X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=643e9710b5cb881e2794551c88390ebe8910529e;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=3cbd73b7dcddc0c75b007f6c899988a808d09b03;hpb=e5817172683acab3d5f51789fdf44f7a9106c8dd;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 3cbd73b..643e971 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,59 +1,58 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, 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.*; /** - * DOCUMENT ME! - * + * Additional formatting methods used by the application in a number of places. + * * @author $author$ * @version $Revision$ */ -public class FormatAdapter - extends AppletFormatAdapter +public class FormatAdapter extends AppletFormatAdapter { - - public String formatSequences(String format, - SequenceI[] seqs, - String[] omitHiddenColumns) + + 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 + * 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) + 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] = new Sequence(seqs[i].getName(), omitHiddenColumns[i], + seqs[i].getStart(), seqs[i].getEnd()); tmp[i].setDescription(seqs[i].getDescription()); } seqs = tmp; @@ -62,15 +61,19 @@ public class FormatAdapter } /** - * 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 - * + * 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) + public String formatSequences(String format, SequenceI[] seqs) { try @@ -80,115 +83,163 @@ public class FormatAdapter if (format.equalsIgnoreCase("FASTA")) { afile = new FastaFile(); - afile.addJVSuffix( - jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true)); + 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)); + 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)); + 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)); + 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)); + 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)); + 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.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)); - }*/ + /* + * 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) + 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"); + 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 jalview.bin.Cache.getDefault(format.toUpperCase() + + "_JVSUFFIX", true); return false; } - public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, ColumnSelection colSel) + + public String formatSequences(String format, AlignmentI alignment, + String[] omitHidden, ColumnSelection colSel) { - return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel, null); + return formatSequences(format, alignment, omitHidden, + getCacheSuffixDefault(format), colSel, null); } - public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp) + + public String formatSequences(String format, AlignmentI alignment, + String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp) { - return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel, 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. + + /** + * 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 + * @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) + public String formatSequences(String format, AlignmentI alignment, + String[] omitHidden, boolean suffix, ColumnSelection colSel) { - return formatSequences(format, alignment, omitHidden, suffix, colSel, null); + 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) + public String formatSequences(String format, AlignmentI alignment, + String[] omitHidden, boolean suffix, ColumnSelection colSel, + jalview.datamodel.SequenceGroup selgp) { - if (omitHidden!=null) + if (omitHidden != null) { - // - Alignment alv = new Alignment(replaceStrings(alignment.getSequencesArray(), omitHidden)); + // 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(); - for (int i=0; i