X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=b427739ca3fc776c60e42ea6bfcf4549261092a1;hb=HEAD;hp=57db830447bec3d1ca24d77ce1dd64d956d77bfa;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index 57db830..b427739 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -20,24 +20,251 @@ */ package jalview.datamodel; -import jalview.util.ShiftList; -import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; -import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField; - import java.util.ArrayList; +import java.util.BitSet; import java.util.Collections; import java.util.List; -import java.util.Vector; +import java.util.regex.PatternSyntaxException; + +import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; +import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField; /** - * 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 { - Vector selected = new Vector(); + /** + * 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; + + /* + * an unmodifiable view of the selected columns list + */ + private List _uorder; + + /** + * bitfield for column selection - allows quick lookup + */ + 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 + */ + void add(int i) + { + if (!selected.get(i)) + { + order.add(Integer.valueOf(i)); + selected.set(i); + } + } + + void clear() + { + order.clear(); + selected.clear(); + } + + void remove(int col) + { + + Integer colInt = Integer.valueOf(col); + + if (selected.get(col)) + { + // if this ever changes to List.remove(), ensure Integer not int + // argument + // as List.remove(int i) removes the i'th item which is wrong + order.remove(colInt); + selected.clear(col); + } + } + + boolean contains(Integer colInt) + { + return selected.get(colInt); + } + + boolean isEmpty() + { + return order.isEmpty(); + } + + /** + * Returns a read-only view of the selected columns list + * + * @return + */ + List getList() + { + return _uorder; + } + + int size() + { + return order.size(); + } + + /** + * gets the column that was selected first, second or i'th + * + * @param i + * @return + */ + int elementAt(int i) + { + return order.get(i); + } + + protected boolean pruneColumnList(final List shifts) + { + int s = 0, t = shifts.size(); + int[] sr = shifts.get(s++); + boolean pruned = false; + int i = 0, j = order.size(); + while (i < j && s <= t) + { + int c = order.get(i++).intValue(); + if (sr[0] <= c) + { + if (sr[1] + sr[0] >= c) + { // sr[1] -ve means inseriton. + order.remove(--i); + selected.clear(c); + j--; + } + else + { + if (s < t) + { + sr = shifts.get(s); + } + s++; + } + } + } + return pruned; + } + + /** + * shift every selected column at or above start by change + * + * @param start + * - leftmost column to be shifted + * @param change + * - delta for shift + */ + void compensateForEdits(int start, int change) + { + BitSet mask = new BitSet(); + for (int i = 0; i < order.size(); i++) + { + int temp = order.get(i); + + if (temp >= start) + { + // clear shifted bits and update List of selected columns + selected.clear(temp); + mask.set(temp - change); + order.set(i, Integer.valueOf(temp - change)); + } + } + // 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; + } + } - // Vector of int [] {startCol, endCol} - Vector hiddenColumns; + private IntList selection = new IntList(); /** * Add a column to the selection @@ -47,11 +274,28 @@ public class ColumnSelection */ public void addElement(int col) { - Integer column = new Integer(col); - if (!selected.contains(column)) + selection.add(col); + } + + /** + * add a series of start,end (inclusive) ranges to the column selection + * + * @param rng + * [start_0, end_0, start_1, end_1, ... ] + * @param baseOne + * - when true, ranges are base 1 and will be mapped to base 0 + */ + public void addRangeOfElements(int[] rng, boolean baseOne) + { + int base = baseOne ? -1 : 0; + for (int c = 0; c < rng.length; c += 2) { - selected.addElement(column); + for (int p = rng[c]; p <= rng[c + 1]; p++) + { + selection.add(base + p); + } } + } /** @@ -59,7 +303,7 @@ public class ColumnSelection */ public void clear() { - selected.removeAllElements(); + selection.clear(); } /** @@ -70,14 +314,7 @@ public class ColumnSelection */ public void removeElement(int col) { - Integer