package jalview.commands;\r
- /*\r
+\r
+/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
\r
import jalview.datamodel.*;\r
\r
-public class RemoveGapsCommand extends EditCommand\r
+public class RemoveGapsCommand\r
+ extends EditCommand\r
{\r
- public RemoveGapsCommand( String description,\r
- SequenceI[] seqs, AlignmentI al)\r
+ public RemoveGapsCommand(String description,\r
+ SequenceI[] seqs, AlignmentI al)\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
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (seqs[i].getLength() > width)\r
+ {\r
width = seqs[i].getLength();\r
+ }\r
+ }\r
\r
findGaps(seqs, 0, width, al);\r
}\r
\r
- public RemoveGapsCommand( String description,\r
- SequenceI[] seqs,\r
- int start, int end, AlignmentI al)\r
+ public RemoveGapsCommand(String description,\r
+ SequenceI[] seqs,\r
+ int start, int end, AlignmentI al)\r
{\r
this.description = description;\r
findGaps(seqs, start, end, al);\r
}\r
\r
- void findGaps(SequenceI [] seqs, int start, int end, AlignmentI al)\r
+ void findGaps(SequenceI[] seqs, int start, int end, AlignmentI al)\r
{\r
\r
int startCol = -1, endCol = -1;\r
edits = new Edit[0];\r
\r
boolean delete = true;\r
- char [] sequence;\r
+ char[] sequence;\r
\r
- for(int s=0; s<seqs.length; s++)\r
+ for (int s = 0; s < seqs.length; s++)\r
{\r
deletedCols = 0;\r
startCol = -1;\r
endCol = -1;\r
- sequence = seqs[s].getSequence(start, end+1);\r
+ sequence = seqs[s].getSequence(start, end + 1);\r
\r
jSize = sequence.length;\r
- for (j=0; j<jSize; j++)\r
+ for (j = 0; j < jSize; j++)\r
{\r
delete = true;\r
\r
-\r
if (!jalview.util.Comparison.isGap(sequence[j]))\r
{\r
if (delete)\r
+ {\r
endCol = j;\r
+ }\r
\r
delete = false;\r
}\r
\r
-\r
if (delete && startCol == -1)\r
{\r
startCol = j;\r
\r
if (!delete && startCol > -1)\r
{\r
- this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]},\r
+ this.appendEdit(DELETE_GAP, new SequenceI[]\r
+ {seqs[s]},\r
start + startCol - deletedCols,\r
endCol - startCol,\r
al,\r
}\r
if (delete && startCol > -1)\r
{\r
- this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]},\r
+ this.appendEdit(DELETE_GAP, new SequenceI[]\r
+ {seqs[s]},\r
start + startCol - deletedCols,\r
jSize - startCol,\r
al,\r