Merge branch 'features/JAL-3417_sdppred_calcs' into features/r2_11_2_JAL-3417_sdppred

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index c4098e2..15423b1 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -21,6 +21,7 @@
 package jalview.datamodel;
 
 import jalview.analysis.AlignmentUtils;
+import jalview.analysis.Conservation;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.io.FastaFile;
 import jalview.util.Comparison;
@@ -71,6 +72,12 @@ public class Alignment implements AlignmentI, AutoCloseable
 
   private List<AlignedCodonFrame> codonFrameList;
 
+  private Conservation conservation;
+
+  private ProfilesI consensus;
+
+  private Hashtable[] codonConsensus, rnaStructureConsensus;
+
   private void initAlignment(SequenceI[] seqs)
   {
     groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
@@ -2032,4 +2039,55 @@ public class Alignment implements AlignmentI, AutoCloseable
     }
   }
 
+  @Override
+  public Hashtable[] getComplementConsensusHash()
+  {
+    return codonConsensus;
+  }
+
+  @Override
+  public Conservation getConservation()
+  {
+    return conservation;
+  }
+
+  @Override
+  public Hashtable[] getRnaStructureConsensusHash()
+  {
+    return rnaStructureConsensus;
+  }
+
+  @Override
+  public ProfilesI getSequenceConsensusHash()
+  {
+    return consensus;
+  }
+
+  @Override
+  public void setComplementConsensusHash(Hashtable[] hconsensus)
+  {
+    codonConsensus = hconsensus;
+
+  }
+
+  @Override
+  public void setConservation(Conservation cons)
+  {
+    conservation = cons;
+
+  }
+
+  @Override
+  public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
+  {
+    rnaStructureConsensus = hStrucConsensus;
+
+  }
+
+  @Override
+  public void setSequenceConsensusHash(ProfilesI hconsensus)
+  {
+    consensus = hconsensus;
+
+  }
 }