X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=15bbffa1e8669610076b4d87363e14f55b33fef9;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=6b9f28d6fb114914e18144ada3f1a0e98e8b2b79;hpb=608832fec5a504b4c56e5837b2b3dfc1993fe734;p=jalview.git diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index 6b9f28d..15bbffa 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -1,510 +1,1392 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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. - * - * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.datamodel; import jalview.util.ShiftList; +import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; +import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +import java.util.Vector; /** * NOTE: Columns are zero based. */ public class ColumnSelection { - Vector selected = new Vector(); + Vector selected = new Vector(); - //Vector of int [] {startCol, endCol} - Vector hiddenColumns; + // Vector of int [] {startCol, endCol} + Vector hiddenColumns; - /** - * Add a column to the selection - * - * @param col index of column - */ - public void addElement(int col) + /** + * 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)) { - Integer column = new Integer(col); - if (!selected.contains(column)) - { - selected.addElement(column); - } + selected.addElement(column); } + } - /** - * clears column selection - */ - public void clear() - { - selected.removeAllElements(); - } + /** + * 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); + /** + * Removes value 'col' from the selection (not the col'th item) + * + * @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); - } + 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); } + } - /** - * 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) + /** + * 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++) { - Integer colInt; - for(int i=start; i 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 selected.elementAt(i).intValue(); + } - /** - * - * @param col index to search for in column selection - * - * @return true if Integer(col) is in selection. - */ - public boolean contains(int col) + /** + * 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++) { - return selected.contains(new Integer(col)); + if (columnAt(i) > max) + { + max = columnAt(i); + } } - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int columnAt(int 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++) { - return ((Integer) selected.elementAt(i)).intValue(); + if (columnAt(i) < min) + { + min = columnAt(i); + } } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int size() + 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 List compensateForEdit(int start, int change) + { + List deletedHiddenColumns = null; + for (int i = 0; i < size(); i++) { - return selected.size(); + int temp = columnAt(i); + + if (temp >= start) + { + // if this ever changes to List.set(), swap parameter order!! + selected.setElementAt(new Integer(temp - change), i); + } } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getMax() + if (hiddenColumns != null) { - int max = -1; + 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; + } - for (int i = 0; i < selected.size(); i++) + if (region[0] > start) { - if (columnAt(i) > max) - { - max = columnAt(i); - } + region[0] -= change; + region[1] -= change; } - return max; + if (region[0] < 0) + { + region[0] = 0; + } + + } + + this.revealHiddenColumns(0); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getMin() + 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 min = 1000000000; + int temp = columnAt(i); - for (int i = 0; i < selected.size(); i++) + if (temp >= start) + { + // if this ever changes to List.set(), swap parameter order!! + selected.setElementAt(new Integer(temp - change), i); + } + } + + if (hiddenColumns != null) + { + for (int i = 0; i < hiddenColumns.size(); i++) + { + int[] region = hiddenColumns.elementAt(i); + if (region[0] >= start) { - if (columnAt(i) < min) - { - min = columnAt(i); - } + region[0] -= change; + } + if (region[1] >= start) + { + region[1] -= change; + } + if (region[1] < region[0]) + { + hiddenColumns.removeElementAt(i--); } - return min; + if (region[0] < 0) + { + region[0] = 0; + } + if (region[1] < 0) + { + region[1] = 0; + } + } } + } - - /** - * propagate shift in alignment columns to column selection - * - * @param start beginning of edit - * @param change shift in edit (-ve or +ve number of columns) - */ - public void compensateForEdit(int start, int change) + /** + * 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) { - for (int i = 0; i < size(); i++) + final List shifts = shiftrecord.getShifts(); + if (shifts != null && shifts.size() > 0) + { + int shifted = 0; + for (int i = 0, j = shifts.size(); i < j; i++) { - int temp = columnAt(i); - - if (temp >= start) - { - selected.setElementAt(new Integer(temp - change), i); - } + int[] sh = shifts.get(i); + // compensateForEdit(shifted+sh[0], sh[1]); + compensateForDelEdits(shifted + sh[0], sh[1]); + shifted -= sh[1]; } + } + return shiftrecord.getInverse(); + } + return null; + } - if(hiddenColumns!