compactor work

[jalview.git] / forester / java / src / org / forester / msa_compactor / MsaCompactor.java

diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index cea2460..687951c 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -143,6 +143,7 @@ public class MsaCompactor {
             System.out.println( "calculating phylogentic tree..." );
             System.out.println();
             phy = calcTree();
+            addSeqs2Tree( _msa, phy );
         }
         if ( !_realign ) {
             _step = -1;
@@ -185,7 +186,26 @@ public class MsaCompactor {
         return msa_props;
     }
 
-    public final void decorateTree( final Phylogeny phy, final List<MsaProperties> msa_props, final boolean chart_only ) {
+    private final static void addSeqs2Tree( final Msa msa, final Phylogeny phy ) {
+        for( int i = 0; i < msa.getNumberOfSequences(); ++i ) {
+            final MolecularSequence seq = msa.getSequence( i );
+            final String seq_name = seq.getIdentifier();
+            final PhylogenyNode n = phy.getNode( seq_name );
+            if ( !n.getNodeData().isHasSequence() ) {
+                n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
+            }
+            else {
+                throw new IllegalArgumentException( "this should not have happened" );
+            }
+            n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
+            n.getNodeData().getSequence().setMolecularSequenceAligned( true );
+            n.getNodeData().getSequence().setName( seq_name );
+        }
+    }
+
+    private final static void decorateTree( final Phylogeny phy,
+                                            final List<MsaProperties> msa_props,
+                                            final boolean chart_only ) {
         final BasicDescriptiveStatistics length_stats = new BasicDescriptiveStatistics();
         for( int i = 0; i < msa_props.size(); ++i ) {
             final MsaProperties msa_prop = msa_props.get( i );
@@ -294,6 +314,7 @@ public class MsaCompactor {
             System.out.println( "calculating phylogentic tree..." );
             System.out.println();
             phy = calcTree();
+            addSeqs2Tree( _msa, phy );
         }
         printTableHeader();
         MsaProperties msa_prop = new MsaProperties( _msa, "", _calculate_shannon_entropy );
@@ -344,6 +365,7 @@ public class MsaCompactor {
             System.out.println( "calculating phylogentic tree..." );
             System.out.println();
             phy = calcTree();
+            addSeqs2Tree( _msa, phy );
         }
         printTableHeader();
         MsaProperties msa_prop = new MsaProperties( _msa, "", _calculate_shannon_entropy );
@@ -395,6 +417,7 @@ public class MsaCompactor {
             System.out.println( "calculating phylogentic tree..." );
             System.out.println();
             phy = calcTree();
+            addSeqs2Tree( _msa, phy );
         }
         printTableHeader();
         MsaProperties msa_prop = new MsaProperties( _msa, "", _calculate_shannon_entropy );
@@ -427,6 +450,11 @@ 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;
     }
@@ -608,6 +636,8 @@ public class MsaCompactor {
         sb.append( msa_properties.getLength() );
         sb.append( "\t" );
         sb.append( NF_4.format( msa_properties.getGapRatio() ) );
+        sb.append( "\t" );
+        sb.append( NF_1.format( msa_properties.getAvgNumberOfGapsPer100() ) );
         if ( _calculate_shannon_entropy ) {
             sb.append( "\t" );
             sb.append( NF_4.format( msa_properties.getEntropy7() ) );
@@ -675,6 +705,8 @@ public class MsaCompactor {
         System.out.print( "\t" );
         System.out.print( "Length" );
         System.out.print( "\t" );
+        System.out.print( "Gap R" );
+        System.out.print( "\t" );
         System.out.print( "Gaps" );
         System.out.print( "\t" );
         if ( _calculate_shannon_entropy ) {