X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=df5353c318c9f003d26519b058c2da21adc73998;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=79a9190a4b997365c522ee8e81e535fbeff2086a;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 79a9190..df5353c 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,23 +1,33 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * 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. - * + * 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 . + * You should have received a copy of the GNU General Public License + * 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. @@ -28,6 +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) { @@ -36,7 +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 @@ -150,8 +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; } @@ -194,7 +226,10 @@ public class FormatAdapter extends AppletFormatAdapter { 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)); AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation(); @@ -220,6 +255,41 @@ public class FormatAdapter extends AppletFormatAdapter return this.formatSequences(format, alignment, suffix); } + public Alignment readFile(String inFile, String type, String format) + throws java.io.IOException + { + Alignment al; + if (format.equals("HTML")) + { + afile = new HtmlFile(inFile, type); + al = new Alignment(afile.getSeqsAsArray()); + afile.addAnnotations(al); + } + 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("HTML")) + { + afile = new HtmlFile(source); + al = new Alignment(afile.getSeqsAsArray()); + afile.addAnnotations(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 @@ -241,4 +311,16 @@ public class FormatAdapter extends AppletFormatAdapter } 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); + } + }