X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=0c8554af6ece5dc20c7aa59d3fdf9254fcc7b9be;hb=ca91ef118ff467dee590a67d8ea762c98451660a;hp=3e5e250c200486f3abafb855b6b779d9c6d7cef5;hpb=128c1c559ce7749ba5a39d30e6108f5ce8f4b99e;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 3e5e250..0c8554a 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,86 +1,109 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program is free software; you can redistribute it and/or +* modify it under the terms of the GNU General Public License +* as published by the Free Software Foundation; either version 2 +* of the License, or (at your option) any later version. +* +* This program is distributed in the hope that it will be useful, +* but WITHOUT ANY WARRANTY; without even the implied warranty of +* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +* GNU General Public License for more details. +* +* You should have received a copy of the GNU General Public License +* along with this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.io; import jalview.datamodel.*; -import java.util.Vector; -public class FormatAdapter -{ - public static Vector formats = new Vector(); - static{ - formats.addElement("FASTA"); - formats.addElement("MSF"); - formats.addElement("PileUp"); - formats.addElement("CLUSTAL"); - formats.addElement("BLC"); - formats.addElement("PIR"); - formats.addElement("PFAM"); - } +import java.util.Vector; - public static SequenceI[] readFile(String inFile, String type, String format) - { - try +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class FormatAdapter extends AppletFormatAdapter +{ + /** + * DOCUMENT ME! + * + * @param format DOCUMENT ME! + * @param seqs DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String formatSequences(String format, Vector seqs) { - AlignFile afile = null; - if (format.equals("FASTA")) - afile = new FastaFile(inFile, type); - else if (format.equals("MSF")) - afile = new MSFfile(inFile, type); - else if (format.equals("PileUp")) - afile = new PileUpfile(inFile, type); - else if (format.equals("CLUSTAL")) - afile = new ClustalFile(inFile, type); - else if (format.equals("BLC")) - afile = new BLCFile(inFile, type); - else if (format.equals("PIR")) - afile = new PIRFile(inFile, type); - else if (format.equals("PFAM")) - afile = new PfamFile(inFile, type); - - return afile.getSeqsAsArray(); - } - catch (Exception e) { - System.err.println("Failed to read alignment using the '"+format+"' reader."); - e.printStackTrace(); - } + SequenceI[] s = new SequenceI[seqs.size()]; - return null; - } + for (int i = 0; i < seqs.size(); i++) + s[i] = (SequenceI) seqs.elementAt(i); + try + { + AlignFile afile = null; - public static String formatSequences(String format, Vector seqs) - { - SequenceI [] s = new SequenceI[seqs.size()]; + if (format.equalsIgnoreCase("FASTA")) + { + afile = new FastaFile(); + afile.addJVSuffix( + jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true)); + } + else if (format.equalsIgnoreCase("MSF")) + { + afile = new MSFfile(); + afile.addJVSuffix( + jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true)); + } + else if (format.equalsIgnoreCase("PileUp")) + { + afile = new PileUpfile(); + afile.addJVSuffix( + jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true)); + } + else if (format.equalsIgnoreCase("CLUSTAL")) + { + afile = new ClustalFile(); + afile.addJVSuffix( + jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true)); + } + else if (format.equalsIgnoreCase("BLC")) + { + afile = new BLCFile(); + afile.addJVSuffix( + jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true)); + } + else if (format.equalsIgnoreCase("PIR")) + { + afile = new PIRFile(); + afile.addJVSuffix( + jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true)); + } + else if (format.equalsIgnoreCase("PFAM")) + { + afile = new PfamFile(); + afile.addJVSuffix( + jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true)); + } - for (int i = 0; i < seqs.size(); i++) - s[i] = (SequenceI) seqs.elementAt(i); + afile.setSeqs(s); - try - { - AlignFile afile = null; - if (format.equals("FASTA")) - afile = new FastaFile(); - else if (format.equals("MSF")) - afile = new MSFfile(); - else if (format.equals("PileUp")) - afile = new PileUpfile(); - else if (format.equals("CLUSTAL")) - afile = new ClustalFile(); - else if (format.equals("BLC")) - afile = new BLCFile(); - else if (format.equals("PIR")) - afile = new PIRFile(); - else if (format.equals("PFAM")) - afile = new PfamFile(); + return afile.print(); + } + catch (Exception e) + { + System.err.println("Failed to write alignment as a '" + format + + "' file\n"); + e.printStackTrace(); + } - afile.setSeqs(s); - return afile.print(); + return null; } - catch (Exception e) { - System.err.println("Failed to write alignment as a '"+format+"' file\n"); - e.printStackTrace(); - } - - return null; - } }