2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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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21 import jalview.datamodel.*;
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23 public class AMSAFile
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24 extends jalview.io.FastaFile
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29 * Creates a new AMSAFile object for output.
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31 public AMSAFile(AlignmentI al)
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39 * @return DOCUMENT ME!
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41 public String print()
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43 super.print(getSeqsAsArray());
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45 AlignmentAnnotation aa;
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46 if (al.getAlignmentAnnotation() != null)
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49 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
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51 aa = al.getAlignmentAnnotation()[i];
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54 if (aa.autoCalculated || !aa.visible)
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59 out.append(">#_" + aa.label);
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60 if (aa.description != null)
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62 out.append(" " + aa.description);
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67 int nochunks = Math.min(aa.annotations.length, al.getWidth())
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70 for (int j = 0; j < nochunks; j++)
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72 int start = j * len;
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73 int end = start + len;
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74 if (end > aa.annotations.length)
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76 end = aa.annotations.length;
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80 for (int k = start; k < end; k++)
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82 if (aa.annotations[k] == null)
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88 ch = aa.annotations[k].displayCharacter;
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98 return out.toString();
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