X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=b427739ca3fc776c60e42ea6bfcf4549261092a1;hb=HEAD;hp=ca54570a09085a98f06ad0b90425e43b7b4ec8f9;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index ca54570..b427739 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -1,1057 +1,887 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.datamodel; - -import java.util.*; - -import jalview.util.*; - -/** - * NOTE: Columns are zero based. - */ -public class ColumnSelection -{ - Vector selected = new Vector(); - - // Vector of int [] {startCol, endCol} - Vector hiddenColumns; - - /** - * Add a column to the selection - * - * @param col - * index of column - */ - public void addElement(int col) - { - Integer column = new Integer(col); - if (!selected.contains(column)) - { - selected.addElement(column); - } - } - - /** - * clears column selection - */ - public void clear() - { - selected.removeAllElements(); - } - - /** - * removes col from selection - * - * @param col - * index of column to be removed - */ - public void removeElement(int col) - { - Integer colInt = new Integer(col); - - if (selected.contains(colInt)) - { - selected.removeElement(colInt); - } - } - - /** - * removes a range of columns from the selection - * - * @param start - * int - first column in range to be removed - * @param end - * int - last col - */ - public void removeElements(int start, int end) - { - Integer colInt; - for (int i = start; i < end; i++) - { - colInt = new Integer(i); - if (selected.contains(colInt)) - { - selected.removeElement(colInt); - } - } - } - - /** - * - * @return Vector containing selected columns as Integers - */ - public Vector getSelected() - { - return selected; - } - - /** - * - * @param col - * index to search for in column selection - * - * @return true if Integer(col) is in selection. - */ - public boolean contains(int col) - { - return selected.contains(new Integer(col)); - } - - /** - * Column number at position i in selection - * - * @param i - * index into selected columns - * - * @return column number in alignment - */ - public int columnAt(int i) - { - return ((Integer) selected.elementAt(i)).intValue(); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int size() - { - return selected.size(); - } - - /** - * rightmost selected column - * - * @return rightmost column in alignment that is selected - */ - public int getMax() - { - int max = -1; - - for (int i = 0; i < selected.size(); i++) - { - if (columnAt(i) > max) - { - max = columnAt(i); - } - } - - return max; - } - - /** - * Leftmost column in selection - * - * @return column index of leftmost column in selection - */ - public int getMin() - { - int min = 1000000000; - - for (int i = 0; i < selected.size(); i++) - { - if (columnAt(i) < min) - { - min = columnAt(i); - } - } - - return min; - } - - /** - * propagate shift in alignment columns to column selection - * - * @param start - * beginning of edit - * @param left - * shift in edit (+ve for removal, or -ve for inserts) - */ - public Vector compensateForEdit(int start, int change) - { - Vector deletedHiddenColumns = null; - for (int i = 0; i < size(); i++) - { - int temp = columnAt(i); - - if (temp >= start) - { - selected.setElementAt(new Integer(temp - change), i); - } - } - - if (hiddenColumns != null) - { - deletedHiddenColumns = new Vector(); - int hSize = hiddenColumns.size(); - for (int i = 0; i < hSize; i++) - { - int[] region = (int[]) hiddenColumns.elementAt(i); - if (region[0] > start && start + change > region[1]) - { - deletedHiddenColumns.addElement(hiddenColumns.elementAt(i)); - - 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); - } - - return deletedHiddenColumns; - } - - /** - * propagate shift in alignment columns to column selection special version of - * compensateForEdit - allowing for edits within hidden regions - * - * @param start - * beginning of edit - * @param left - * shift in edit (+ve for removal, or -ve for inserts) - */ - private void compensateForDelEdits(int start, int change) - { - for (int i = 0; i < size(); i++) - { - int temp = columnAt(i); - - if (temp >= start) - { - selected.setElementAt(new Integer(temp - change), i); - } - } - - if (hiddenColumns != null) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = (int[]) 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; - } - } - } - } - - /** - * Adjust hidden column boundaries based on a series of column additions or - * deletions in visible regions. - * - * @param shiftrecord - * @return - */ - public ShiftList compensateForEdits(ShiftList shiftrecord) - { - if (shiftrecord != null) - { - Vector shifts = shiftrecord.shifts; - if (shifts != null && shifts.size() > 0) - { - int shifted = 0; - for (int i = 0, j = shifts.size(); i < j; i++) - { - int[] sh = (int[]) shifts.elementAt(i); - // compensateForEdit(shifted+sh[0], sh[1]); - compensateForDelEdits(shifted + sh[0], sh[1]); - shifted -= sh[1]; - } - } - return shiftrecord.getInverse(); - } - return null; - } - - /** - * removes intersection of position,length ranges in deletions from the - * start,end regions marked in intervals. - * - * @param deletions - * @param intervals - * @return - */ - private boolean pruneIntervalVector(Vector deletions, Vector intervals) - { - boolean pruned = false; - int i = 0, j = intervals.size() - 1, s = 0, t = deletions.size() - 1; - int hr[] = (int[]) intervals.elementAt(i); - int sr[] = (int[]) deletions.elementAt(s); - while (i <= j && s <= t) - { - boolean trailinghn = hr[1] >= sr[0]; - if (!trailinghn) - { - if (i < j) - { - hr = (int[]) 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 = (int[]) deletions.elementAt(++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 = (int[]) 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 = (int[]) deletions.elementAt(++s); - } - else - { - s++; - } - continue; - } - } - } - return pruned; // true if any interval was removed or modified by - // operations. - } - - private boolean pruneColumnList(Vector deletion, Vector list) - { - int s = 0, t = deletion.size(); - int[] sr = (int[]) list.elementAt(s++); - boolean pruned = false; - int i = 0, j = list.size(); - while (i < j && s <= t) - { - int c = ((Integer) 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 = (int[]) deletion.elementAt(s); - } - s++; - } - } - } - return pruned; - } - - /** - * remove any hiddenColumns or selected columns and shift remaining based on a - * series of position, range deletions. - * - * @param deletions - */ - public void pruneDeletions(ShiftList deletions) - { - if (deletions != null) - { - Vector shifts = deletions.shifts; - 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) - { - pruneColumnList(shifts, selected); - if (selected != null && selected.size() == 0) - { - selected = null; - } - } - // and shift the rest. - this.compensateForEdits(deletions); - } - } - } - - /** - * This Method is used to return all the HiddenColumn regions less than the - * given index. - * - * @param end - * int - * @return Vector - */ - public Vector getHiddenColumns() - { - return 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) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = (int[]) hiddenColumns.elementAt(i); - if (result >= region[0]) - { - result += region[1] - region[0] + 1; - } - } - } - return result; - } - - /** - * Use this method to find out where a visible column is in the alignment when - * hidden columns exist - * - * @param hiddenColumn - * int - * @return int - */ - public int findColumnPosition(int hiddenColumn) - { - int result = hiddenColumn; - if (hiddenColumns != null) - { - int index = 0; - int gaps = 0; - do - { - int[] region = (int[]) hiddenColumns.elementAt(index); - if (hiddenColumn > region[1]) - { - result -= region[1] + 1 - region[0]; - } - index++; - } while (index < hiddenColumns.size()); - - result -= gaps; - } - - return result; - } - - /** - * 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 = (int[]) 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 = (int[]) 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 = (int[]) hiddenColumns.elementAt(index); - if (alPos > region[1]) - { - return region[1]; - } - - index--; - } while (index > -1); - } - - return alPos; - - } - - public void hideSelectedColumns() - { - while (size() > 0) - { - int column = ((Integer) 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 = (int[]) 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 = (int[]) hiddenColumns.elementAt(i); - for (int j = region[0]; j < region[1] + 1; j++) - { - addElement(j); - } - } - } - - hiddenColumns = null; - } - - public void revealHiddenColumns(int res) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = (int[]) hiddenColumns.elementAt(i); - if (res == 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 i = 0; i < hiddenColumns.size(); i++) - { - int[] region = (int[]) hiddenColumns.elementAt(i); - if (column >= region[0] && column <= region[1]) - { - return false; - } - } - - return true; - } - - /** - * Copy constructor - * - * @param copy - */ - public ColumnSelection(ColumnSelection copy) - { - 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 = (int[]) copy.hiddenColumns.elementAt(i); - if (rh != null) - { - cp = new int[rh.length]; - System.arraycopy(rh, 0, cp, 0, rh.length); - hiddenColumns.addElement(cp); - } - } - } - } - } - - /** - * ColumnSelection - */ - public 