X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=3cbd73b7dcddc0c75b007f6c899988a808d09b03;hb=ce886100c1eae01eac7d59c961e694f4493d4bcb;hp=dba0c61d3e84677672b8e0d78a53b782d7180d43;hpb=b3f66e3a4fd8d3f24a5a44f8716a41c84c4d1cb3;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index dba0c61..3cbd73b 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,81 +1,194 @@ -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("CLUSTAL"); - formats.addElement("BLC"); - formats.addElement("PIR"); - formats.addElement("PFAM"); - } - - public static SequenceI[] readFile(String inFile, String type, String format) - { - - try - { - 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("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; - } - - - public static String formatSequences(String format, Vector seqs) - { - 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.equals("FASTA")) - afile = new FastaFile(); - else if (format.equals("MSF")) - afile = new MSFfile(); - 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(); - - 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; - } -} +/* + * 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.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class FormatAdapter + extends AppletFormatAdapter +{ + + public String formatSequences(String format, + SequenceI[] seqs, + String[] omitHiddenColumns) + { + + return formatSequences(format, replaceStrings(seqs, omitHiddenColumns)); + } + + /** + * create sequences with each seuqence string replaced with the one given in omitHiddenCOlumns + * @param seqs + * @param omitHiddenColumns + * @return new sequences + */ + public SequenceI[] replaceStrings(SequenceI[] seqs, String[] omitHiddenColumns) + { + if (omitHiddenColumns != null) + { + 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; + } + return seqs; + } + + /** + * Format a vector of sequences as a flat alignment file. + * + * @param format Format string as givien in the AppletFormatAdaptor list (exact match to name of class implementing file io for that format) + * @param seqs vector of sequences to write + * + * @return String containing sequences in desired format + */ + public String formatSequences(String format, + SequenceI[] seqs) + { + + try + { + 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)); + } + /* amsa is not supported by this function - it requires an alignment rather than a sequence vector + else if (format.equalsIgnoreCase("AMSA")) + { + afile = new AMSAFile(); + afile.addJVSuffix( + jalview.bin.Cache.getDefault("AMSA_JVSUFFIX", true)); + }*/ + + afile.setSeqs(seqs); + + return afile.print(); + } + catch (Exception e) + { + System.err.println("Failed to write alignment as a '" + format + + "' file\n"); + e.printStackTrace(); + } + + return null; + } + public boolean getCacheSuffixDefault(String format) + { + if (isValidFormat(format)) + return jalview.bin.Cache.getDefault(format.toUpperCase()+"_JVSUFFIX", true); + return false; + } + public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, ColumnSelection colSel) + { + return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel, null); + } + public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp) + { + return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel, sgp); + } + /** + * hack function to replace seuqences with visible sequence strings before generating a + * string of the alignment in the given format. + * @param format + * @param alignment + * @param omitHidden sequence strings to write out in order of sequences in alignment + * @param colSel defines hidden columns that are edited out of annotation + * @return string representation of the alignment formatted as format + */ + public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, boolean suffix, ColumnSelection colSel) + { + return formatSequences(format, alignment, omitHidden, suffix, colSel, null); + } + + public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, boolean suffix, + ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp) + { + if (omitHidden!=null) + { + // + Alignment alv = new Alignment(replaceStrings(alignment.getSequencesArray(), omitHidden)); + AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation(); + for (int i=0; i