colInt = new Integer(col); - - if (selected.contains(colInt)) - { - // if this ever changes to List.remove(), ensure Integer not int argument - // as List.remove(int i) removes the i'th item which is wrong - selected.removeElement(colInt); - } + selection.remove(col); } /** @@ -93,21 +330,38 @@ public class ColumnSelection Integer colInt; for (int i = start; i < end; i++) { - colInt = new Integer(i); - if (selected.contains(colInt)) + colInt = Integer.valueOf(i); + if (selection.contains(colInt)) { - selected.removeElement(colInt); + selection.remove(colInt); } } } /** - * - * @return Vector containing selected columns as Integers + * Returns a read-only view of the (possibly empty) list of selected columns + * (base 1) + *

+ * The list contains no duplicates but is not necessarily ordered. Columns are + * reported in alignment coordinates (base 1), so may also 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 selection.getList(); + } + + /** + * @return list of int arrays containing start and end column position for + * runs of selected columns ordered from right to left. */ - public Vector getSelected() + public List getSelectedRanges() { - return selected; + return selection.getRanges(); } /** @@ -115,34 +369,35 @@ 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; } /** - * Column number at position i in selection * - * @param i - * index into selected columns - * - * @return column number in alignment */ - public int columnAt(int i) + public boolean intersects(int from, int to) { - return selected.elementAt(i).intValue(); + // TODO: do this in a more efficient bitwise way + for (int f = from; f <= to; f++) + { + if (selection.isSelected(f)) + { + return true; + } + } + return false; } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Answers true if no columns are selected, else false */ - public int size() + public boolean isEmpty() { - return selected.size(); + return selection == null || selection.isEmpty(); } /** @@ -152,17 +407,11 @@ public class ColumnSelection */ public int getMax() { - int max = -1; - - for (int i = 0; i < selected.size(); i++) + if (selection.isEmpty()) { - if (columnAt(i) > max) - { - max = columnAt(i); - } + return -1; } - - return max; + return selection.getMaxColumn(); } /** @@ -172,1221 +421,467 @@ public class ColumnSelection */ public int getMin() { - int min = 1000000000; + if (selection.isEmpty()) + { + return 1000000000; + } + return selection.getMinColumn(); + } - for (int i = 0; i < selected.size(); i++) + public void hideSelectedColumns(AlignmentI al) + { + synchronized (selection) { - if (columnAt(i) < min) + for (int[] selregions : selection.getRanges()) { - min = columnAt(i); + al.getHiddenColumns().hideColumns(selregions[0], selregions[1]); } + selection.clear(); } - return min; } /** - * propagate shift in alignment columns to column selection + * Hides the specified column and any adjacent selected columns * - * @param start - * beginning of edit - * @param left - * shift in edit (+ve for removal, or -ve for inserts) + * @param res + * int */ - public List compensateForEdit(int start, int change) + public void hideSelectedColumns(int col, HiddenColumns hidden) { - List deletedHiddenColumns = null; - for (int i = 0; i < size(); i++) - { - int temp = columnAt(i); + /* + * deselect column (whether selected or not!) + */ + removeElement(col); - if (temp >= start) - { - // if this ever changes to List.set(), swap parameter order!! - selected.setElementAt(new Integer(temp - change), i); - } + /* + * find adjacent selected columns + */ + int min = col - 1, max = col + 1; + while (contains(min)) + { + removeElement(min); + min--; } - if (hiddenColumns != null) + while (contains(max)) { - 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; - } - - } + removeElement(max); + max++; + } - this.revealHiddenColumns(0); + /* + * min, max are now the closest unselected columns + */ + min++; + max--; + if (min > max) + { + min = max; } - return deletedHiddenColumns; + hidden.hideColumns(min, max); } /** - * propagate shift in alignment columns to column selection special version of - * compensateForEdit - allowing for edits within hidden regions + * Copy constructor * - * @param start - * beginning of edit - * @param left - * shift in edit (+ve for removal, or -ve for inserts) + * @param copy */ - private void compensateForDelEdits(int start, int change) + public ColumnSelection(ColumnSelection copy) { - for (int i = 0; i < size(); i++) + if (copy != null) { - int temp = columnAt(i); - - if (temp >= start) - { - // if this ever changes to List.set(), swap parameter order!! - selected.setElementAt(new Integer(temp - change), i); - } + selection = new IntList(copy.selection); } + } - 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; - } - } - } + /** + * ColumnSelection + */ + public ColumnSelection() + { } /** - * Adjust hidden column boundaries based on a series of column additions or - * deletions in visible regions. + * Invert the column selection from first to end-1. leaves hiddenColumns + * untouched (and unselected) * - * @param shiftrecord - * @return + * @param first + * @param end */ - public ShiftList compensateForEdits(ShiftList shiftrecord) + public void invertColumnSelection(int first, int width, AlignmentI al) { - if (shiftrecord != null) + boolean hasHidden = al.getHiddenColumns().hasHiddenColumns(); + for (int i = first; i < width; i++) { - final List shifts = shiftrecord.getShifts(); - if (shifts != null && shifts.size() > 0) + if (contains(i)) + { + removeElement(i); + } + else { - int shifted = 0; - for (int i = 0, j = shifts.size(); i < j; i++) + if (!hasHidden || al.getHiddenColumns().isVisible(i)) { - int[] sh = shifts.get(i); - // compensateForEdit(shifted+sh[0], sh[1]); - compensateForDelEdits(shifted + sh[0], sh[1]); - shifted -= sh[1]; + addElement(i); } } - return shiftrecord.getInverse(); } - return null; } /** - * removes intersection of position,length ranges in deletions from the - * start,end regions marked in intervals. + * set the selected columns to the given column selection, excluding any + * columns that are hidden. * - * @param shifts - * @param intervals - * @return + * @param colsel */ - private boolean pruneIntervalVector(final List shifts, - Vector intervals) + public void setElementsFrom(ColumnSelection colsel, + HiddenColumns hiddenColumns) { - 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) + selection = new IntList(); + if (colsel.selection != null && colsel.selection.size() > 0) { - boolean trailinghn = hr[1] >= sr[0]; - if (!trailinghn) + if (hiddenColumns.hasHiddenColumns()) { - 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 + // only select visible columns in this columns selection + for (Integer col : colsel.getSelected()) { - 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) + if (hiddenColumns != null + && hiddenColumns.isVisible(col.intValue())) { - hr = intervals.elementAt(i); + selection.add(col); } - continue; - } - if (leadinghc) - { - hr[0] = endshift; // clip c terminal region - leadinghn = !leadinghn; - pruned = true; } } - if (!leadinghn) + else { - if (trailinghc) - { - if (trailinghn) - { - hr[1] = sr[0] - 1; - pruned = true; - } - } - else + // add everything regardless + for (Integer col : colsel.getSelected()) { - // sr contained in hr - if (s < t) - { - sr = shifts.get(++s); - } - else - { - s++; - } - continue; + addElement(col); } } } - return pruned; // true if any interval was removed or modified by - // operations. } - private boolean pruneColumnList(final List shifts, - Vector list) + /** + * + * @return true if there are columns marked + */ + public boolean hasSelectedColumns() { - int s = 0, t = shifts.size(); - int[] sr = shifts.get(s++); - boolean pruned = false; - int i = 0, j = list.size(); - while (i < j && s <= t) - { - int c = list.elementAt(i++).intValue(); - if (sr[0] <= c) - { - if (sr[1] + sr[0] >= c) - { // sr[1] -ve means inseriton. - list.removeElementAt(--i); - j--; - } - else - { - if (s < t) - { - sr = shifts.get(s); - } - s++; - } - } - } - return pruned; + return (selection != null && selection.size() > 0); } /** - * remove any hiddenColumns or selected columns and shift remaining based on a - * series of position, range deletions. + * Selects columns where the given annotation matches the provided filter + * condition(s). Any existing column selections are first cleared. Answers the + * number of columns added. * - * @param deletions + * @param