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(); - Vector regions = getHiddenColumns(); - - int blockStart = start, blockEnd = end; - int[] region; - int hideStart, hideEnd; - - for (int j = 0; j < regions.size(); j++) - { - region = (int[]) regions.elementAt(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) - { - Vector visiblecontigs = new Vector(); - Vector regions = getHiddenColumns(); - - int vstart = start; - int[] region; - int hideStart, hideEnd; - - for (int j = 0; vstart < end && j < regions.size(); j++) - { - region = (int[]) regions.elementAt(j); - hideStart = region[0]; - hideEnd = region[1]; - - if (hideEnd < vstart) - { - continue; - } - if (hideStart > vstart) - { - visiblecontigs.addElement(new int[] - { vstart, hideStart - 1 }); - } - vstart = hideEnd + 1; - } - - if (vstart < end) - { - visiblecontigs.addElement(new int[] - { vstart, end - 1 }); - } - int[] vcontigs = new int[visiblecontigs.size() * 2]; - for (int i = 0, j = visiblecontigs.size(); i < j; i++) - { - int[] vc = (int[]) visiblecontigs.elementAt(i); - visiblecontigs.setElementAt(null, i); - vcontigs[i * 2] = vc[0]; - vcontigs[i * 2 + 1] = vc[1]; - } - visiblecontigs.removeAllElements(); - 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; - Vector regions = getHiddenColumns(); - int blockStart = start, blockEnd = end; - int[] region; - int hideStart, hideEnd, w = 0; - - for (int j = 0; j < regions.size(); j++) - { - region = (int[]) regions.elementAt(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 (end - blockStart + 1 <= alignmentAnnotation.annotations.length) - { - System.arraycopy(alignmentAnnotation.annotations, blockStart, - els, 0, els.length); - } - else - { - System.arraycopy(alignmentAnnotation.annotations, blockStart, - els, 0, (end - blockStart + 1)); - } - w += els.length; - } - if (w == 0) - return; - Enumeration e = annels.elements(); - alignmentAnnotation.annotations = new Annotation[w]; - w = 0; - while (e.hasMoreElements()) - { - Annotation[] chnk = (Annotation[]) e.nextElement(); - 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)) - { - removeElement(i); - } - else - { - if (!hasHidden || isVisible(i)) - { - addElement(i); - } - } - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import java.util.ArrayList; +import java.util.BitSet; +import java.util.Collections; +import java.util.List; +import java.util.regex.PatternSyntaxException; + +import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; +import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField; + +/** + * 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; + + /* + * 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; + } + } + + private IntList selection = new IntList(); + + /** + * Add a column to the selection + * + * @param col + * index of column + */ + public void addElement(int col) + { + 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) + { + for (int p = rng[c]; p <= rng[c + 1]; p++) + { + selection.add(base + p); + } + } + + } + + /** + * clears column selection + */ + public void clear() + { + selection.clear(); + } + + /** + * Removes value 'col' from the selection (not the col'th item) + * + * @param col + * index of column to be removed + */ + public void removeElement(int col) + { + selection.remove(col); + } + + /** + * removes a range of columns from the selection + * + * @param start + * int - first column in range to be removed + * @param end + * int - last col + */ + public void removeElements(int start, int end) + { + Integer colInt; + for (int i = start; i < end; i++) + { + colInt = Integer.valueOf(i); + if (selection.contains(colInt)) + { + selection.remove(colInt); + } + } + } + + /** + * 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 List getSelectedRanges() + { + return selection.getRanges(); + } + + /** + * + * @param col + * index to search for in column selection + * + * @return true if col is selected + */ + public boolean contains(int col) + { + return (col > -1) ? selection.isSelected(col) : false; + } + + /** + * + */ + public boolean intersects(int from, int to) + { + // TODO: do this in a more efficient bitwise way + for (int f = from; f <= to; f++) + { + if (selection.isSelected(f)) + { + return true; + } + } + return false; + } + + /** + * Answers true if no columns are selected, else false + */ + public boolean isEmpty() + { + return selection == null || selection.isEmpty(); + } + + /** + * rightmost selected column + * + * @return rightmost column in alignment that is selected + */ + public int getMax() + { + if (selection.isEmpty()) + { + return -1; + } + return selection.getMaxColumn(); + } + + /** + * Leftmost column in selection + * + * @return column index of leftmost column