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 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;
}
// 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);
{
if (hmmFile.length() == 0L)
{
- Cache.log.error("Error: hmmbuild produced empty hmm file");
+ Console.error("Error: hmmbuild produced empty hmm file");
return;
}