/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
+ * This file is part of Jalview.\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
+ * Jalview 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 3 of the License, or (at your option) any later version.\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
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.datamodel;\r
\r
* any of cigar are actually CigarArrays.\r
* \r
* @param cigar\r
- * Cigar[]\r
+ * Cigar[]\r
*/\r
public CigarArray(CigarSimple[] cigars)\r
{\r
/**\r
* @see Cigar.getSequenceAndDeletions\r
* @param GapChar\r
- * char\r
+ * char\r
* @return Object[][]\r
*/\r
protected Object[][] getArrayofSequenceAndDeletions(char GapChar)\r
* @return String formed by newline concatenated results of applying CIGAR\r
* operations to each reference object in turn.\r
* @param GapChar\r
- * char\r
+ * char\r
* @return '\n' separated strings (empty results included as \n\n)\r
*/\r
public String getSequenceString(char GapChar)\r
* return string results of applying cigar string to all reference cigars\r
* \r
* @param GapChar\r
- * char\r
+ * char\r
* @return String[]\r
*/\r
public String[] getSequenceStrings(char GapChar)\r
* \r
* @return Cigar[]\r
* \r
- * public CigarBase[] getEditedCigars() {\r
+ * public CigarBase[] getEditedCigars() {\r
* \r
- * return new CigarBase[] {}; }\r
+ * return new CigarBase[] {}; }\r
*/\r
/**\r
* applyDeletions edits underlying refCigars to propagate deleted regions, and\r
int delstart = cursor, delend = cursor + range[i] - 1; // inclusive\r
delpos.addElement(new int[]\r
{ vcursor + offset, range[i] }); // index of right hand column after\r
- // hidden region boundary\r
+ // 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