2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.datamodel;
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20 public class CigarCigar extends CigarSimple
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25 * Apply CIGAR operations to the result of another cigar
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30 CigarCigar(SeqCigar cigar)
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38 * @return String formed by applying CIGAR operations to the reference object
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41 * @todo Implement this jalview.datamodel.Cigar method
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43 public String getSequenceString(char GapChar)
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49 String refString = refCigar.getSequenceString(GapChar);
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50 if (refString != null)
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52 return (length == 0) ? "" : (String) getSequenceAndDeletions(
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53 refString, GapChar)[0];
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