in selection + */ + public int getMin() + { + if (selection.isEmpty()) + { + return 1000000000; + } + return selection.getMinColumn(); + } + + public void hideSelectedColumns(AlignmentI al) + { + synchronized (selection) + { + for (int[] selregions : selection.getRanges()) + { + al.getHiddenColumns().hideColumns(selregions[0], selregions[1]); + } + selection.clear(); + } + + } + + /** + * Hides the specified column and any adjacent selected columns + * + * @param res + * int + */ + public void hideSelectedColumns(int col, HiddenColumns hidden) + { + /* + * deselect column (whether selected or not!) + */ + removeElement(col); + + /* + * find adjacent selected columns + */ + int min = col - 1, max = col + 1; + while (contains(min)) + { + removeElement(min); + min--; + } + + while (contains(max)) + { + removeElement(max); + max++; + } + + /* + * min, max are now the closest unselected columns + */ + min++; + max--; + if (min > max) + { + min = max; + } + + hidden.hideColumns(min, max); + } + + /** + * Copy constructor + * + * @param copy + */ + public ColumnSelection(ColumnSelection copy) + { + if (copy != null) + { + selection = new IntList(copy.selection); + } + } + + /** + * ColumnSelection + */ + public ColumnSelection() + { + } + + /** + * 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, AlignmentI al) + { + boolean hasHidden = al.getHiddenColumns().hasHiddenColumns(); + for (int i = first; i < width; i++) + { + if (contains(i)) + { + removeElement(i); + } + else + { + if (!hasHidden || al.getHiddenColumns().isVisible(i)) + { + addElement(i); + } + } + } + } + + /** + * set the selected columns to the given column selection, excluding any + * columns that are hidden. + * + * @param colsel + */ + public void setElementsFrom(ColumnSelection colsel, + HiddenColumns hiddenColumns) + { + selection = new IntList(); + if (colsel.selection != null && colsel.selection.size() > 0) + { + if (hiddenColumns.hasHiddenColumns()) + { + // only select visible columns in this columns selection + for (Integer col : colsel.getSelected()) + { + if (hiddenColumns != null + && hiddenColumns.isVisible(col.intValue())) + { + selection.add(col); + } + } + } + else + { + // add everything regardless + for (Integer col : colsel.getSelected()) + { + addElement(col); + } + } + } + } + + /** + * + * @return true if there are columns marked + */ + public boolean hasSelectedColumns() + { + return (selection != null && selection.size() > 0); + } + + /** + * 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 annotations + * @param filterParams + * @return + */ + public int filterAnnotations(AlignmentAnnotation ann_row, + AnnotationFilterParameter filterParams) + { + 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)) + { + float tVal = filterParams.getThresholdValue(); + if (ann_row.sequenceRef != null) + { + // TODO - get ContactList from AlignmentView for non-seq-ref associatd + for (int column = 0; column < annotations.length; column++) + { + if (ann_row.annotations[column] == null) + { + continue; + } + + 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++) + { + 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); + } + } + } + } + return selection.size(); + } + + int addedCount = 0; + int column = 0; + do + { + Annotation ann = annotations[column]; + if (ann != null) + { + float value = ann.value; + boolean matched = false; + + /* + * filter may have multiple conditions - + * these are or'd until a match is found + */ + if (filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD + && value > filterParams.getThresholdValue()) + { + matched = true; + } + + if (!matched && filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD + && value < filterParams.getThresholdValue()) + { + matched = true; + } + + if (!matched && filterParams.isFilterAlphaHelix() + && ann.secondaryStructure == 'H') + { + matched = true; + } + + if (!matched && filterParams.isFilterBetaSheet() + && ann.secondaryStructure == 'E') + { + matched = true; + } + + if (!matched && filterParams.isFilterTurn() + && ann.secondaryStructure == 'S') + { + matched = true; + } + + String regexSearchString = filterParams.getRegexString(); + if (!matched && regexSearchString != null) + { + 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; + } + } + } + } + + if (matched) + { + this.addElement(column); + addedCount++; + } + } + column++; + } while (column < annotations.length); + + return addedCount; + } + + /** + * Returns a hashCode built from selected columns ranges + */ + @Override + public int hashCode() + { + return selection.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 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); + } + } + } +}