X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMBuild.java;h=cb087fad8de3a0e0558e8e29b6ea717513ed2301;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=0c47c1dd8011fc05ef682d1f39fb113439eb94ac;hpb=0d519ae0c45b0b9962b4589e84c262a71bb2f346;p=jalview.git

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 0c47c1d..cb087fa 100644
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -1,7 +1,9 @@
 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;
@@ -22,6 +24,7 @@ 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.
@@ -58,7 +61,7 @@ public class HMMBuild extends HmmerCommand
   {
     if (params == null || params.isEmpty())
     {
-      Cache.log.error("No parameters to HMMBuild!|");
+      Console.error("No parameters to HMMBuild!|");
       return;
     }
 
@@ -201,7 +204,7 @@ 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);
 
@@ -330,7 +333,7 @@ public class HMMBuild extends HmmerCommand
   {
     if (hmmFile.length() == 0L)
     {
-      Cache.log.error("Error: hmmbuild produced empty hmm file");
+      Console.error("Error: hmmbuild produced empty hmm file");
       return;
     }