From 8b08ad675b71e43e127d7be3b65c6d2f9d9094db Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 10 Oct 2006 10:44:03 +0000 Subject: [PATCH] 1.1 compatible --- src/jalview/datamodel/ColumnSelection.java | 1552 ++++++++++++++-------------- 1 file changed, 776 insertions(+), 776 deletions(-) diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index c895b2f..c35ff46 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -1,776 +1,776 @@ -/* - * 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 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]