X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHmmerCommand.java;h=e24100811d3ea8fcfdce13e46dcd4b4114038980;hb=ca9ab48d85c35112da4d9bf6273a41e734d0872b;hp=02403525aef6d62ebac586a2414b71a314e6b467;hpb=5d28c907a598716ca90eaa8a625420e2c0c694f0;p=jalview.git

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index 0240352..e241008 100644
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -1,6 +1,7 @@
 package jalview.hmmer;
 
 import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -30,6 +31,7 @@ import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 /**
  * Base class for hmmbuild, hmmalign and hmmsearch
@@ -127,7 +129,7 @@ public abstract class HmmerCommand implements Runnable
    * 
    * @param seqs
    */
-  protected Hashtable stashSequences(SequenceI[] seqs)
+  protected Map<String, SequenceInfo> stashSequences(SequenceI[] seqs)
   {
     return SeqsetUtils.uniquify(seqs, true);
   }
@@ -135,12 +137,12 @@ public abstract class HmmerCommand implements Runnable
   /**
    * 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);
   }
 
   /**