3 import jalview.api.AlignViewportI;
4 import jalview.bin.Cache;
5 import jalview.datamodel.Alignment;
6 import jalview.datamodel.AlignmentI;
7 import jalview.datamodel.AlignmentView;
8 import jalview.datamodel.AnnotatedCollectionI;
9 import jalview.datamodel.SequenceGroup;
10 import jalview.datamodel.SequenceI;
11 import jalview.gui.AlignFrame;
12 import jalview.gui.JvOptionPane;
13 import jalview.io.DataSourceType;
14 import jalview.io.FileParse;
15 import jalview.io.HMMFile;
16 import jalview.util.FileUtils;
17 import jalview.util.MessageManager;
18 import jalview.ws.params.ArgumentI;
21 import java.io.IOException;
22 import java.util.ArrayList;
23 import java.util.Hashtable;
24 import java.util.List;
27 * A class that runs the hmmbuild command as a separate process.
32 public class HMMBuild extends HmmerCommand
34 static final String ARG_AMINO = "--amino";
36 static final String ARG_DNA = "--dna";
38 static final String ARG_RNA = "--rna";
46 public HMMBuild(AlignFrame alignFrame, List<ArgumentI> args)
48 super(alignFrame, args);
52 * Builds a HMM from an alignment (and/or groups), then imports and adds it to
53 * the alignment (and/or groups). Call this method directly to execute
54 * synchronously, or via start() in a new Thread for asynchronously.
59 if (params == null || params.isEmpty())
61 Cache.log.error("No parameters to HMMBuild!|");
65 long msgID = System.currentTimeMillis();
66 af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
69 AlignViewportI viewport = af.getViewport();
73 * run hmmbuild for alignment and/or groups as selected
75 List<AnnotatedCollectionI> runBuildFor = parseParameters(viewport);
77 for (AnnotatedCollectionI grp : runBuildFor)
83 af.setProgressBar("", msgID);
84 viewport.alignmentChanged(af.alignPanel);
85 af.buildColourMenu(); // to enable HMMER colour schemes
90 * Scans the parameters to determine whether to run hmmmbuild for the whole
91 * alignment or specified subgroup(s) or both
96 protected List<AnnotatedCollectionI> parseParameters(
97 AlignViewportI viewport)
99 List<AnnotatedCollectionI> runBuildFor = new ArrayList<>();
100 boolean foundArg = false;
102 for (ArgumentI arg : params)
104 String name = arg.getName();
105 if (MessageManager.getString("label.hmmbuild_for").equals(name))
108 String value = arg.getValue();
110 if (MessageManager.getString("label.alignment").equals(value))
112 runBuildFor.add(viewport.getAlignmentView(false)
113 .getVisibleAlignment('-'));
115 else if (MessageManager.getString("label.groups_and_alignment")
118 AlignmentView av = viewport.getAlignmentView(true);
119 runBuildFor.add(av.getVisibleAlignment('-'));
120 runBuildFor.addAll(av.getVisibleGroups('-'));
122 else if (MessageManager.getString("label.groups").equals(value))
124 AlignmentView av = viewport.getAlignmentView(false);
125 runBuildFor.addAll(av.getVisibleGroups('-'));
127 else if (MessageManager.getString("label.selected_group")
130 AlignmentView av = viewport.getAlignmentView(true);
131 runBuildFor.add(av.getVisibleAlignment('-'));
134 else if (MessageManager.getString("label.use_reference")
137 // todo disable this option if no RF annotation on alignment
138 if (!af.getViewport().hasReferenceAnnotation())
140 JvOptionPane.showInternalMessageDialog(af, MessageManager
141 .getString("warn.no_reference_annotation"));
148 * default is to build for the whole alignment
152 runBuildFor.add(alignment);
159 * Runs hmmbuild on the given sequences (alignment or group)
163 private void runHMMBuild(AnnotatedCollectionI ac)
166 File alignmentFile = null;
169 hmmFile = FileUtils.createTempFile("hmm", ".hmm");
170 alignmentFile = FileUtils.createTempFile("output", ".sto");
172 if (ac instanceof Alignment)
174 AlignmentI al = (Alignment) ac;
175 // todo pad gaps in an unaligned SequenceGroup as well?
