X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=92e5810c71f123183a0f68534f739cdced07ded6;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=15d4dc3ce87dae93a7dd779b7fef60c6b586fad6;hpb=ed8d18abc302ac802ad1d0611f3fe2fef570ab5e;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 15d4dc3..92e5810 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,126 +1,346 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 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) - { - if(omitHiddenColumns!=null) - { - SequenceI [] tmp = new SequenceI[seqs.length]; - for(int i=0; i. + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.io; + +import jalview.api.AlignExportSettingI; +import jalview.api.AlignmentViewPanel; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; + +/** + * Additional formatting methods used by the application in a number of places. + * + * @author $author$ + * @version $Revision$ + */ +public class FormatAdapter extends AppletFormatAdapter +{ + public FormatAdapter(AlignmentViewPanel viewpanel) + { + super(viewpanel); + init(); + } + + public FormatAdapter() + { + super(); + init(); + } + + public FormatAdapter(AlignmentViewPanel alignPanel, + AlignExportSettingI settings) + { + super(alignPanel, settings); + } + + private void init() + { + if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true)) + { + annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN", + true); + localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN", + true); + serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW", + true); + } + else + { + // disable all PDB annotation options + annotFromStructure = false; + localSecondaryStruct = false; + serviceSecondaryStruct = false; + } + } + + public String formatSequences(String format, SequenceI[] seqs, + String[] omitHiddenColumns, int[] exportRange) + { + + return formatSequences(format, + replaceStrings(seqs, omitHiddenColumns, exportRange)); + } + + /** + * 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, int[] startEnd) + { + if (omitHiddenColumns != null) + { + SequenceI[] tmp = new SequenceI[seqs.length]; + + int startRes; + int endRes; + int startIndex; + int endIndex; + for (int i = 0; i < seqs.length; i++) + { + startRes = seqs[i].getStart(); + endRes = seqs[i].getEnd(); + if (startEnd != null) + { + startIndex = startEnd[0]; + endIndex = startEnd[1]; + // get first non-gaped residue start position + while (jalview.util.Comparison.isGap(seqs[i] + .getCharAt(startIndex)) && startIndex < endIndex) + { + startIndex++; + } + + // get last non-gaped residue end position + while (jalview.util.Comparison.isGap(seqs[i].getCharAt(endIndex)) + && endIndex > startIndex) + { + endIndex--; + } + + startRes = seqs[i].findPosition(startIndex); + endRes = seqs[i].findPosition(endIndex); + } + + tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i], + startRes, endRes); + 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, int[] exportRange, ColumnSelection colSel) + { + return formatSequences(format, alignment, omitHidden, exportRange, + getCacheSuffixDefault(format), colSel, null); + } + + public String formatSequences(String format, AlignmentI alignment, + String[] omitHidden, int[] exportRange, ColumnSelection colSel, + SequenceGroup sgp) + { + return formatSequences(format, alignment, omitHidden, exportRange, + 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, int[] exportRange, boolean suffix, + ColumnSelection colSel) + { + return formatSequences(format, alignment, omitHidden, exportRange, + suffix, colSel, null); + } + + public String formatSequences(String format, AlignmentI alignment, + String[] omitHidden, int[] exportRange, 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 + // TODO: JAL-1486 - set start and end for output correctly. basically, + // AlignmentView.getVisibleContigs does this. + Alignment alv = new Alignment(replaceStrings( + alignment.getSequencesArray(), omitHidden, exportRange)); + 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); + } + + /** + * Create a flat file representation of a given view or selected region of a + * view + * + * @param format + * @param ap + * alignment panel originating the view + * @return String containing flat file + */ + public String formatSequences(String format, AlignmentViewPanel ap, + boolean selectedOnly) + { + return formatSequences(format, getCacheSuffixDefault(format), ap, + selectedOnly); + } + +}