3 import jalview.api.AlignViewportI;
4 import jalview.bin.Cache;
5 import jalview.datamodel.Alignment;
6 import jalview.datamodel.AlignmentI;
7 import jalview.datamodel.AnnotatedCollectionI;
8 import jalview.datamodel.SequenceGroup;
9 import jalview.datamodel.SequenceI;
10 import jalview.gui.AlignFrame;
11 import jalview.gui.JvOptionPane;
12 import jalview.io.DataSourceType;
13 import jalview.io.FileParse;
14 import jalview.io.HMMFile;
15 import jalview.util.FileUtils;
16 import jalview.util.MessageManager;
17 import jalview.ws.params.ArgumentI;
20 import java.io.IOException;
21 import java.util.ArrayList;
22 import java.util.Hashtable;
23 import java.util.List;
26 * A class that runs the hmmbuild command as a separate process.
31 public class HMMBuild extends HmmerCommand
33 static final String ARG_AMINO = "--amino";
35 static final String ARG_DNA = "--dna";
37 static final String ARG_RNA = "--rna";
45 public HMMBuild(AlignFrame alignFrame, List<ArgumentI> args)
47 super(alignFrame, args);
51 * Builds a HMM from an alignment (and/or groups), then imports and adds it to
52 * the alignment (and/or groups). Call this method directly to execute
53 * synchronously, or via start() in a new Thread for asynchronously.
58 if (params == null || params.isEmpty())
60 Cache.log.error("No parameters to HMMBuild!|");
64 long msgID = System.currentTimeMillis();
65 af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
68 AlignViewportI viewport = af.getViewport();
72 * run hmmbuild for alignment and/or groups as selected
74 List<AnnotatedCollectionI> runBuildFor = parseParameters(viewport);
76 for (AnnotatedCollectionI grp : runBuildFor)
82 af.setProgressBar("", msgID);
83 viewport.alignmentChanged(af.alignPanel);
84 af.buildColourMenu(); // to enable HMMER colour schemes
89 * Scans the parameters to determine whether to run hmmmbuild for the whole
90 * alignment or specified subgroup(s) or both
95 protected List<AnnotatedCollectionI> parseParameters(
96 AlignViewportI viewport)
98 List<AnnotatedCollectionI> runBuildFor = new ArrayList<>();
99 boolean foundArg = false;
101 for (ArgumentI arg : params)
103 String name = arg.getName();
104 if (MessageManager.getString("label.hmmbuild_for").equals(name))
107 String value = arg.getValue();
108 if (MessageManager.getString("label.alignment").equals(value))
110 runBuildFor.add(alignment);
112 else if (MessageManager.getString("label.groups_and_alignment")
115 runBuildFor.add(alignment);
116 runBuildFor.addAll(viewport.getAlignment().getGroups());
118 else if (MessageManager.getString("label.groups").equals(value))
120 runBuildFor.addAll(viewport.getAlignment().getGroups());
122 else if (MessageManager.getString("label.selected_group")
125 runBuildFor.add(viewport.getSelectionGroup());
128 else if (MessageManager.getString("label.use_reference")
131 // todo disable this option if no RF annotation on alignment
132 if (!af.getViewport().hasReferenceAnnotation())
134 JvOptionPane.showInternalMessageDialog(af, MessageManager
135 .getString("warn.no_reference_annotation"));
142 * default is to build for the whole alignment
146 runBuildFor.add(alignment);
153 * Runs hmmbuild on the given sequences (alignment or group)
157 private void runHMMBuild(AnnotatedCollectionI ac)
160 File alignmentFile = null;
163 hmmFile = FileUtils.createTempFile("hmm", ".hmm");
164 alignmentFile = FileUtils.createTempFile("output", ".sto");
166 if (ac instanceof Alignment)
168 AlignmentI al = (Alignment) ac;
169 // todo pad gaps in an unaligned SequenceGroup as well?