182 deleteHmmSequences(ac);
184 List<SequenceI> copy = new ArrayList<>();
185 if (ac instanceof Alignment)
187 copy.addAll(ac.getSequences());
191 SequenceI[] sel = ((SequenceGroup) ac)
192 .getSelectionAsNewSequences((AlignmentI) ac.getContext(),
194 for (SequenceI seq : sel)
200 SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
201 Hashtable sequencesHash = stashSequences(copyArray);
203 exportStockholm(copyArray, alignmentFile, ac);
205 recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));
207 boolean ran = runCommand(alignmentFile, hmmFile, ac);
210 JvOptionPane.showInternalMessageDialog(af, MessageManager
211 .formatMessage("warn.command_failed", "hmmbuild"));
214 importData(hmmFile, ac);
215 } catch (Exception e)
224 if (alignmentFile != null)
226 alignmentFile.delete();
232 * A helper method that deletes any HMM consensus sequence from the given
233 * collection, and from the parent alignment if <code>ac</code> is a subgroup
237 void deleteHmmSequences(AnnotatedCollectionI ac)
239 List<SequenceI> hmmSeqs = ac.getHmmSequences();
240 for (SequenceI hmmSeq : hmmSeqs)
242 if (ac instanceof SequenceGroup)
244 ((SequenceGroup) ac).deleteSequence(hmmSeq, false);
245 AnnotatedCollectionI context = ac.getContext();
246 if (context != null && context instanceof AlignmentI)
248 ((AlignmentI) context).deleteSequence(hmmSeq);
253 ((AlignmentI) ac).deleteSequence(hmmSeq);
259 * Constructs and executes the hmmbuild command as a separate process
261 * @param sequencesFile
262 * the alignment from which the HMM is built
264 * the output file to which the HMM is written
266 * alignment or group for which the hmm is generated
269 * @throws IOException
271 private boolean runCommand(File sequencesFile, File hmmFile,
272 AnnotatedCollectionI group) throws IOException
274 String cmd = getCommandPath(HMMBUILD);
277 return false; // executable not found
279 List<String> args = new ArrayList<>();
283 * HMM name (will be given to consensus sequence) is
284 * - as specified by an input parameter if set
285 * - else group name with _HMM appended (if for a group)
286 * - else align frame title with _HMM appended (if title is not too long)
287 * - else "Alignment_HMM"
293 for (ArgumentI arg : params)
295 String argName = arg.getName();
299 name = arg.getValue().trim();
301 case "Use Reference Annotation":
308 if (group instanceof SequenceGroup)
310 name = ((SequenceGroup) group).getName() + "_HMM";
315 if (af != null && af.getTitle().length() < 15)
317 name = af.getTitle();
321 name = "Alignment_HMM";
326 args.add(name.replace(' ', '_'));
327 if (!alignment.isNucleotide())
329 args.add(ARG_AMINO); // TODO check for rna
336 args.add(getFilePath(hmmFile));
337 args.add(getFilePath(sequencesFile));
339 return runCommand(args);
343 * Imports the .hmm file produced by hmmbuild, and inserts the HMM consensus
344 * sequence (with attached HMM profile) as the first sequence in the alignment
345 * or group for which it was generated
349 * (optional) the group for which the hmm was generated
350 * @throws IOException
352 private void importData(File hmmFile, AnnotatedCollectionI ac)
355 if (hmmFile.length() == 0L)
357 Cache.log.error("Error: hmmbuild produced empty hmm file");
361 HMMFile file = new HMMFile(
362 new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
363 SequenceI hmmSeq = file.getHMM().getConsensusSequence();
367 // hmmbuild failure not detected earlier
371 if (ac instanceof SequenceGroup)
373 SequenceGroup grp = (SequenceGroup) ac;
374 char gapChar = alignment.getGapCharacter();
375 hmmSeq.insertCharAt(0, ac.getStartRes(), gapChar);
376 hmmSeq.insertCharAt(ac.getEndRes() + 1,
377 alignment.getWidth() - ac.getEndRes() - 1, gapChar);
378 SequenceI topSeq = grp.getSequencesInOrder(alignment)[0];
379 int topIndex = alignment.findIndex(topSeq);
380 alignment.insertSequenceAt(topIndex, hmmSeq);
381 ac.setSeqrep(hmmSeq);
382 grp.addSequence(hmmSeq, false);
386 alignment.insertSequenceAt(0, hmmSeq);