annotations + * @param filterParams + * @return */ - public void pruneDeletions(ShiftList deletions) + public int filterAnnotations(AlignmentAnnotation ann_row, + AnnotationFilterParameter filterParams) { - if (deletions != null) + Annotation[] annotations = ann_row.annotations; + // JBPNote - this method needs to be refactored to become independent of + // viewmodel package + this.clear(); + + if (ann_row.graph == AlignmentAnnotation.CONTACT_MAP && (filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD + || filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD)) { - final List shifts = deletions.getShifts(); - if (shifts != null && shifts.size() > 0) + float tVal = filterParams.getThresholdValue(); + if (ann_row.sequenceRef != null) { - // delete any intervals intersecting. - if (hiddenColumns != null) + // TODO - get ContactList from AlignmentView for non-seq-ref associatd + for (int column = 0; column < annotations.length; column++) { - pruneIntervalVector(shifts, hiddenColumns); - if (hiddenColumns != null && hiddenColumns.size() == 0) + if (ann_row.annotations[column] == null) { - hiddenColumns = null; + continue; } - } - if (selected != null && selected.size() > 0) - { - pruneColumnList(shifts, selected); - if (selected != null && selected.size() == 0) + + int cpos = ann_row.sequenceRef.findPosition(column) - 1; + ContactListI clist = ann_row.sequenceRef + .getContactListFor(ann_row, cpos); + for (int row = column + 8, rowEnd = clist + .getContactHeight(); row < rowEnd; row++) { - selected = null; + if (filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD + ? (clist.getContactAt(row) > tVal) + : (clist.getContactAt(row) < tVal)) + { + addElement(column); + break; + // int column_forrowpos = ann_row.sequenceRef.findIndex(row + 1); + // addElement(column_forrowpos); + } } } - // and shift the rest. - this.compensateForEdits(deletions); } + return selection.size(); } - } - /** - * 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) - { - int result = column; - if (hiddenColumns != null) + int addedCount = 0; + int column = 0; + do { - for (int i = 0; i < hiddenColumns.size(); i++) + Annotation ann = annotations[column]; + if (ann != null) { - int[] region = hiddenColumns.elementAt(i); - if (result >= region[0]) - { - result += region[1] - region[0] + 1; - } - } - } - return result; - } + float value = ann.value; + boolean matched = false; - /** - * 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]) + /* + * filter may have multiple conditions - + * these are or'd until a match is found + */ + if (filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD + && value > filterParams.getThresholdValue()) { - result -= region[1] + 1 - region[0]; + matched = true; } - } 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) + if (!matched && filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD + && value < filterParams.getThresholdValue()) { - return region[0]; + matched = true; } - 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]) + if (!matched && filterParams.isFilterAlphaHelix() + && ann.secondaryStructure == 'H') { - return region[0]; + matched = true; } - 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]) + if (!matched && filterParams.isFilterBetaSheet() + && ann.secondaryStructure == 'E') { - return region[1]; + matched = true; } - index--; - } while (index > -1); - } - - return alPos; - - } - - public void hideSelectedColumns() - { - while (size() > 0) - { - int column = getSelected().firstElement().intValue(); - hideColumns(column); - } - - } - - public void hideColumns(int start, int end) - { - if (hiddenColumns == null) - { - hiddenColumns = new Vector(); - } - - boolean added = false; - boolean overlap = false; - - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - if (start <= region[1] && end >= region[0]) - { - hiddenColumns.removeElementAt(i); - overlap = true; - break; - } - else if (end < region[0] && start < region[0]) - { - hiddenColumns.insertElementAt(new int[] { start, end }, i); - added = true; - break; - } - } - - if (overlap) - { - hideColumns(start, end); - } - else if (!added) - { - hiddenColumns.addElement(new int[] { start, end }); - } - - } - - /** - * This method will find a range of selected