X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=74410a186d56b127812138108093f65b46073e8e;hb=2a42323bc7b92e39c676fc46768f28d032f2f686;hp=17a5c6841134da0acfe58f7b5fd17d87b97d64bb;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 17a5c68..74410a1 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,24 +1,33 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; -import jalview.datamodel.*; +import jalview.api.AlignViewportI; +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. @@ -29,6 +38,26 @@ import jalview.datamodel.*; public class FormatAdapter extends AppletFormatAdapter { + public FormatAdapter() + { + super(); + 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) { @@ -37,7 +66,7 @@ public class FormatAdapter extends AppletFormatAdapter } /** - * create sequences with each seuqence string replaced with the one given in + * create sequences with each sequence string replaced with the one given in * omitHiddenCOlumns * * @param seqs @@ -62,14 +91,15 @@ public class FormatAdapter extends AppletFormatAdapter } /** - * Format a vector of sequences as a flat alignment file. + * 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) + * 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 + * vector of sequences to write * * @return String containing sequences in desired format */ @@ -124,14 +154,19 @@ public class FormatAdapter extends AppletFormatAdapter } /* * 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( + * 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(); + 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 @@ -145,8 +180,10 @@ public class FormatAdapter extends AppletFormatAdapter public boolean getCacheSuffixDefault(String format) { if (isValidFormat(format)) + { return jalview.bin.Cache.getDefault(format.toUpperCase() + "_JVSUFFIX", true); + } return false; } @@ -171,10 +208,9 @@ public class FormatAdapter extends AppletFormatAdapter * @param format * @param alignment * @param omitHidden - * sequence strings to write out in order of sequences in - * alignment + * sequence strings to write out in order of sequences in alignment * @param colSel - * defines hidden columns that are edited out of annotation + * 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, @@ -190,26 +226,106 @@ public class FormatAdapter extends AppletFormatAdapter { 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 + // TODO: JAL-1486 - set start and end for output correctly. basically, + // AlignmentView.getVisibleContigs does this. + Alignment alv = new Alignment(replaceStrings( + alignment.getSequencesArray(), omitHidden)); AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation(); - for (int i = 0; i < ala.length; i++) + if (ala != null) { - AlignmentAnnotation na = new AlignmentAnnotation(ala[i]); - if (selgp != null) - { - colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp - .getEndRes(), na); - } - else + for (int i = 0; i < ala.length; i++) { - colSel.makeVisibleAnnotation(na); + AlignmentAnnotation na = new AlignmentAnnotation(ala[i]); + if (selgp != null) + { + colSel.makeVisibleAnnotation(selgp.getStartRes(), + selgp.getEndRes(), na); + } + else + { + colSel.makeVisibleAnnotation(na); + } + alv.addAnnotation(na); } - alv.addAnnotation(na); } return this.formatSequences(format, alv, suffix); } return this.formatSequences(format, alignment, suffix); } + + public Alignment readFile(String inFile, String type, String format) + throws java.io.IOException + { + Alignment al; + if (format.equals(JSONFile.FILE_DESC)) + { + afile = new JSONFile(inFile, type); + al = new Alignment(afile.getSeqsAsArray()); + afile.addAnnotations(al); + for (SequenceGroup sg : afile.getSeqGroups()) + { + al.addGroup(sg); + } + } + else + { + al = super.readFile(inFile, type, format); + } + return al; + } + + public AlignmentI readFromFile(FileParse source, String format) + throws java.io.IOException + { + Alignment al; + if (format.equals(JSONFile.FILE_DESC)) + { + afile = new JSONFile(source); + al = new Alignment(afile.getSeqsAsArray()); + afile.addAnnotations(al); + afile.addSeqGroups(al); + } + else + { + al = (Alignment) super.readFromFile(source, format); + } + return al; + } + + /** + * 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 av + * @return String containing flat file + */ + public String formatSequences(String format, AlignViewportI av, boolean selectedOnly) + { + return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly); + } + + }