JAL-2805 added getter in trees for retrieving all node sequences

[jalview.git] / src / jalview / ext / forester / DataConversions.java

diff --git a/src/jalview/ext/forester/DataConversions.java b/src/jalview/ext/forester/DataConversions.java
index b084382..ceeecde 100644 (file)
--- a/src/jalview/ext/forester/DataConversions.java
+++ b/src/jalview/ext/forester/DataConversions.java
@@ -17,13 +17,14 @@ public final class DataConversions
     {
       foresterSeq.setName(jalviewSequence.getDescription());
     }
-    foresterSeq.setMolecularSequenceAligned(sequenceIsAligned); // all tree
-                                                              // sequences
-                                                              // should
-                                                   // be aligned already
+
+    // all tree sequences should be aligned already
+    foresterSeq.setMolecularSequenceAligned(sequenceIsAligned);
+
     foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
-    if (jalviewSequence.isProtein()) // add checks for DNA or RNA (infer from
-                                     // forester itself?)
+    
+    // add checks for DNA or RNA (infer from forester itself?)
+    if (jalviewSequence.isProtein())
     {
       try
       {
@@ -56,10 +57,6 @@ public final class DataConversions
           final MatrixI jalviewInputMatrix,
           final String[] matrixIdentifiers)
   {
-    if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
-    {
-      // some kind of warning?
-    }
 
     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
             matrixIdentifiers);
@@ -71,13 +68,11 @@ public final class DataConversions
           final MatrixI jalviewInputMatrix,
           final SequenceI[] matrixSequences)
   {
-    if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
-    {
-      // some kind of warning?
-    }
     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
             matrixSequences);
     return foresterMatrix;
 
   }
+
+
 }