From: amwaterhouse Date: Tue, 25 Jul 2006 15:49:42 +0000 (+0000) Subject: 1.1 compatible X-Git-Tag: Release_2_1~211 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0da4baaa746b174c1ec4776cdff7abfb2a019154;p=jalview.git 1.1 compatible --- diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java new file mode 100644 index 0000000..1dafcf0 --- /dev/null +++ b/src/jalview/datamodel/ColumnSelection.java @@ -0,0 +1,419 @@ +/* + * 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 + * 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.*; + +/** + * NOTE: Columns are zero based. + */ +public class ColumnSelection +{ + Vector selected = new Vector(); + + //Vector of int [] {startCol, endCol} + Vector hiddenColumns; + + /** + * DOCUMENT ME! + * + * @param col DOCUMENT ME! + */ + public void addElement(int col) + { + if (!selected.contains(new Integer(col))) + { + selected.addElement(new Integer(col)); + } + } + + /** + * DOCUMENT ME! + */ + public void clear() + { + selected.removeAllElements(); + } + + /** + * DOCUMENT ME! + * + * @param col DOCUMENT ME! + */ + public void removeElement(int col) + { + Integer colInt = new Integer(col); + + if (selected.contains(colInt)) + { + selected.removeElement(colInt); + } + } + + 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; + } + + + /** + * DOCUMENT ME! + * + * @param start DOCUMENT ME! + * @param change DOCUMENT ME! + */ + 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; + } + } + } + + /** + * 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; + } + + 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 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 hideColumns(int res) + { + if(hiddenColumns==null) + hiddenColumns = new Vector(); + + // First find out range of columns to hide + int min = res, max = res+1; + while( contains(min) ) + { removeElement(min); min --; } + + while( contains(max) ) + { removeElement(max); max ++; } + + min++; max--; + + boolean added = false; + for(int i=0; i= region[0] && column <= region[1]) + { + return false; + } + } + return true; + } + +}