2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
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3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.datamodel;
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21 public class CigarCigar extends CigarSimple
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26 * Apply CIGAR operations to the result of another cigar
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31 CigarCigar(SeqCigar cigar)
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39 * @return String formed by applying CIGAR operations to the reference object
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42 * @todo Implement this jalview.datamodel.Cigar method
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44 public String getSequenceString(char GapChar)
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50 String refString = refCigar.getSequenceString(GapChar);
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51 if (refString != null)
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53 return (length == 0) ? "" : (String) getSequenceAndDeletions(
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54 refString, GapChar)[0];
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