Merge branch 'alpha/origin_2022_JAL-3066_Jalview_212_slivka-integration' into spike...

[jalview.git] / src / jalview / hmmer / HMMBuild.java

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 0c47c1d..fa9cd92 100644 (file)
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -1,5 +1,6 @@
 package jalview.hmmer;
 
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -22,6 +23,7 @@ import java.io.IOException;
 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.
@@ -201,7 +203,7 @@ public class HMMBuild extends HmmerCommand
       // 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);