-package jalview.commands;\r
- /*\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
-\r
-import jalview.datamodel.*;\r
-\r
-public class RemoveGapsCommand extends EditCommand\r
-{\r
- public RemoveGapsCommand( String description,\r
- SequenceI[] seqs, char gapChar)\r
- {\r
- this.description = description;\r
- int width = 0;\r
- for(int i=0; i<seqs.length; i++)\r
- if(seqs[i].getLength()>width)\r
- width = seqs[i].getLength();\r
-\r
- findGaps(seqs, 0, width, gapChar);\r
- }\r
-\r
- public RemoveGapsCommand( String description,\r
- SequenceI[] seqs,\r
- int start, int end, char gapChar)\r
- {\r
- this.description = description;\r
- findGaps(seqs, start, end, gapChar);\r
- }\r
-\r
- void findGaps(SequenceI [] seqs, int start, int end, char gapChar)\r
- {\r
-\r
- int startCol = -1, endCol = -1;\r
- int deletedCols = 0;\r
-\r
- edits = new Edit[0];\r
-\r
- boolean delete = true;\r
- char [] sequence;\r
- for(int s=0; s<seqs.length; s++)\r
- {\r
- deletedCols = 0;\r
- startCol = -1;\r
- endCol = -1;\r
- sequence = seqs[s].getSequence().toCharArray();\r
- for (int i = start; i < end; i++)\r
- {\r
- delete = true;\r
-\r
- if (!jalview.util.Comparison.isGap(sequence[i]))\r
- {\r
- if (delete)\r
- endCol = i;\r
-\r
- delete = false;\r
- }\r
-\r
- if (delete && startCol == -1)\r
- {\r
- startCol = i;\r
- }\r
-\r
- if (!delete && startCol > -1)\r
- {\r
- this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]},\r
- startCol - deletedCols,\r
- endCol - startCol,\r
- gapChar,\r
- false);\r
-\r
- deletedCols += (endCol - startCol);\r
- startCol = -1;\r
- endCol = -1;\r
- }\r
- }\r
- if (delete && startCol > -1)\r
- {\r
- int width = end - endCol;\r
-\r
- if (endCol == -1)\r
- width = end - start + 1;\r
-\r
- //This is the end of the region.\r
- this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]},\r
- startCol - deletedCols,\r
- width,\r
- gapChar,\r
- false);\r
- }\r
-\r
- }\r
-\r
- performEdit(0);\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.commands;
+
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer Copyright (C) 2007 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
+ */
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+public class RemoveGapsCommand extends EditCommand
+{
+ public RemoveGapsCommand(String description, SequenceI[] seqs,
+ AlignmentI al)
+ {
+ this.description = description;
+ int width = 0;
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i].getLength() > width)
+ {
+ width = seqs[i].getLength();
+ }
+ }
+
+ findGaps(seqs, 0, width, al);
+ }
+
+ public RemoveGapsCommand(String description, SequenceI[] seqs, int start,
+ int end, AlignmentI al)
+ {
+ this.description = description;
+ findGaps(seqs, start, end, al);
+ }
+
+ void findGaps(SequenceI[] seqs, int start, int end, AlignmentI al)
+ {
+
+ int startCol = -1, endCol = -1;
+ int deletedCols = 0;
+
+ int j, jSize;
+
+ clearEdits();
+
+ boolean delete = true;
+ char[] sequence;
+
+ for (int s = 0; s < seqs.length; s++)
+ {
+ deletedCols = 0;
+ startCol = -1;
+ endCol = -1;
+ sequence = seqs[s].getSequence(start, end + 1);
+
+ jSize = sequence.length;
+ for (j = 0; j < jSize; j++)
+ {
+ delete = true;
+
+ if (!jalview.util.Comparison.isGap(sequence[j]))
+ {
+ if (delete)
+ {
+ endCol = j;
+ }
+
+ delete = false;
+ }
+
+ if (delete && startCol == -1)
+ {
+ startCol = j;
+ }
+
+ if (!delete && startCol > -1)
+ {
+ this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] },
+ start + startCol - deletedCols, endCol - startCol, al,
+ false, null);
+
+ deletedCols += (endCol - startCol);
+ startCol = -1;
+ endCol = -1;
+ }
+ }
+ if (delete && startCol > -1)
+ {
+ this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] },
+ start + startCol - deletedCols, jSize - startCol, al,
+ false, null);
+ }
+
+ }
+
+ performEdit(0, null);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff