package jalview.hmmer;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
+import jalview.bin.Console;
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 java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
/**
* A class that runs the hmmbuild command as a separate process.
{
if (params == null || params.isEmpty())
{
- Cache.log.error("No parameters to HMMBuild!|");
+ Console.error("No parameters to HMMBuild!|");
return;
}
{
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))
else
{
SequenceI[] sel = ((SequenceGroup) ac)
- .getSelectionAsNewSequences((AlignmentI) ac.getContext());
+ .getSelectionAsNewSequences((AlignmentI) ac.getContext());
for (SequenceI seq : sel)
{
- copy.add(seq);
+ 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);
}
/**
- * A helper method that deletes any HMM consensus sequence from the given
- * collection, and from the parent alignment if <code>ac</code> is a subgroup
- *
- * @param ac
- */
- void deleteHmmSequences(AnnotatedCollectionI ac)
- {
- List<SequenceI> hmmSeqs = ac.getHmmSequences();
- for (SequenceI hmmSeq : hmmSeqs)
- {
- if (ac instanceof SequenceGroup)
- {
- ((SequenceGroup) ac).deleteSequence(hmmSeq, false);
- AnnotatedCollectionI context = ac.getContext();
- if (context != null && context instanceof AlignmentI)
- {
- ((AlignmentI) context).deleteSequence(hmmSeq);
- }
- }
- else
- {
- ((AlignmentI) ac).deleteSequence(hmmSeq);
- }
- }
- }
-
- /**
* Constructs and executes the hmmbuild command as a separate process
*
* @param sequencesFile
args.add(ARG_DNA);
}
- args.add(getFilePath(hmmFile));
- args.add(getFilePath(sequencesFile));
+ args.add(getFilePath(hmmFile, true));
+ args.add(getFilePath(sequencesFile, true));
return runCommand(args);
}
{
if (hmmFile.length() == 0L)
{
- Cache.log.error("Error: hmmbuild produced empty hmm file");
+ Console.error("Error: hmmbuild produced empty hmm file");
return;
}
new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
SequenceI hmmSeq = file.getHMM().getConsensusSequence();
+
+
+ ResidueCount counts = new ResidueCount(alignment.getSequences());
+ hmmSeq.getHMM().setBackgroundFrequencies(counts);
+
if (hmmSeq == null)
{
// hmmbuild failure not detected earlier