columns around the column - * specified - * - * @param res - * int - */ - public void hideColumns(int col) - { - // First find out range of columns to hide - int min = col, max = col + 1; - while (contains(min)) - { - removeElement(min); - min--; - } - - while (contains(max)) - { - removeElement(max); - max++; - } - - min++; - max--; - if (min > max) - { - min = max; - } - - hideColumns(min, max); - } - - 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++) + if (!matched && filterParams.isFilterTurn() + && ann.secondaryStructure == 'S') { - addElement(j); + matched = true; } - } - } - hiddenColumns = null; - } - - public void revealHiddenColumns(int res) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - if (res == region[0]) - { - for (int j = region[0]; j < region[1] + 1; j++) + String regexSearchString = filterParams.getRegexString(); + if (!matched && regexSearchString != null) { - addElement(j); + List fields = filterParams + .getRegexSearchFields(); + for (SearchableAnnotationField field : fields) + { + String compareTo = field == SearchableAnnotationField.DISPLAY_STRING + ? ann.displayCharacter // match 'Label' + : ann.description; // and/or 'Description' + if (compareTo != null) + { + try + { + if (compareTo.matches(regexSearchString)) + { + matched = true; + } + } catch (PatternSyntaxException pse) + { + if (compareTo.equals(regexSearchString)) + { + matched = true; + } + } + if (matched) + { + break; + } + } + } } - hiddenColumns.removeElement(region); - break; - } - } - if (hiddenColumns.size() == 0) - { - hiddenColumns = null; - } - } - - public boolean isVisible(int column) - { - if (hiddenColumns != null) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - if (column >= region[0] && column <= region[1]) + if (matched) { - return false; + this.addElement(column); + addedCount++; } } - } + column++; + } while (column < annotations.length); - return true; + return addedCount; } /** - * Copy constructor - * - * @param copy + * Returns a hashCode built from selected columns ranges */ - public ColumnSelection(ColumnSelection copy) + @Override + public int hashCode() { - if (copy != null) - { - if (copy.selected != null) - { - selected = new Vector(); - for (int i = 0, j = copy.selected.size(); i < j; i++) - { - selected.addElement(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); - } - } - } - } + return selection.hashCode(); } /** - * ColumnSelection + * Answers true if comparing to a ColumnSelection with the same selected + * columns and hidden columns, else false */ - public ColumnSelection() + @Override + public boolean equals(Object obj) { - } - - 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) + if (!(obj instanceof ColumnSelection)) { - 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 false; } + ColumnSelection that = (ColumnSelection) obj; - 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) + /* + * check columns selected are either both null, or match + */ + if (this.selection == null) { - 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++) + if (that.selection != null) { - int[] vc = visiblecontigs.get(i); - visiblecontigs.set(i, null); - vcontigs[i * 2] = vc[0]; - vcontigs[i * 2 + 1] = vc[1]; + return false; } - visiblecontigs.clear(); - return vcontigs; } - else + if (!this.selection.equals(that.selection)) { - return new int[] { start, end - 1 }; + return false; } - } - /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). - * - * @param alignmentAnnotation - */ - public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation) - { - makeVisibleAnnotation(-1, -1, alignmentAnnotation); + return true; } /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). + * Updates the column selection depending on the parameters, and returns true + * if any change was made to the selection * - * @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 + * @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 void makeVisibleAnnotation(int start, int end, - AlignmentAnnotation alignmentAnnotation) + public boolean markColumns(BitSet markedColumns, int startCol, int endCol, + boolean invert, boolean extendCurrent, boolean toggle) { - if (alignmentAnnotation.annotations == null) - { - return; - } - if (start == end && end == -1) + boolean changed = false; + if (!extendCurrent && !toggle) { - start = 0; - end = alignmentAnnotation.annotations.length; + changed = !this.isEmpty(); + clear(); } - if (hiddenColumns != null && hiddenColumns.size() > 0) + if (invert) { - // 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) + // invert only in the currently selected sequence region + int i = markedColumns.nextClearBit(startCol); + int ibs = markedColumns.nextSetBit(startCol); + while (i >= startCol && i <= endCol) { - annels.addElement(els = new Annotation[end - blockStart + 1]); - if ((els.length + blockStart) <= alignmentAnnotation.annotations.length) + if (ibs < 0 || i < ibs) { - // copy just the visible segment of the annotation row - System.arraycopy(alignmentAnnotation.annotations, blockStart, - els, 0, els.length); + changed = true; + if (toggle && contains(i)) + { + removeElement(i++); + } + else + { + addElement(i++); + } } else { - // copy to the end of the annotation row - System.arraycopy(alignmentAnnotation.annotations, blockStart, - els, 0, - (alignmentAnnotation.annotations.length - blockStart)); + i = markedColumns.nextClearBit(ibs); + ibs = markedColumns.nextSetBit(i); } - 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 - * untouched (and unselected) - * - * @param first - * @param end - */ - public void invertColumnSelection(int first, int width) - { - boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0; - for (int i = first; i < width; i++) - { - if (contains(i)) + int i = markedColumns.nextSetBit(startCol); + while (i >= startCol && i <= endCol) { - removeElement(i); - } - else - { - if (!hasHidden || isVisible(i)) + changed = true; + if (toggle && contains(i)) + { + removeElement(i); + } + else { addElement(i); } + i = markedColumns.nextSetBit(i + 1); } } + return changed; } /** - * add in any unselected columns from the given column selection, excluding - * any that are hidden. + * 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 colsel + * @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 addElementsFrom(ColumnSelection colsel) + public void stretchGroup(int res, SequenceGroup sg, int min, int max) { - if (colsel != null && colsel.size() > 0) + if (!contains(res)) { - for (Integer col : colsel.getSelected()) - { - if (hiddenColumns != null && isVisible(col.intValue())) - { - if (!selected.contains(col)) - { - selected.addElement(col); - } - } - } + addElement(res); } - } - /** - * set the selected columns the given column selection, excluding any columns - * that are hidden. - * - * @param colsel - */ - public void setElementsFrom(ColumnSelection colsel) - { - selected = new Vector(); - if (colsel.selected != null && colsel.selected.size() > 0) + if (res > sg.getStartRes()) { - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - // only select visible columns in this columns selection - addElementsFrom(colsel); - } - else - { - // add everything regardless - for (Integer col : colsel.getSelected()) - { - addElement(col); - } - } + // expand selection group to the right + sg.setEndRes(res); } - } - - /** - * Add gaps into the sequences aligned to profileseq under the given - * AlignmentView - * - * @param profileseq - * @param al - * - alignment to have gaps inserted into it - * @param input - * - alignment view where sequence corresponding to profileseq is - * first entry - * @return new Column selection for new alignment view, with insertions into - * profileseq marked as hidden. - */ - public static ColumnSelection propagateInsertions(SequenceI profileseq, - AlignmentI al, AlignmentView input) - { - int profsqpos = 0; - - // return propagateInsertions(profileseq, al, ) - char gc = al.getGapCharacter(); - Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc); - ColumnSelection nview = (ColumnSelection) alandcolsel[1]; - SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos]; - nview.propagateInsertions(profileseq, al, origseq); - return nview; - } - - /** - * - * @param profileseq - * - sequence in al which corresponds to origseq - * @param al - * - alignment which is to have gaps inserted into it - * @param origseq - * - sequence corresponding to profileseq which defines gap map for - * modifying al - */ - public 