From b2d54d33d6313efd9da96bd7586dfaa7a0d7a182 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 22 Aug 2006 08:34:04 +0000 Subject: [PATCH] hidden region recovery in JPred and new hidden region pruning function --- src/jalview/datamodel/ColumnSelection.java | 1181 ++++++++++++++++------------ src/jalview/util/ShiftList.java | 248 +++--- src/jalview/ws/JPredClient.java | 4 +- 3 files changed, 792 insertions(+), 641 deletions(-) diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index 39d7a8d..bd06ca3 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -1,510 +1,671 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 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 jalview.util.ShiftList; - -import java.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 max) - { - max = columnAt(i); - } - } - - return max; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - 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 change shift in edit (-ve or +ve number of columns) - */ - public void compensateForEdit(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 start) - { - region[0] -= change; - region[1] -= change; - } - if(region[0]<0) - region[0] = 0; - if(region[1] <0) - region[1] = 0; - } - } - } - 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]) - { - 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 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) - { - 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--; - - 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= 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 max) + { + max = columnAt(i); + } + } + + return max; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + 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 void compensateForEdit(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 start) + { + region[0] -= change; + region[1] -= change; + } + if(region[0]<0) + region[0] = 0; + if(region[1] <0) + region[1] = 0; + } + } + } + /** + * 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= start) + { + region[0] -= change; + } + if (region[1]>= start) { + region[1] -=change; + } + if (region[1]