=null) + /** + * removes intersection of position,length ranges in deletions from the + * start,end regions marked in intervals. + * + * @param shifts + * @param intervals + * @return + */ + private boolean pruneIntervalVector(final List shifts, + Vector intervals) + { + boolean pruned = false; + int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1; + int hr[] = intervals.elementAt(i); + int sr[] = shifts.get(s); + while (i <= j && s <= t) + { + boolean trailinghn = hr[1] >= sr[0]; + if (!trailinghn) + { + if (i < j) + { + hr = intervals.elementAt(++i); + } + else + { + i++; + } + continue; + } + int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert + if (endshift < hr[0] || endshift < sr[0]) + { // leadinghc disjoint or not a deletion + if (s < t) { - for(int i=0; i= 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) { - int[] region = (int[]) hiddenColumns.elementAt(i); - if(region[0] > start) - { - region[0] -= change; - region[1] -= change; - } - if(region[0]<0) - region[0] = 0; - if(region[1] <0) - region[1] = 0; + hr = intervals.elementAt(i); } + continue; } - } - public ShiftList compensateForEdits(ShiftList shiftrecord) { - if (shiftrecord!=null) { - Vector shifts = shiftrecord.shifts; - if (shifts!=null && shifts.size()>0) { - for (int i=0,j=shifts.size(); i= region[0]) + // sr contained in hr + if (s < t) + { + sr = shifts.get(++s); + } + else { - result += region[1] - region[0] + 1; + s++; } + continue; } } - return result; } + return pruned; // true if any interval was removed or modified by + // operations. + } - /** - * 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) + private boolean pruneColumnList(final List shifts, + Vector list) + { + 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 result = hiddenColumn; - if (hiddenColumns != null) + int c = list.elementAt(i++).intValue(); + if (sr[0] <= c) { - int index = 0; - int gaps = 0; - do + if (sr[1] + sr[0] >= c) + { // sr[1] -ve means inseriton. + list.removeElementAt(--i); + j--; + } + else { - int[] region = (int[]) hiddenColumns.elementAt(index); - if (hiddenColumn > region[1]) + if (s < t) { - result -= region[1]+1-region[0]; + sr = shifts.get(s); } - index++; + s++; } - while (index < hiddenColumns.size()); - - result -= gaps; } - - return result; } + return pruned; + } - /** - * Use this method to determine where the next hiddenRegion starts - */ - public int findHiddenRegionPosition(int hiddenRegion) + /** + * 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) { - int result = 0; - if (hiddenColumns != null) + final List shifts = deletions.getShifts(); + if (shifts != null && shifts.size() > 0) { - int index = 0; - int gaps = 0; - do + // delete any intervals intersecting. + if (hiddenColumns != null) { - int[] region = (int[]) hiddenColumns.elementAt(index); - if(hiddenRegion==0) + pruneIntervalVector(shifts, hiddenColumns); + if (hiddenColumns != null && hiddenColumns.size() == 0) { - return region[0]; + hiddenColumns = null; } - - gaps += region[1] +1 - region[0]; - result = region[1] +1; - index++; } - while(index < hiddenRegion+1); - - result -= gaps; + if (selected != null && selected.size() > 0) + { + pruneColumnList(shifts, selected); + if (selected != null && selected.size() == 0) + { + selected = null; + } + } + // and shift the rest. + this.compensateForEdits(deletions); } - - return result; } + } + + /** + * 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; + } - /** - * 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) + /** + * 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) { - if (hiddenColumns != null) + for (int i = 0; i < hiddenColumns.size(); i++) { - int index = 0; - do + int[] region = hiddenColumns.elementAt(i); + if (result >= region[0]) { - int[] region = (int[]) hiddenColumns.elementAt(index); - if(alPos < region[0]) - return region[0]; + result += region[1] - region[0] + 1; + } + } + } + return result; + } - index++; + /** + * Use this method to find out where a column will appear in the visible + * alignment when hidden columns exist. If the column is not visible, then the + * left-most visible column will always be returned. + * + * @param