X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=92e5810c71f123183a0f68534f739cdced07ded6;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=6514e609c0ffc7ab6aa989c6b96f6044c2db63d4;hpb=facdb659200d855348d884f55e465a8b7d49add2;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 6514e60..92e5810 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,24 +1,34 @@ /* - * 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 2.9.0b2) + * Copyright (C) 2015 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.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. @@ -28,16 +38,54 @@ import jalview.datamodel.*; */ 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) + String[] omitHiddenColumns, int[] exportRange) { - return formatSequences(format, replaceStrings(seqs, omitHiddenColumns)); + return formatSequences(format, + replaceStrings(seqs, omitHiddenColumns, exportRange)); } /** - * 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 @@ -45,15 +93,44 @@ public class FormatAdapter extends AppletFormatAdapter * @return new sequences */ public SequenceI[] replaceStrings(SequenceI[] seqs, - String[] omitHiddenColumns) + 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], - seqs[i].getStart(), seqs[i].getEnd()); + startRes, endRes); tmp[i].setDescription(seqs[i].getDescription()); } seqs = tmp; @@ -62,14 +139,15 @@ 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 +202,19 @@ 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 @@ -145,22 +228,25 @@ public class FormatAdapter extends AppletFormatAdapter 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) + String[] omitHidden, int[] exportRange, ColumnSelection colSel) { - return formatSequences(format, alignment, omitHidden, + return formatSequences(format, alignment, omitHidden, exportRange, getCacheSuffixDefault(format), colSel, null); } public String formatSequences(String format, AlignmentI alignment, - String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp) + String[] omitHidden, int[] exportRange, ColumnSelection colSel, + SequenceGroup sgp) { - return formatSequences(format, alignment, omitHidden, + return formatSequences(format, alignment, omitHidden, exportRange, getCacheSuffixDefault(format), colSel, sgp); } @@ -171,42 +257,48 @@ 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, - String[] omitHidden, boolean suffix, ColumnSelection colSel) + String[] omitHidden, int[] exportRange, boolean suffix, + ColumnSelection colSel) { - return formatSequences(format, alignment, omitHidden, suffix, colSel, - null); + return formatSequences(format, alignment, omitHidden, exportRange, + suffix, colSel, null); } public String formatSequences(String format, AlignmentI alignment, - String[] omitHidden, boolean suffix, ColumnSelection colSel, - jalview.datamodel.SequenceGroup selgp) + String[] omitHidden, int[] exportRange, boolean suffix, + ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp) { 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, exportRange)); AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation(); - for (int i = 0; i < ala.length; i++) + if (ala != null) { - AlignmentAnnotation na = new AlignmentAnnotation(ala[i]); - if (selgp != null) + for (int i = 0; i < ala.length; i++) { - colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp - .getEndRes(), na); + AlignmentAnnotation na = new AlignmentAnnotation(ala[i]); + if (selgp != null) + { + colSel.makeVisibleAnnotation(selgp.getStartRes(), + selgp.getEndRes(), na); + } + else + { + colSel.makeVisibleAnnotation(na); + } + alv.addAnnotation(na); } - else - { - colSel.makeVisibleAnnotation(na); - } - alv.addAnnotation(na); } return this.formatSequences(format, alv, suffix); } @@ -219,10 +311,10 @@ public class FormatAdapter extends AppletFormatAdapter * 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) + * 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. + * when true, format is checked against list of writable formats. * @return true if format is valid */ public static final boolean isValidIOFormat(String format, @@ -234,4 +326,21 @@ 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 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); + } + }