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 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) + if (res < sg.getStartRes()) { - if (viscontigs[v] > spos) - { - StringBuffer sb = new StringBuffer(); - for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++) - { - sb.append(gc); - } - for (int s = 0, ns = al.getHeight(); s < ns; s++) - { - SequenceI sqobj = al.getSequenceAt(s); - if (sqobj != profileseq) - { - String sq = al.getSequenceAt(s).getSequenceAsString(); - if (sq.length() <= spos + offset) - { - // pad sequence - int diff = spos + offset - sq.length() - 1; - if (diff > 0) - { - // pad gaps - sq = sq + sb; - while ((diff = spos + offset - sq.length() - 1) > 0) - { - // sq = sq - // + ((diff >= sb.length()) ? sb.toString() : sb - // .substring(0, diff)); - if (diff >= sb.length()) - { - sq += sb.toString(); - } - else - { - char[] buf = new char[diff]; - sb.getChars(0, diff, buf, 0); - sq += buf.toString(); - } - } - } - sq += sb.toString(); - } - else - { - al.getSequenceAt(s).setSequence( - sq.substring(0, spos + offset) + sb.toString() - + sq.substring(spos + offset)); - } - } - } - // offset+=sb.length(); - } - spos = viscontigs[v + 1] + 1; + // expand selection group to the left + sg.setStartRes(res); } - if ((offset + spos) < profileseq.getLength()) + + /* + * expand or shrink column selection to match the + * range of the drag operation + */ + for (int col = min; col <= max; col++) { - // pad the final region with gaps. - StringBuffer sb = new StringBuffer(); - for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++) + if (col < sg.getStartRes() || col > sg.getEndRes()) { - sb.append(gc); + // shrinking drag - remove from selection + removeElement(col); } - for (int s = 0, ns = al.getHeight(); s < ns; s++) + else { - SequenceI sqobj = al.getSequenceAt(s); - if (sqobj == profileseq) - { - continue; - } - String sq = sqobj.getSequenceAsString(); - // pad sequence - int diff = origseq.getLength() - sq.length(); - while (diff > 0) - { - // sq = sq - // + ((diff >= sb.length()) ? sb.toString() : sb - // .substring(0, diff)); - if (diff >= sb.length()) - { - sq += sb.toString(); - } - else - { - char[] buf = new char[diff]; - sb.getChars(0, diff, buf, 0); - sq += buf.toString(); - } - diff = origseq.getLength() - sq.length(); - } + // expanding drag - add to selection + addElement(col); } } } - - /** - * - * @return true if there are columns marked - */ - public boolean hasSelectedColumns() - { - return (selected != null && selected.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(); - this.clear(); - int count = 0; - do - { - if (annotations[count] != null) - { - - boolean itemMatched = false; - - if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD - && annotations[count].value >= filterParams - .getThresholdValue()) - { - itemMatched = true; - } - if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD - && annotations[count].value <= filterParams - .getThresholdValue()) - { - itemMatched = true; - } - - if (filterParams.isFilterAlphaHelix() - && annotations[count].secondaryStructure == 'H') - { - itemMatched = true; - } - - if (filterParams.isFilterBetaSheet() - && annotations[count].secondaryStructure == 'E') - { - itemMatched = true; - } - - if (filterParams.isFilterTurn() - && annotations[count].secondaryStructure == 'S') - { - itemMatched = true; - } - - String regexSearchString = filterParams.getRegexString(); - if (regexSearchString != null - && !filterParams.getRegexSearchFields().isEmpty()) - { - List fields = filterParams - .getRegexSearchFields(); - try - { - if (fields.contains(SearchableAnnotationField.DISPLAY_STRING) - && annotations[count].displayCharacter - .matches(regexSearchString)) - { - itemMatched = true; - } - } catch (java.util.regex.PatternSyntaxException pse) - { - if (annotations[count].displayCharacter - .equals(regexSearchString)) - { - itemMatched = true; - } - } - if (fields.contains(SearchableAnnotationField.DESCRIPTION) - && annotations[count].description != null - && annotations[count].description - .matches(regexSearchString)) - { - itemMatched = true; - } - } - - if (itemMatched) - { - this.addElement(count); - } - } - count++; - } while (count < annotations.length); - return false; - } }