X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=3cd93458dcc58e2423a2920f43f7919abc92e32d;hb=4dd44779e0d1ffa07b52b67bd8178ad45801bb4f;hp=61c2331465e952492f73174cc456fff1376a5ac3;hpb=008ad05ffd2964c864cdab0f18dff2fb36c82242;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 61c2331..3cd9345 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,28 +1,25 @@ /* -* 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 -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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; - - /** * DOCUMENT ME! * @@ -30,137 +27,99 @@ import java.util.Vector; * @version $Revision$ */ public class FormatAdapter + extends AppletFormatAdapter { - /** DOCUMENT ME!! */ - public static final Vector formats = new Vector(); - static + public String formatSequences(String format, + SequenceI[] seqs, + String[] omitHiddenColumns) + { + if (omitHiddenColumns != null) { - formats.addElement("FASTA"); - formats.addElement("MSF"); - formats.addElement("PileUp"); - formats.addElement("CLUSTAL"); - formats.addElement("BLC"); - formats.addElement("PIR"); - formats.addElement("PFAM"); + SequenceI[] tmp = new SequenceI[seqs.length]; + for (int i = 0; i < seqs.length; i++) + { + tmp[i] = new Sequence( + seqs[i].getName(), omitHiddenColumns[i], + seqs[i].getStart(), seqs[i].getEnd()); + tmp[i].setDescription(seqs[i].getDescription()); + } + seqs = tmp; } - AlignFile afile = null; - - /** - * DOCUMENT ME! - * - * @param inFile DOCUMENT ME! - * @param type DOCUMENT ME! - * @param format DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceI[] readFile(String inFile, String type, String format) + return formatSequences(format, seqs); + } + + /** + * DOCUMENT ME! + * + * @param format DOCUMENT ME! + * @param seqs DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String formatSequences(String format, + SequenceI[] seqs) + { + + try { - try - { - 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(); - } - - return null; + AlignFile afile = null; + + 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)); + } + + afile.setSeqs(seqs); + + return afile.print(); } - - - /** - * DOCUMENT ME! - * - * @param format DOCUMENT ME! - * @param seqs DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String formatSequences(String format, Vector seqs) + catch (Exception e) { - SequenceI[] s = new SequenceI[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) - s[i] = (SequenceI) seqs.elementAt(i); - - try - { - AlignFile afile = null; - - if (format.equalsIgnoreCase("FASTA")) - { - afile = new FastaFile(); - } - else if (format.equalsIgnoreCase("MSF")) - { - afile = new MSFfile(); - } - else if (format.equalsIgnoreCase("PileUp")) - { - afile = new PileUpfile(); - } - else if (format.equalsIgnoreCase("CLUSTAL")) - { - afile = new ClustalFile(); - } - else if (format.equalsIgnoreCase("BLC")) - { - afile = new BLCFile(); - } - else if (format.equalsIgnoreCase("PIR")) - { - afile = new PIRFile(); - } - else if (format.equalsIgnoreCase("PFAM")) - { - afile = new PfamFile(); - } - - afile.setSeqs(s); - - return afile.print(); - } - catch (Exception e) - { - System.err.println("Failed to write alignment as a '" + format + - "' file\n"); - e.printStackTrace(); - } - - return null; + System.err.println("Failed to write alignment as a '" + format + + "' file\n"); + e.printStackTrace(); } + + return null; + } }