X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=97bc5a3b7e3a62edff41d05e9a6fdab98591c1cc;hb=4bb1a8a4b8fc08ed5b0d51f0ea03d9a9ad7dc419;hp=aaf70b888a245a9e5c50d892f2734872362dce68;hpb=528191d2feb45cd42c5b4f48420687346705119d;p=jalview.git diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index aaf70b8..97bc5a3 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -45,19 +45,52 @@ public class ColumnSelection /* * 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)) { @@ -66,13 +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); @@ -87,22 +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(); } @@ -113,7 +151,7 @@ public class ColumnSelection * @param i * @return */ - public int elementAt(int i) + int elementAt(int i) { return order.get(i); } @@ -156,7 +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++) @@ -175,17 +213,17 @@ public class ColumnSelection selected.or(mask); } - public boolean isSelected(int column) + boolean isSelected(int column) { return selected.get(column); } - public int getMaxColumn() + int getMaxColumn() { return selected.length() - 1; } - public int getMinColumn() + int getMinColumn() { return selected.get(0) ? 0 : selected.nextSetBit(0); } @@ -193,7 +231,7 @@ public class ColumnSelection /** * @return a series of selection intervals along the range */ - public List getRanges() + List getRanges() { List rlist = new ArrayList(); if (selected.isEmpty()) @@ -288,9 +326,14 @@ public class ColumnSelection } /** - * Returns a list of selected columns. The list contains no duplicates but is - * not necessarily ordered. It also may include columns hidden from the - * current view + * 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() { @@ -647,8 +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) { @@ -665,15 +708,89 @@ 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. } /** + * Find the visible column which is a given visible number of columns to the + * left of another visible column. i.e. for a startColumn x, the column which + * is distance 1 away will be column x-1. + * + * @param visibleDistance + * the number of visible columns to offset by + * @param startColumn + * the column to start from + * @return the position of the column in the visible alignment + */ + public int subtractVisibleColumns(int visibleDistance, int startColumn) + { + int distance = visibleDistance; + + // in case startColumn is in a hidden region, move it to the left + int start = adjustForHiddenColumns(findColumnPosition(startColumn)); + + // get index of hidden region to left of start + int index = getHiddenIndexLeft(start); + if (index == -1) + { + // no hidden regions to left of startColumn + return start - distance; + } + + // walk backwards through the alignment subtracting the counts of visible + // columns from distance + int[] region; + int gap = 0; + int nextstart = start; + + while ((index > -1) && (distance - gap > 0)) + { + // subtract the gap to right of region from distance + distance -= gap; + start = nextstart; + + // calculate the next gap + region = hiddenColumns.get(index); + gap = start - region[1]; + + // set start to just to left of current region + nextstart = region[0] - 1; + index--; + } + + if (distance - gap > 0) + { + // fell out of loop because there are no more hidden regions + distance -= gap; + return nextstart - distance; + } + return start - distance; + + } + + /** * Use this method to determine where the next hiddenRegion starts * * @param hiddenRegion @@ -762,6 +879,35 @@ public class ColumnSelection } + /** + * This method returns the index of the hidden region to the left of a column + * position. If the column is in a hidden region it returns the index of the + * region to the left. If there is no hidden region to the left it returns -1. + * + * @param pos + * int + */ + private int getHiddenIndexLeft(int pos) + { + if (hiddenColumns != null) + { + int index = hiddenColumns.size() - 1; + do + { + int[] region = hiddenColumns.elementAt(index); + if (pos > region[1]) + { + return index; + } + + index--; + } while (index > -1); + } + + return -1; + + } + public void hideSelectedColumns() { synchronized (selection) @@ -823,6 +969,24 @@ 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; } } @@ -948,14 +1112,7 @@ public class ColumnSelection { if (copy != null) { - if (copy.selection != null) - { - selection = new IntList(); - for (int i = 0, j = copy.selection.size(); i < j; i++) - { - selection.add(copy.selection.elementAt(i)); - } - } + selection = new IntList(copy.selection); if (copy.hiddenColumns != null) { hiddenColumns = new Vector(copy.hiddenColumns.size()); @@ -985,7 +1142,7 @@ 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++) @@ -1027,18 +1184,18 @@ 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; } /** @@ -1112,9 +1269,9 @@ public class ColumnSelection */ public int[] locateVisibleBoundsOfSequence(SequenceI seq) { - int fpos=seq.getStart(),lpos= seq.getEnd(); + 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; @@ -1703,4 +1860,129 @@ public class ColumnSelection 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); + } + } + } }