176 deleteHmmSequences(ac);
178 List<SequenceI> copy = new ArrayList<>();
179 if (ac instanceof Alignment)
181 copy.addAll(ac.getSequences());
185 SequenceI[] sel = ((SequenceGroup) ac)
186 .getSelectionAsNewSequences((AlignmentI) ac.getContext());
187 for (SequenceI seq : sel)
193 SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
194 Hashtable sequencesHash = stashSequences(copyArray);
196 exportStockholm(copyArray, alignmentFile, ac);
198 recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));
200 boolean ran = runCommand(alignmentFile, hmmFile, ac);
203 JvOptionPane.showInternalMessageDialog(af, MessageManager
204 .formatMessage("warn.command_failed", "hmmbuild"));
207 importData(hmmFile, ac);
208 } catch (Exception e)
217 if (alignmentFile != null)
219 alignmentFile.delete();
225 * A helper method that deletes any HMM consensus sequence from the given
226 * collection, and from the parent alignment if <code>ac</code> is a subgroup
230 void deleteHmmSequences(AnnotatedCollectionI ac)
232 List<SequenceI> hmmSeqs = ac.getHmmSequences();
233 for (SequenceI hmmSeq : hmmSeqs)
235 if (ac instanceof SequenceGroup)
237 ((SequenceGroup) ac).deleteSequence(hmmSeq, false);
238 AnnotatedCollectionI context = ac.getContext();
239 if (context != null && context instanceof AlignmentI)
241 ((AlignmentI) context).deleteSequence(hmmSeq);
246 ((AlignmentI) ac).deleteSequence(hmmSeq);
252 * Constructs and executes the hmmbuild command as a separate process
254 * @param sequencesFile
255 * the alignment from which the HMM is built
257 * the output file to which the HMM is written
259 * alignment or group for which the hmm is generated
262 * @throws IOException
264 private boolean runCommand(File sequencesFile, File hmmFile,
265 AnnotatedCollectionI group) throws IOException
267 String cmd = getCommandPath(HMMBUILD);
270 return false; // executable not found
272 List<String> args = new ArrayList<>();
276 * HMM name (will be given to consensus sequence) is
277 * - as specified by an input parameter if set
278 * - else group name with _HMM appended (if for a group)
279 * - else align frame title with _HMM appended (if title is not too long)
280 * - else "Alignment_HMM"
286 for (ArgumentI arg : params)
288 String argName = arg.getName();
292 name = arg.getValue().trim();
294 case "Use Reference Annotation":
301 if (group instanceof SequenceGroup)
303 name = ((SequenceGroup) group).getName() + "_HMM";
308 if (af != null && af.getTitle().length() < 15)
310 name = af.getTitle();
314 name = "Alignment_HMM";
319 args.add(name.replace(' ', '_'));
320 if (!alignment.isNucleotide())
322 args.add(ARG_AMINO); // TODO check for rna
329 args.add(getFilePath(hmmFile));
330 args.add(getFilePath(sequencesFile));
332 return runCommand(args);
336 * Imports the .hmm file produced by hmmbuild, and inserts the HMM consensus
337 * sequence (with attached HMM profile) as the first sequence in the alignment
338 * or group for which it was generated
342 * (optional) the group for which the hmm was generated
343 * @throws IOException
345 private void importData(File hmmFile, AnnotatedCollectionI ac)
348 if (hmmFile.length() == 0L)
350 Cache.log.error("Error: hmmbuild produced empty hmm file");
354 HMMFile file = new HMMFile(
355 new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
356 SequenceI hmmSeq = file.getHMM().getConsensusSequence();
360 // hmmbuild failure not detected earlier
364 if (ac instanceof SequenceGroup)
366 SequenceGroup grp = (SequenceGroup) ac;
367 char gapChar = alignment.getGapCharacter();
368 hmmSeq.insertCharAt(0, ac.getStartRes(), gapChar);
369 hmmSeq.insertCharAt(ac.getEndRes() + 1,
370 alignment.getWidth() - ac.getEndRes() - 1, gapChar);
371 SequenceI topSeq = grp.getSequencesInOrder(alignment)[0];
372 int topIndex = alignment.findIndex(topSeq);
373 alignment.insertSequenceAt(topIndex, hmmSeq);
374 ac.setSeqrep(hmmSeq);
375 grp.addSequence(hmmSeq, false);
379 alignment.insertSequenceAt(0, hmmSeq);