X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=28745f18c50a48cb50de027cd7eeb1f70bc670cb;hb=956ae1ec0680e5567994197641be358d6bd15a83;hp=168e43f3e30509ed3ba92ac0d2ed3cc714afcd75;hpb=48538fac92d607c3b88b10b3d901539da00108e2;p=jalview.git diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index 168e43f..28745f1 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -20,6 +20,7 @@ */ package jalview.datamodel; +import jalview.util.Comparison; import jalview.util.ShiftList; import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField; @@ -31,28 +32,65 @@ 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 +99,13 @@ 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 +120,27 @@ 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 +151,7 @@ public class ColumnSelection * @param i * @return */ - public int elementAt(int i) + int elementAt(int i) { return order.get(i); } @@ -151,7 +194,7 @@ 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++) @@ -170,18 +213,61 @@ public class ColumnSelection selected.or(mask); } - public int getMaxColumn() + boolean isSelected(int column) + { + return selected.get(column); + } + + int getMaxColumn() { return selected.length() - 1; } - public int getMinColumn() + 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(); + IntList selection = new IntList(); + /* * list of hidden column [start, end] ranges; the list is maintained in * ascending start column order @@ -196,7 +282,7 @@ public class ColumnSelection */ public void addElement(int col) { - selected.add(col); + selection.add(col); } /** @@ -204,7 +290,7 @@ public class ColumnSelection */ public void clear() { - selected.clear(); + selection.clear(); } /** @@ -215,7 +301,7 @@ public class ColumnSelection */ public void removeElement(int col) { - selected.remove(col); + selection.remove(col); } /** @@ -232,20 +318,35 @@ 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(); } /** @@ -253,11 +354,11 @@ 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; } /** @@ -265,7 +366,7 @@ public class ColumnSelection */ public boolean isEmpty() { - return selected == null || selected.isEmpty(); + return selection == null || selection.isEmpty(); } /** @@ -275,11 +376,11 @@ public class ColumnSelection */ public int getMax() { - if (selected.isEmpty()) + if (selection.isEmpty()) { return -1; } - return selected.getMaxColumn(); + return selection.getMaxColumn(); } /** @@ -289,11 +390,11 @@ public class ColumnSelection */ public int getMin() { - if (selected.isEmpty()) + if (selection.isEmpty()) { return 1000000000; } - return selected.getMinColumn(); + return selection.getMinColumn(); } /** @@ -307,7 +408,7 @@ public class ColumnSelection public List compensateForEdit(int start, int change) { List deletedHiddenColumns = null; - selected.compensateForEdits(start, change); + selection.compensateForEdits(start, change); if (hiddenColumns != null) { @@ -357,7 +458,7 @@ public class ColumnSelection private void compensateForDelEdits(int start, int change) { - selected.compensateForEdits(start, change); + selection.compensateForEdits(start, change); if (hiddenColumns != null) { @@ -534,12 +635,12 @@ public class ColumnSelection hiddenColumns = null; } } - if (selected != null && selected.size() > 0) + 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. @@ -563,7 +664,7 @@ public class ColumnSelection * Return absolute column index for a visible column index * * @param column - * int column index in alignment view + * int column index in alignment view (count from zero) * @return alignment column index for column */ public int adjustForHiddenColumns(int column) @@ -589,8 +690,8 @@ public class ColumnSelection * left-most visible column will always be returned. * * @param hiddenColumn - * int - * @return int + * the column index in the full alignment including hidden columns + * @return the position of the column in the visible alignment */ public int findColumnPosition(int hiddenColumn) { @@ -607,9 +708,26 @@ public class ColumnSelection 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; + + if (hiddenColumn >= region[0] && hiddenColumn <= region[1]) + { + // Here the hidden column is within a region, so + // we want to return the position of region[0]-1, adjusted for any + // earlier hidden columns. + // Calculate the difference between the actual hidden col position + // and region[0]-1, and then subtract from result to convert result from + // the adjusted hiddenColumn value to the adjusted region[0]-1 value + + // However, if the region begins at 0 we cannot return region[0]-1 + // just return 0 + if (region[0] == 0) + { + return 0; + } + else + { + return result - (hiddenColumn - region[0] + 1); + } } } return result; // return the shifted position after removing hidden columns. @@ -617,6 +735,10 @@ public class ColumnSelection /** * Use this method to determine where the next hiddenRegion starts + * + * @param hiddenRegion + * index of hidden region (counts from 0) + * @return column number in visible view */ public int findHiddenRegionPosition(int hiddenRegion) { @@ -636,7 +758,7 @@ public class ColumnSelection gaps += region[1] + 1 - region[0]; result = region[1] + 1; index++; - } while (index < hiddenRegion + 1); + } while (index <= hiddenRegion); result -= gaps; } @@ -702,10 +824,13 @@ public class ColumnSelection public void hideSelectedColumns() { - while (!selected.isEmpty()) + synchronized (selection) { - int column = selected.elementAt(0); - hideColumns(column); + for (int[] selregions : selection.getRanges()) + { + hideColumns(selregions[0], selregions[1]); + } + selection.clear(); } } @@ -758,6 +883,24 @@ public class ColumnSelection */ region[0] = Math.min(region[0], start); region[1] = Math.max(region[1], end); + + /* + * also update or remove any subsequent ranges + * that are overlapped + */ + while (i < hiddenColumns.size() - 1) + { + int[] nextRegion = hiddenColumns.get(i + 1); + if (nextRegion[0] > end + 1) + { + /* + * gap to next hidden range - no more to update + */ + break; + } + region[1] = Math.max(nextRegion[1], end); + hiddenColumns.remove(i + 1); + } return; } } @@ -765,7 +908,7 @@ public class ColumnSelection /* * remaining case is that the new range follows everything else */ - hiddenColumns.addElement(new int[] { start, end }); + hiddenColumns.addElement(new int[] { start, end }); } /** @@ -883,14 +1026,7 @@ 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)); - } - } + selection = new IntList(copy.selection); if (copy.hiddenColumns != null) { hiddenColumns = new Vector(copy.hiddenColumns.size()); @@ -920,7 +1056,7 @@ public class ColumnSelection SequenceI[] seqs) { int i, iSize = seqs.length; - String selection[] = new String[iSize]; + String selections[] = new String[iSize]; if (hiddenColumns != null && hiddenColumns.size() > 0) { for (i = 0; i < iSize; i++) @@ -962,18 +1098,18 @@ public class ColumnSelection visibleSeq.append(seqs[i].getSequence(blockStart, end)); } - selection[i] = visibleSeq.toString(); + selections[i] = visibleSeq.toString(); } } else { for (i = 0; i < iSize; i++) { - selection[i] = seqs[i].getSequenceAsString(start, end); + selections[i] = seqs[i].getSequenceAsString(start, end); } } - return selection; + return selections; } /** @@ -1036,6 +1172,84 @@ public class ColumnSelection } /** + * Locate the first and last position visible for this sequence. if seq isn't + * visible then return the position of the left and right of the hidden + * boundary region, and the corresponding alignment column indices for the + * extent of the sequence + * + * @param seq + * @return int[] { visible start, visible end, first seqpos, last seqpos, + * alignment index for seq start, alignment index for seq end } + */ + public int[] locateVisibleBoundsOfSequence(SequenceI seq) + { + int fpos = seq.getStart(), lpos = seq.getEnd(); + int start = 0; + + if (hiddenColumns == null || hiddenColumns.size() == 0) + { + int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1; + return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos }; + } + + // Simply walk along the sequence whilst watching for hidden column + // boundaries + List regions = getHiddenColumns(); + int spos = fpos, lastvispos = -1, rcount = 0, hideStart = seq + .getLength(), hideEnd = -1; + int visPrev = 0, visNext = 0, firstP = -1, lastP = -1; + boolean foundStart = false; + for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd() + && p < pLen; p++) + { + if (!Comparison.isGap(seq.getCharAt(p))) + { + // keep track of first/last column + // containing sequence data regardless of visibility + if (firstP == -1) + { + firstP = p; + } + lastP = p; + // update hidden region start/end + while (hideEnd < p && rcount < regions.size()) + { + int[] region = regions.get(rcount++); + visPrev = visNext; + visNext += region[0] - visPrev; + hideStart = region[0]; + hideEnd = region[1]; + } + if (hideEnd < p) + { + hideStart = seq.getLength(); + } + // update visible boundary for sequence + if (p < hideStart) + { + if (!foundStart) + { + fpos = spos; + start = p; + foundStart = true; + } + lastvispos = p; + lpos = spos; + } + // look for next sequence position + spos++; + } + } + if (foundStart) + { + return new int[] { findColumnPosition(start), + findColumnPosition(lastvispos), fpos, lpos, firstP, lastP }; + } + // otherwise, sequence was completely hidden + return new int[] { visPrev, visNext, 0, 0, firstP, lastP }; + } + + /** * delete any columns in alignmentAnnotation that are hidden (including * sequence associated annotation). * @@ -1185,7 +1399,7 @@ public class ColumnSelection { if (hiddenColumns != null && isVisible(col.intValue())) { - selected.add(col); + selection.add(col); } } } @@ -1199,8 +1413,8 @@ 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) { @@ -1367,7 +1581,7 @@ public class ColumnSelection */ public boolean hasSelectedColumns() { - return (selected != null && selected.size() > 0); + return (selection != null && selection.size() > 0); } /** @@ -1406,6 +1620,8 @@ public class ColumnSelection public boolean filterAnnotations(Annotation[] annotations, AnnotationFilterParameter filterParams) { + // JBPNote - this method needs to be refactored to become independent of + // viewmodel package this.revealAllHiddenColumns(); this.clear(); int count = 0; @@ -1487,4 +1703,200 @@ 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(); + if (hiddenColumns != null) + { + for (int[] hidden : hiddenColumns) + { + hashCode = 31 * hashCode + hidden[0]; + hashCode = 31 * hashCode + hidden[1]; + } + } + return 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; + } + + /* + * check hidden columns are either both null, or match + */ + if (this.hiddenColumns == null) + { + return (that.hiddenColumns == null); + } + if (that.hiddenColumns == null + || that.hiddenColumns.size() != this.hiddenColumns.size()) + { + return false; + } + int i = 0; + for (int[] thisRange : hiddenColumns) + { + int[] thatRange = that.hiddenColumns.get(i++); + if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1]) + { + return false; + } + } + return true; + } + + /** + * 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); + } + } + } }