package jalview.hmmer;
import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
/**
* Base class for hmmbuild, hmmalign and hmmsearch
*
* @param seqs
*/
- protected Hashtable stashSequences(SequenceI[] seqs)
+ protected Map<String, SequenceInfo> stashSequences(SequenceI[] seqs)
{
return SeqsetUtils.uniquify(seqs, true);
}
/**
* Restores the sequence data lost by uniquifying
*
- * @param hashtable
+ * @param sequencesHash
* @param seqs
*/
- protected void recoverSequences(Hashtable hashtable, SequenceI[] seqs)
+ protected void recoverSequences(Map<String, SequenceInfo> sequencesHash, SequenceI[] seqs)
{
- SeqsetUtils.deuniquify(hashtable, seqs);
+ SeqsetUtils.deuniquify(sequencesHash, seqs);
}
/**
int exitValue = p.exitValue();
if (exitValue != 0)
{
- Cache.log.error("Command failed, return code = " + exitValue);
- Cache.log.error("Command/args were: " + args.toString());
+ Console.error("Command failed, return code = " + exitValue);
+ Console.error("Command/args were: " + args.toString());
}
return exitValue == 0; // 0 is success, by convention
} catch (Exception e)
Cache.getProperty(Preferences.CYGWIN_PATH));
if (bash == null)
{
- Cache.log.error("Cygwin shell not found");
+ Console.error("Cygwin shell not found");
return commands;
}