X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=81460ebd29860998a2be2f60a97b1918b153f611;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=e59c191879b5f8a1e3ff74cdff6c76712de40781;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index e59c191..81460eb 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,105 +1,245 @@ -/* -* 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"); - } - - 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("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; - } - - 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("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(); - } - - 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 (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview 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 3 of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . + */ +package jalview.io; + +import jalview.datamodel.*; + +/** + * Additional formatting methods used by the application in a number of places. + * + * @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 sequence 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. TODO: allow caller + * to detect errors and warnings encountered when generating output + * + * + * @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); + String afileresp = afile.print(); + if (afile.hasWarningMessage()) + { + System.err.println("Warning raised when writing as " + format + + " : " + afile.getWarningMessage()); + } + return afileresp; + } 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) + { + // TODO consider using AlignmentView to prune to visible region + // TODO prune sequence annotation and groups to visible region + Alignment alv = new Alignment(replaceStrings( + alignment.getSequencesArray(), omitHidden)); + AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation(); + if (ala != null) + { + for (int i = 0; i < ala.length; i++) + { + AlignmentAnnotation na = new AlignmentAnnotation(ala[i]); + if (selgp != null) + { + colSel.makeVisibleAnnotation(selgp.getStartRes(), + selgp.getEndRes(), na); + } + else + { + colSel.makeVisibleAnnotation(na); + } + alv.addAnnotation(na); + } + } + return this.formatSequences(format, alv, suffix); + } + return this.formatSequences(format, alignment, suffix); + } + + /** + * validate format is valid for IO in Application. This is basically the + * AppletFormatAdapter.isValidFormat call with additional checks for + * Application only formats like 'Jalview'. + * + * @param format + * a format string to be compared with list of readable or writable + * formats (READABLE_FORMATS or WRITABLE_FORMATS) + * @param forwriting + * when true, format is checked against list of writable formats. + * @return true if format is valid + */ + public static final boolean isValidIOFormat(String format, + boolean forwriting) + { + if (format.equalsIgnoreCase("jalview")) + { + return true; + } + return AppletFormatAdapter.isValidFormat(format, forwriting); + } +}