigs = hiddenColumns.getVisibleContigs(0, + profileseq.getLength()); int spos = 0; int offset = 0; - // input.pruneDeletions(ShiftList.parseMap(((SequenceI[]) - // alandcolsel[0])[0].gapMap())) + // add profile to visible contigs for (int v = 0; v < viscontigs.length; v += 2) { @@ -1369,46 +786,17 @@ public class ColumnSelection */ public boolean hasSelectedColumns() { - return (selected != null && selected.size() > 0); + return (selection != null && selection.size() > 0); } - /** - * - * @return true if there are columns hidden - */ - public boolean hasHiddenColumns() - { - return hiddenColumns != null && hiddenColumns.size() > 0; - } - - /** - * - * @return true if there are more than one set of columns hidden - */ - public boolean hasManyHiddenColumns() - { - return hiddenColumns != null && hiddenColumns.size() > 1; - } - /** - * mark the columns corresponding to gap characters as hidden in the column - * selection - * - * @param sr - */ - public void hideInsertionsFor(SequenceI sr) - { - List inserts = sr.getInsertions(); - for (int[] r : inserts) - { - hideColumns(r[0], r[1]); - } - } public boolean filterAnnotations(Annotation[] annotations, AnnotationFilterParameter filterParams) { - this.revealAllHiddenColumns(); + // JBPNote - this method needs to be refactored to become independent of + // viewmodel package + hiddenColumns.revealAllHiddenColumns(this); this.clear(); int count = 0; do @@ -1489,4 +877,171 @@ public class ColumnSelection } while (count < annotations.length); return false; } + + /** + * Returns a hashCode built from selected columns and hidden column ranges + */ + @Override + public int hashCode() + { + int hashCode = selection.hashCode(); + return hiddenColumns.hashCode(hashCode); + } + + /** + * Answers true if comparing to a ColumnSelection with the same selected + * columns and hidden columns, else false + */ + @Override + public boolean equals(Object obj) + { + if (!(obj instanceof ColumnSelection)) + { + return false; + } + ColumnSelection that = (ColumnSelection) obj; + + /* + * check columns selected are either both null, or match + */ + if (this.selection == null) + { + if (that.selection != null) + { + return false; + } + } + if (!this.selection.equals(that.selection)) + { + return false; + } + + return this.hiddenColumns.equals(that.hiddenColumns); + } + + /** + * Updates the column selection depending on the parameters, and returns true + * if any change was made to the selection + * + * @param markedColumns + * a set identifying marked columns (base 0) + * @param startCol + * the first column of the range to operate over (base 0) + * @param endCol + * the last column of the range to operate over (base 0) + * @param invert + * if true, deselect marked columns and select unmarked + * @param extendCurrent + * if true, extend rather than replacing the current column selection + * @param toggle + * if true, toggle the selection state of marked columns + * + * @return + */ + public boolean markColumns(BitSet markedColumns, int startCol, + int endCol, boolean invert, boolean extendCurrent, boolean toggle) + { + boolean changed = false; + if (!extendCurrent && !toggle) + { + changed = !this.isEmpty(); + clear(); + } + if (invert) + { + // invert only in the currently selected sequence region + int i = markedColumns.nextClearBit(startCol); + int ibs = markedColumns.nextSetBit(startCol); + while (i >= startCol && i <= endCol) + { + if (ibs < 0 || i < ibs) + { + changed = true; + if (toggle && contains(i)) + { + removeElement(i++); + } + else + { + addElement(i++); + } + } + else + { + i = markedColumns.nextClearBit(ibs); + ibs = markedColumns.nextSetBit(i); + } + } + } + else + { + int i = markedColumns.nextSetBit(startCol); + while (i >= startCol && i <= endCol) + { + changed = true; + if (toggle && contains(i)) + { + removeElement(i); + } + else + { + addElement(i); + } + i = markedColumns.nextSetBit(i + 1); + } + } + return changed; + } + + /** + * Adjusts column selections, and the given selection group, to match the + * range of a stretch (e.g. mouse drag) operation + *

+ * Method refactored from ScalePanel.mouseDragged + * + * @param res + * current column position, adjusted for hidden columns + * @param sg + * current selection group + * @param min + * start position of the stretch group + * @param max + * end position of the stretch group + */ + public void stretchGroup(int res, SequenceGroup sg, int min, int max) + { + if (!contains(res)) + { + addElement(res); + } + + if (res > sg.getStartRes()) + { + // expand selection group to the right + sg.setEndRes(res); + } + if (res < sg.getStartRes()) + { + // expand selection group to the left + sg.setStartRes(res); + } + + /* + * expand or shrink column selection to match the + * range of the drag operation + */ + for (int col = min; col <= max; col++) + { + if (col < sg.getStartRes() || col > sg.getEndRes()) + { + // shrinking drag - remove from selection + removeElement(col); + } + else + { + // expanding drag - add to selection + addElement(col); + } + } + } }