-\r
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2007 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
-package jalview.commands;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class SlideSequencesCommand extends EditCommand\r
-{\r
- boolean gapsInsertedBegin = false;\r
-\r
- public SlideSequencesCommand(String description,\r
- SequenceI[] seqsLeft,\r
- SequenceI[] seqsRight,\r
- int slideSize,\r
- char gapChar)\r
- {\r
- this.description = description;\r
-\r
- int lSize = seqsLeft.length;\r
- gapsInsertedBegin = false;\r
- int i, j;\r
- for (i = 0; i < lSize; i++)\r
- {\r
- for (j = 0; j < slideSize; j++)\r
- if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j)))\r
- {\r
- gapsInsertedBegin = true;\r
- break;\r
- }\r
- }\r
-\r
- if (!gapsInsertedBegin)\r
- edits = new Edit[]\r
- { new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar)};\r
- else\r
- edits = new Edit[]\r
- { new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar)};\r
-\r
- performEdit(0);\r
- }\r
-\r
- public boolean getGapsInsertedBegin()\r
- {\r
- return gapsInsertedBegin;\r
- }\r
-\r
- public boolean appendSlideCommand(SlideSequencesCommand command)\r
- {\r
- boolean same = false;\r
-\r
- if(command.edits[0].seqs.length==edits[0].seqs.length)\r
- {\r
- same = true;\r
- for (int i = 0; i < command.edits[0].seqs.length; i++)\r
- {\r
- if (edits[0].seqs[i] != command.edits[0].seqs[i])\r
- {\r
- same = false;\r
- }\r
- }\r
- }\r
-\r
- if(same)\r
- {\r
- Edit[] temp = new Edit[command.edits.length + 1];\r
- System.arraycopy(command.edits, 0, temp, 0, command.edits.length);\r
- command.edits = temp;\r
- command.edits[command.edits.length - 1] = edits[0];\r
- }\r
-\r
- return same;\r
- }\r
-}\r
-\r
-\r
+
+/*
+* 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
+*/
+
+package jalview.commands;
+
+import jalview.datamodel.*;
+
+public class SlideSequencesCommand extends EditCommand
+{
+ boolean gapsInsertedBegin = false;
+
+ public SlideSequencesCommand(String description,
+ SequenceI[] seqsLeft,
+ SequenceI[] seqsRight,
+ int slideSize,
+ char gapChar)
+ {
+ this.description = description;
+
+ int lSize = seqsLeft.length;
+ gapsInsertedBegin = false;
+ int i, j;
+ for (i = 0; i < lSize; i++)
+ {
+ for (j = 0; j < slideSize; j++)
+ if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j)))
+ {
+ gapsInsertedBegin = true;
+ break;
+ }
+ }
+
+ if (!gapsInsertedBegin)
+ edits = new Edit[]
+ { new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar)};
+ else
+ edits = new Edit[]
+ { new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar)};
+
+ performEdit(0,null);
+ }
+
+ public boolean getGapsInsertedBegin()
+ {
+ return gapsInsertedBegin;
+ }
+
+ public boolean appendSlideCommand(SlideSequencesCommand command)
+ {
+ boolean same = false;
+
+ if(command.edits[0].seqs.length==edits[0].seqs.length)
+ {
+ same = true;
+ for (int i = 0; i < command.edits[0].seqs.length; i++)
+ {
+ if (edits[0].seqs[i] != command.edits[0].seqs[i])
+ {
+ same = false;
+ }
+ }
+ }
+
+ if(same)
+ {
+ Edit[] temp = new Edit[command.edits.length + 1];
+ System.arraycopy(command.edits, 0, temp, 0, command.edits.length);
+ command.edits = temp;
+ command.edits[command.edits.length - 1] = edits[0];
+ }
+
+ return same;
+ }
+}
+
+