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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27 * @version $Revision$
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29 public class FormatAdapter
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30 extends AppletFormatAdapter
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33 public String formatSequences(String format,
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35 String[] omitHiddenColumns)
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37 if (omitHiddenColumns != null)
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39 SequenceI[] tmp = new SequenceI[seqs.length];
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40 for (int i = 0; i < seqs.length; i++)
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42 tmp[i] = new Sequence(
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43 seqs[i].getName(), omitHiddenColumns[i],
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44 seqs[i].getStart(), seqs[i].getEnd());
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45 tmp[i].setDescription(seqs[i].getDescription());
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50 return formatSequences(format, seqs);
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56 * @param format DOCUMENT ME!
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57 * @param seqs DOCUMENT ME!
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59 * @return DOCUMENT ME!
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61 public String formatSequences(String format,
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67 AlignFile afile = null;
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69 if (format.equalsIgnoreCase("FASTA"))
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71 afile = new FastaFile();
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73 jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));
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75 else if (format.equalsIgnoreCase("MSF"))
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77 afile = new MSFfile();
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79 jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true));
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81 else if (format.equalsIgnoreCase("PileUp"))
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83 afile = new PileUpfile();
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85 jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true));
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87 else if (format.equalsIgnoreCase("CLUSTAL"))
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89 afile = new ClustalFile();
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91 jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));
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93 else if (format.equalsIgnoreCase("BLC"))
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95 afile = new BLCFile();
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97 jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));
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99 else if (format.equalsIgnoreCase("PIR"))
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101 afile = new PIRFile();
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103 jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true));
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105 else if (format.equalsIgnoreCase("PFAM"))
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107 afile = new PfamFile();
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109 jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));
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112 afile.setSeqs(seqs);
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114 return afile.print();
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116 catch (Exception e)
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118 System.err.println("Failed to write alignment as a '" + format +
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120 e.printStackTrace();
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