X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa_compactor%2FMsaCompactor.java;h=b4d2fe7a5eda0a04fc7586bd74df36f606c5c328;hb=97358f7a982d67831aedc14d5ab193727f6bdc83;hp=6209da11161ff7b40581f2c67ce267fcfa101353;hpb=4d33637f6bc5a76ca65dea7e21c9e2f7267ab2a3;p=jalview.git

diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index 6209da1..b4d2fe7 100644
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -179,6 +179,7 @@ public class MsaCompactor {
             }
             ++i;
         }
+        
         if ( _phylogentic_inference ) {
             decorateTree( phy, msa_props, true );
             displayTree( phy );
@@ -350,7 +351,14 @@ public class MsaCompactor {
         if ( _phylogentic_inference ) {
             decorateTree( phy, msa_props, false );
             displayTree( phy );
-        }
+            System.out.println( "calculating phylogentic tree..." );
+            System.out.println();
+            final Phylogeny phy2 = calcTree();
+            addSeqs2Tree( _msa, phy2 );
+            displayTree( phy2 );
+        }   
+      
+       
         return msa_props;
     }
 
@@ -401,7 +409,13 @@ public class MsaCompactor {
         if ( _phylogentic_inference ) {
             decorateTree( phy, msa_props, false );
             displayTree( phy );
-        }
+            System.out.println( "calculating phylogentic tree..." );
+            System.out.println();
+            final Phylogeny phy2 = calcTree();
+            addSeqs2Tree( _msa, phy2 );
+            displayTree( phy2 );
+        }   
+       
         return msa_props;
     }
 
@@ -456,7 +470,8 @@ public class MsaCompactor {
             final Phylogeny phy2 = calcTree();
             addSeqs2Tree( _msa, phy2 );
             displayTree( phy2 );
-        }
+        }   
+       
         return msa_props;
     }