package jalview.hmmer;
import jalview.analysis.AlignmentSorter;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import javax.swing.JInternalFrame;
int job = 0;
for (SequenceI[] seqs : subAlignments)
{
- Hashtable sequencesHash = stashSequences(seqs);
+ Map<String, SequenceInfo> sequencesHash = stashSequences(seqs);
try
{
File modelFile = FileUtils.createTempFile("hmm", ".hmm");
File alignmentFile = FileUtils.createTempFile("output", ".sto");
File resultFile = FileUtils.createTempFile("input", ".sto");
- exportStockholm(seqs, alignmentFile.getAbsoluteFile(), null, false);
+ exportStockholm(seqs, alignmentFile.getAbsoluteFile(), null);
exportHmm(hmm, modelFile.getAbsoluteFile());
boolean ran = runCommand(modelFile, alignmentFile, resultFile);