package jalview.hmmer;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ResidueCount;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.HMMFile;
+import jalview.util.FileUtils;
import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.ArgumentI;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Hashtable;
-import java.util.Iterator;
import java.util.List;
+import java.util.Map;
/**
* A class that runs the hmmbuild command as a separate process.
@Override
public void run()
{
- if (params == null)
+ if (params == null || params.isEmpty())
{
Cache.log.error("No parameters to HMMBuild!|");
return;
AlignViewportI viewport)
{
List<AnnotatedCollectionI> runBuildFor = new ArrayList<>();
+ boolean foundArg = false;
+
for (ArgumentI arg : params)
{
String name = arg.getName();
if (MessageManager.getString("label.hmmbuild_for").equals(name))
{
+ foundArg = true;
String value = arg.getValue();
+
if (MessageManager.getString("label.alignment").equals(value))
{
- runBuildFor.add(alignment);
+ runBuildFor.add(viewport.getAlignmentView(false)
+ .getVisibleAlignment('-'));
}
else if (MessageManager.getString("label.groups_and_alignment")
.equals(value))
{
- runBuildFor.add(alignment);
+ runBuildFor.add(viewport.getAlignmentView(false)
+ .getVisibleAlignment('-'));
runBuildFor.addAll(viewport.getAlignment().getGroups());
}
else if (MessageManager.getString("label.groups").equals(value))
}
}
}
+
+ /*
+ * default is to build for the whole alignment
+ */
+ if (!foundArg)
+ {
+ runBuildFor.add(alignment);
+ }
+
return runBuildFor;
}
File alignmentFile = null;
try
{
- hmmFile = createTempFile("hmm", ".hmm");
- alignmentFile = createTempFile("output", ".sto");
- List<SequenceI> seqs = ac.getSequences();
- List<SequenceI> copy = new ArrayList<>();
- copy.addAll(seqs);
+ hmmFile = FileUtils.createTempFile("hmm", ".hmm");
+ alignmentFile = FileUtils.createTempFile("output", ".sto");
if (ac instanceof Alignment)
{
}
}
- /*
- * copy over sequences, excluding hmm consensus sequences
- * hmm sequences are also deleted in preparation for
- * re-adding them when recalculated; Information annotation is not
- * deleted, it will be updated to reference the new hmm sequence
- * by InformationThread.findOrCreateAnnotation
- */
- Iterator<SequenceI> it = copy.iterator();
- while (it.hasNext())
+ deleteHmmSequences(ac);
+
+ List<SequenceI> copy = new ArrayList<>();
+ if (ac instanceof Alignment)
+ {
+ copy.addAll(ac.getSequences());
+ }
+ else
{
- SequenceI seq = it.next();
- if (seq.isHMMConsensusSequence())
+ SequenceI[] sel = ((SequenceGroup) ac)
+ .getSelectionAsNewSequences((AlignmentI) ac.getContext());
+ for (SequenceI seq : sel)
{
- alignment.deleteSequence(seq);
- it.remove();
+ if (seq != null)
+ {
+ copy.add(seq);
+ }
}
}
+ // TODO rather than copy alignment data we should anonymize in situ -
+ // export/File import could use anonymization hash to reinstate references
+ // at import level ?
SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
- Hashtable sequencesHash = stashSequences(copyArray);
+ Map<String, SequenceInfo> sequencesHash = stashSequences(copyArray);
exportStockholm(copyArray, alignmentFile, ac);
- recoverSequences(sequencesHash, seqs.toArray(new SequenceI[] {}));
+ recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));
boolean ran = runCommand(alignmentFile, hmmFile, ac);
if (!ran)
{
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .formatMessage("warn.command_failed", "hmmbuild"));
return;
}
importData(hmmFile, ac);
* HMM name (will be given to consensus sequence) is
* - as specified by an input parameter if set
* - else group name with _HMM appended (if for a group)
- * - else align fame title with _HMM appended (if title is not too long)
+ * - else align frame title with _HMM appended (if title is not too long)
* - else "Alignment_HMM"
*/
String name = "";
args.add(ARG_DNA);
}
- args.add(hmmFile.getAbsolutePath());
- args.add(sequencesFile.getAbsolutePath());
+ args.add(getFilePath(hmmFile, true));
+ args.add(getFilePath(sequencesFile, true));
return runCommand(args);
}
private void importData(File hmmFile, AnnotatedCollectionI ac)
throws IOException
{
+ if (hmmFile.length() == 0L)
+ {
+ Cache.log.error("Error: hmmbuild produced empty hmm file");
+ return;
+ }
+
HMMFile file = new HMMFile(
new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
- SequenceI[] seqs = file.getSeqsAsArray();
- SequenceI hmmSeq = seqs[0];
- hmmSeq.createDatasetSequence();
+ SequenceI hmmSeq = file.getHMM().getConsensusSequence();
+
+
+
+ ResidueCount counts = new ResidueCount(alignment.getSequences());
+ hmmSeq.getHMM().setBackgroundFrequencies(counts);
+
+ if (hmmSeq == null)
+ {
+ // hmmbuild failure not detected earlier
+ return;
+ }
+
if (ac instanceof SequenceGroup)
{
SequenceGroup grp = (SequenceGroup) ac;
- hmmSeq.insertCharAt(0, ac.getStartRes(), '-');
+ char gapChar = alignment.getGapCharacter();
+ hmmSeq.insertCharAt(0, ac.getStartRes(), gapChar);
hmmSeq.insertCharAt(ac.getEndRes() + 1,
- alignment.getWidth() - ac.getEndRes() - 1, '-');
- hmmSeq.updateHMMMapping();
+ alignment.getWidth() - ac.getEndRes() - 1, gapChar);
SequenceI topSeq = grp.getSequencesInOrder(alignment)[0];
int topIndex = alignment.findIndex(topSeq);
alignment.insertSequenceAt(topIndex, hmmSeq);
ac.setSeqrep(hmmSeq);
grp.addSequence(hmmSeq, false);
- grp.setHmmConsensus(hmmSeq);
}
else
{
alignment.insertSequenceAt(0, hmmSeq);
- alignment.setHmmConsensus(hmmSeq);
- }
-
- if (af.getSelectedHMM() == null)
- {
- af.setSelectedHMMSequence(hmmSeq);
}
}
}
git://source.jalview.org / jalview.git / blobdiff