+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.datamodel;\r
\r
public class CigarArray extends CigarBase\r
* applyDeletions\r
* edits underlying refCigars to propagate deleted regions, and removes deletion\r
* operations from CigarArray operation list.\r
- * @return int[] position where deletion occured in cigarArray or null if none occured\r
+ * @return int[] position after deletion occured and range of deletion in cigarArray or null if none occured\r
*/\r
public int[] applyDeletions()\r
{\r
return null;\r
int cursor=0; // range counter for deletions\r
int vcursor=0; // visible column index\r
- for (int i=0; i<length; i++) {\r
+ int offset=0; // shift in visible column index as deletions are made\r
+ int i=0;\r
+ while (i<length) {\r
if (operation[i]!=D) {\r
if (operation[i]==M)\r
cursor+=range[i];\r
- vcursor+=range[i];\r
+ vcursor+=range[i++];\r
}\r
else\r
{\r
if (delpos==null)\r
delpos=new java.util.Vector();\r
int delstart=cursor, delend=cursor+range[i]-1; // inclusive\r
- delpos.addElement(new Integer(vcursor-1)); // index of left hand column of hidden region boundary\r
+ delpos.addElement(new int[] { vcursor+offset, range[i]}); // index of right hand column after hidden region boundary\r
+ offset+=range[i]-1; // shift in visible column coordinates\r
System.arraycopy(operation, i+1, operation, i, length-i);\r
System.arraycopy(range, i+1, range, i, length-i);\r
length--;\r
+ /* int dmax=0;\r
+ for (int s=0; s<refCigars.length; s++) {\r
+ int d = refCigars[s].deleteRange(delstart, delend);\r
+ if (d>dmax)\r
+ dmax=d;\r
+ }\r
+ offset+=dmax; // shift in visible column coordinates\r
+ */\r
for (int s=0; s<refCigars.length; s++) {\r
- refCigars[s].deleteRange(delstart, delend);\r
+ int d = refCigars[s].deleteRange(delstart, delend);\r
}\r
+\r
}\r
}\r
if (delpos!=null)\r
{\r
- int[] pos=new int[delpos.size()];\r
+ int[] pos=new int[delpos.size()*2];\r
for (int k = 0, l = delpos.size(); k < l; k++) {\r
- pos[k] = ((Integer) delpos.elementAt(k)).intValue();\r
+ int[] dr = ((int[]) delpos.elementAt(k));\r
+ pos[k*2] = dr[0];\r
+ pos[k*2+1] = dr[1];\r
delpos.setElementAt(null,k);\r
}\r
delpos=null;\r