hiddenColumn + * int + * @return int + */ + public int findColumnPosition(int hiddenColumn) + { + int result = hiddenColumn; + if (hiddenColumns != null) + { + int index = 0; + int[] region; + do + { + region = hiddenColumns.elementAt(index++); + if (hiddenColumn > region[1]) + { + result -= region[1] + 1 - region[0]; } - while(index < hiddenColumns.size()); + } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size())); + if (hiddenColumn > region[0] && hiddenColumn < region[1]) + { + return region[0] + hiddenColumn - result; } + } + return result; // return the shifted position after removing hidden columns. + } + + /** + * Use this method to determine where the next hiddenRegion starts + */ + public int findHiddenRegionPosition(int hiddenRegion) + { + int result = 0; + if (hiddenColumns != null) + { + int index = 0; + int gaps = 0; + do + { + int[] region = hiddenColumns.elementAt(index); + if (hiddenRegion == 0) + { + return region[0]; + } - return alPos; + gaps += region[1] + 1 - region[0]; + result = region[1] + 1; + index++; + } while (index < hiddenRegion + 1); + result -= gaps; } - /** - * 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 getHiddenBoundaryLeft(int alPos) + + 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) { - if (hiddenColumns != null) + int index = 0; + do { - int index = hiddenColumns.size()-1; - do + int[] region = hiddenColumns.elementAt(index); + if (alPos < region[0]) { - int[] region = (int[]) hiddenColumns.elementAt(index); - if(alPos > region[1]) - return region[1]; + return region[0]; + } - index--; + index++; + } while (index < hiddenColumns.size()); + } + + return alPos; + + } + + /** + * This method returns the leftmost limit of a region of an alignment with + * hidden columns. In otherwords, the previous hidden column. + * + * @param index + * int + */ + public int getHiddenBoundaryLeft(int alPos) + { + if (hiddenColumns != null) + { + int index = hiddenColumns.size() - 1; + do + { + int[] region = hiddenColumns.elementAt(index); + if (alPos > region[1]) + { + return region[1]; } - while(index >-1); - } - return alPos; + index--; + } while (index > -1); + } + + return alPos; + } + + public void hideSelectedColumns() + { + while (size() > 0) + { + int column = getSelected().firstElement().intValue(); + hideColumns(column); } - public void hideSelectedColumns() + } + + public void hideColumns(int start, int end) + { + if (hiddenColumns == null) { - while (size() > 0) + 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]) { - int column = ( (Integer) getSelected().firstElement()).intValue(); - hideColumns(column); + 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--; } - public void hideColumns(int start, int end) + while (contains(max)) { - if(hiddenColumns==null) - hiddenColumns = new Vector(); + removeElement(max); + max++; + } - boolean added = false; - boolean overlap = false; + 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); - if ( start<=region[1] && end>=region[0]) + int[] region = hiddenColumns.elementAt(i); + for (int j = region[0]; j < region[1] + 1; j++) { - hiddenColumns.removeElementAt(i); - overlap = true; - break; + addElement(j); } - else if (end < region[0] && start < region[0]) + } + } + + 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++) { - hiddenColumns.insertElementAt(new int[] - {start, end}, i); - added = true; - break; + addElement(j); } + + hiddenColumns.removeElement(region); + break; } + } + if (hiddenColumns.size() == 0) + { + hiddenColumns = null; + } + } - if(overlap) + public boolean isVisible(int column) + { + if (hiddenColumns != null) + { + for (int i = 0; i < hiddenColumns.size(); i++) { - hideColumns(start, end); + int[] region = hiddenColumns.elementAt(i); + if (column >= region[0] && column <= region[1]) + { + return false; + } } - else if (!added) - hiddenColumns.addElement(new int[] {start, end}); + } + + 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 = copy.hiddenColumns.elementAt(i); + if (rh != null) + { + cp = new int[rh.length]; + System.arraycopy(rh, 0, cp, 0, rh.length); + hiddenColumns.addElement(cp); + } + } + } } + } - /** - * This method will find a range of selected columns - * around the column specified - * @param res int - */ - public void hideColumns(int col) + /** + * 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) { - // First find out range of columns to hide - int min = col, max = col+1; - while( contains(min) ) - { removeElement(min); min --; } + for (i = 0; i < iSize; i++) + { + StringBuffer visibleSeq = new StringBuffer(); + List regions = getHiddenColumns(); - while( contains(max) ) - { removeElement(max); max ++; } + int blockStart = start, blockEnd = end; + int[] region; + int hideStart, hideEnd; - min++; max--; + 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; + } - hideColumns(min, max); + 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); + } } - public void revealAllHiddenColumns() + 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) { - if(hiddenColumns!