1 package jalview.commands;
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3 * Jalview - A Sequence Alignment Editor and Viewer
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4 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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6 * This program is free software; you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License
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8 * as published by the Free Software Foundation; either version 2
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9 * of the License, or (at your option) any later version.
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11 * This program is distributed in the hope that it will be useful,
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12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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14 * GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License
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17 * along with this program; if not, write to the Free Software
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18 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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21 import jalview.datamodel.*;
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23 public class RemoveGapColCommand extends EditCommand
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26 public RemoveGapColCommand(String description,
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28 int start, int end, AlignmentI al)
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30 this.description = description;
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32 int j, jSize = seqs.length;
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34 int startCol = -1, endCol = -1;
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37 edits = new Edit[0];
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39 boolean delete = true;
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40 for (int i = start; i <= end; i++)
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44 for (j = 0; j < jSize; j++)
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46 if (seqs[j].getLength() > i)
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48 if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
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59 if (delete && startCol == -1)
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64 if (!delete && startCol > -1)
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66 this.appendEdit(DELETE_GAP, seqs,
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67 startCol - columnsDeleted,
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72 columnsDeleted += (endCol - startCol);
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78 if (delete && startCol > -1)
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80 //This is for empty columns at the
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81 //end of the alignment
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83 this.appendEdit(DELETE_GAP, seqs,
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84 startCol - columnsDeleted,
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89 columnsDeleted += (end - startCol +1);
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96 public int getSize()
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98 //We're interested in the number of columns deleted,
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99 //Not the number of sequence edits.
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100 return columnsDeleted;
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