2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 import jalview.datamodel.*;
23 public class AMSAFile extends jalview.io.FastaFile
29 * Creates a new AMSAFile object for output.
31 public AMSAFile(AlignmentI al)
39 * @return DOCUMENT ME!
43 super.print(getSeqsAsArray());
45 AlignmentAnnotation aa;
46 if (al.getAlignmentAnnotation() != null)
49 for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
51 aa = al.getAlignmentAnnotation()[i];
53 if (aa.autoCalculated || !aa.visible)
58 out.append(">#_" + aa.label);
59 if (aa.description != null)
61 out.append(" " + aa.description);
66 int nochunks = Math.min(aa.annotations.length, al.getWidth()) / len
69 for (int j = 0; j < nochunks; j++)
72 int end = start + len;
73 if (end > aa.annotations.length)
75 end = aa.annotations.length;
79 for (int k = start; k < end; k++)
81 if (aa.annotations[k] == null)
87 ch = aa.annotations[k].displayCharacter;
91 this.warningMessage = "Truncated column annotation to first letter.";
92 ch = ch.substring(0, 1);
101 return out.toString();