2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignExportSettingI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.bin.Cache;
26 import jalview.datamodel.Alignment;
27 import jalview.datamodel.AlignmentAnnotation;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.ColumnSelection;
30 import jalview.datamodel.Sequence;
31 import jalview.datamodel.SequenceGroup;
32 import jalview.datamodel.SequenceI;
33 import jalview.util.Comparison;
35 import java.io.IOException;
38 * Additional formatting methods used by the application in a number of places.
43 public class FormatAdapter extends AppletFormatAdapter
45 public FormatAdapter(AlignmentViewPanel viewpanel)
51 public FormatAdapter()
57 public FormatAdapter(AlignmentViewPanel alignPanel,
58 AlignExportSettingI settings)
60 super(alignPanel, settings);
65 if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
67 annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
69 localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
71 serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
76 // disable all PDB annotation options
77 annotFromStructure = false;
78 localSecondaryStruct = false;
79 serviceSecondaryStruct = false;
83 public String formatSequences(FileFormatI format, SequenceI[] seqs,
84 String[] omitHiddenColumns, int[] exportRange)
87 return formatSequences(format,
88 replaceStrings(seqs, omitHiddenColumns, exportRange));
92 * create sequences with each sequence string replaced with the one given in
96 * @param omitHiddenColumns
97 * @return new sequences
99 public SequenceI[] replaceStrings(SequenceI[] seqs,
100 String[] omitHiddenColumns, int[] startEnd)
102 if (omitHiddenColumns != null)
104 SequenceI[] tmp = new SequenceI[seqs.length];
110 for (int i = 0; i < seqs.length; i++)
112 startRes = seqs[i].getStart();
113 endRes = seqs[i].getEnd();
114 if (startEnd != null)
116 startIndex = startEnd[0];
117 endIndex = startEnd[1];
118 // get first non-gaped residue start position
119 while (Comparison.isGap(seqs[i]
120 .getCharAt(startIndex)) && startIndex < endIndex)
125 // get last non-gaped residue end position
126 while (Comparison.isGap(seqs[i].getCharAt(endIndex))
127 && endIndex > startIndex)
132 startRes = seqs[i].findPosition(startIndex);
133 endRes = seqs[i].findPosition(endIndex);
136 tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
138 tmp[i].setDescription(seqs[i].getDescription());
146 * Format a vector of sequences as a flat alignment file. TODO: allow caller
147 * to detect errors and warnings encountered when generating output
152 * vector of sequences to write
154 * @return String containing sequences in desired format
156 public String formatSequences(FileFormatI format, SequenceI[] seqs)
161 boolean withSuffix = getCacheSuffixDefault(format);
162 return format.getAlignmentFile().print(seqs, withSuffix);
165 // if (format.equalsIgnoreCase("FASTA"))
167 // afile = new FastaFile();
168 // afile.addJVSuffix(jalview.bin.Cache.getDefault("FASTA_JVSUFFIX",
171 // else if (format.equalsIgnoreCase("MSF"))
173 // afile = new MSFfile();
174 // afile.addJVSuffix(jalview.bin.Cache
175 // .getDefault("MSF_JVSUFFIX", true));
177 // else if (format.equalsIgnoreCase("PileUp"))
179 // afile = new PileUpfile();
180 // afile.addJVSuffix(jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX",
183 // else if (format.equalsIgnoreCase("CLUSTAL"))
185 // afile = new ClustalFile();
186 // afile.addJVSuffix(jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX",
189 // else if (format.equalsIgnoreCase("BLC"))
191 // afile = new BLCFile();
192 // afile.addJVSuffix(jalview.bin.Cache
193 // .getDefault("BLC_JVSUFFIX", true));
195 // else if (format.equalsIgnoreCase("PIR"))
197 // afile = new PIRFile();
198 // afile.addJVSuffix(jalview.bin.Cache
199 // .getDefault("PIR_JVSUFFIX", true));
201 // else if (format.equalsIgnoreCase("PFAM"))
203 // afile = new PfamFile();
204 // afile.addJVSuffix(jalview.bin.Cache.getDefault("PFAM_JVSUFFIX",
208 // * amsa is not supported by this function - it requires an alignment
209 // * rather than a sequence vector else if
210 // (format.equalsIgnoreCase("AMSA"))
211 // * { afile = new AMSAFile(); afile.addJVSuffix(
212 // * jalview.bin.Cache.getDefault("AMSA_JVSUFFIX", true)); }
215 // afile.setSeqs(seqs);
216 // String afileresp = afile.print();
217 // if (afile.hasWarningMessage())
219 // System.err.println("Warning raised when writing as " + format
220 // + " : " + afile.getWarningMessage());
223 // } catch (Exception e)
225 // System.err.println("Failed to write alignment as a '" + format
227 // e.printStackTrace();
233 public boolean getCacheSuffixDefault(FileFormatI format)
235 return Cache.getDefault(format.toString() + "_JVSUFFIX", true);
238 public String formatSequences(FileFormatI format, AlignmentI alignment,
239 String[] omitHidden, int[] exportRange, ColumnSelection colSel)
241 return formatSequences(format, alignment, omitHidden, exportRange,
242 getCacheSuffixDefault(format), colSel, null);
246 * hack function to replace seuqences with visible sequence strings before
247 * generating a string of the alignment in the given format.
252 * sequence strings to write out in order of sequences in alignment
254 * defines hidden columns that are edited out of annotation
255 * @return string representation of the alignment formatted as format
257 public String formatSequences(FileFormatI format, AlignmentI alignment,
258 String[] omitHidden, int[] exportRange, boolean suffix,
259 ColumnSelection colSel)
261 return formatSequences(format, alignment, omitHidden, exportRange,
262 suffix, colSel, null);
265 public String formatSequences(FileFormatI format, AlignmentI alignment,
266 String[] omitHidden, int[] exportRange, boolean suffix,
267 ColumnSelection colSel, SequenceGroup selgp)
269 if (omitHidden != null)
271 // TODO consider using AlignmentView to prune to visible region
272 // TODO prune sequence annotation and groups to visible region
273 // TODO: JAL-1486 - set start and end for output correctly. basically,
274 // AlignmentView.getVisibleContigs does this.
275 Alignment alv = new Alignment(replaceStrings(
276 alignment.getSequencesArray(), omitHidden, exportRange));
277 AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
280 for (int i = 0; i < ala.length; i++)
282 AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
285 colSel.makeVisibleAnnotation(selgp.getStartRes(),
286 selgp.getEndRes(), na);
290 colSel.makeVisibleAnnotation(na);
292 alv.addAnnotation(na);
295 return this.formatSequences(format, alv, suffix);
297 return this.formatSequences(format, alignment, suffix);
301 public AlignmentI readFile(String file, DataSourceType sourceType,
302 FileFormatI fileFormat) throws IOException
304 AlignmentI al = super.readFile(file, sourceType, fileFormat);
309 public AlignmentI readFromFile(FileParse source, FileFormatI format)
312 AlignmentI al = super.readFromFile(source, format);
317 * Create a flat file representation of a given view or selected region of a
322 * alignment panel originating the view
323 * @return String containing flat file
325 public String formatSequences(FileFormatI format, AlignmentViewPanel ap,
326 boolean selectedOnly)
328 return formatSequences(format, getCacheSuffixDefault(format), ap,
332 public AlignmentI readFromFile(AlignmentFileI source, FileFormatI format)
335 FileParse fp = new FileParse(source.getInFile(),
336 source.getDataSourceType());
337 return readFromFile(fp, format);