X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=9913428b0937f183f74d79eda02b6fcdcc06f4d5;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=25e2fead225df2ea6cf010de36b8d29b4da66b52;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java index 25e2fea..9913428 100755 --- a/src/jalview/io/FormatAdapter.java +++ b/src/jalview/io/FormatAdapter.java @@ -1,20 +1,22 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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; @@ -37,7 +39,7 @@ 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 +64,15 @@ 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 +127,19 @@ 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 @@ -171,10 +179,9 @@ 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, @@ -190,23 +197,29 @@ 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); } @@ -219,10 +232,10 @@ 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,