=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++) { - for (int i = 0; i < hiddenColumns.size(); i++) + region = regions.get(j); + hideStart = region[0]; + hideEnd = region[1]; + + if (hideEnd < vstart) { - int[] region = (int[]) hiddenColumns.elementAt(i); - for (int j = region[0]; j < region[1]+1; j++) - { - addElement(j); - } + continue; + } + if (hideStart > vstart) + { + visiblecontigs.add(new int[] { vstart, hideStart - 1 }); } + vstart = hideEnd + 1; } - hiddenColumns = null; + if (vstart < end) + { + visiblecontigs.add(new int[] { vstart, end - 1 }); + } + int[] vcontigs = new int[visiblecontigs.size() * 2]; + for (int i = 0, j = visiblecontigs.size(); i < j; i++) + { + int[] vc = visiblecontigs.get(i); + visiblecontigs.set(i, null); + vcontigs[i * 2] = vc[0]; + vcontigs[i * 2 + 1] = vc[1]; + } + visiblecontigs.clear(); + return vcontigs; + } + else + { + return new int[] { start, end - 1 }; } + } - public void revealHiddenColumns(int res) + /** + * 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) { - for(int i=0; i 0) + { + // then mangle the alignmentAnnotation annotation array + Vector annels = new Vector(); + Annotation[] els = null; + List regions = getHiddenColumns(); + int blockStart = start, blockEnd = end; + int[] region; + int hideStart, hideEnd, w = 0; + + for (int j = 0; j < regions.size(); j++) { - int [] region = (int[])hiddenColumns.elementAt(i); - if( res == region[0]) + region = regions.get(j); + hideStart = region[0]; + hideEnd = region[1]; + + if (hideStart < start) { - for (int j = region[0]; j < region[1]+1; j++) - { - addElement(j); - } + continue; + } + + blockStart = Math.min(blockStart, hideEnd + 1); + blockEnd = Math.min(blockEnd, hideStart); - hiddenColumns.removeElement(region); + if (blockStart > blockEnd) + { break; } + + annels.addElement(els = new Annotation[blockEnd - blockStart]); + System.arraycopy(alignmentAnnotation.annotations, blockStart, els, + 0, els.length); + w += els.length; + blockStart = hideEnd + 1; + blockEnd = end; + } + + if (end > blockStart) + { + annels.addElement(els = new Annotation[end - blockStart + 1]); + if ((els.length + blockStart) <= alignmentAnnotation.annotations.length) + { + // copy just the visible segment of the annotation row + System.arraycopy(alignmentAnnotation.annotations, blockStart, + els, 0, els.length); + } + else + { + // copy to the end of the annotation row + System.arraycopy(alignmentAnnotation.annotations, blockStart, + els, 0, + (alignmentAnnotation.annotations.length - blockStart)); + } + w += els.length; + } + if (w == 0) + { + return; + } + + alignmentAnnotation.annotations = new Annotation[w]; + w = 0; + + for (Annotation[] chnk : annels) + { + System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, + chnk.length); + w += chnk.length; } - if(hiddenColumns.size()==0) - hiddenColumns = null; } + else + { + alignmentAnnotation.restrict(start, end); + } + } - public boolean isVisible(int column) + /** + * 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++) { - for(int i=0; i= region[0] && column <= region[1]) + if (!hasHidden || isVisible(i)) { - return false; + addElement(i); } } - 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 0) + { + for (Integer col : colsel.getSelected()) + { + if (hiddenColumns != null && isVisible(col.intValue())) + { + if (!selected.contains(col)) + { + selected.addElement(col); } } - if (copy.hiddenColumns!=null) { - hiddenColumns=new Vector(); - for (int i=0,j=copy.hiddenColumns.size(); i(); + if (colsel.selected != null && colsel.selected.size() > 0) + { + 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); + } + } + } + } + + /** + * 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 (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; } + if ((offset + spos) < profileseq.getLength()) + { + // pad the final region with gaps. + StringBuffer sb = new StringBuffer(); + for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++) + { + sb.append(gc); + } + for (int s = 0, ns = al.getHeight(); s < ns; s++) + { + 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(); + } + } + } + } /** - * ColumnSelection + * + * @return true if there are columns marked */ - public ColumnSelection() + 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; } }