in progress

[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 6209da1..8a13b5c 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -82,7 +82,7 @@ public class MsaCompactor {
     //
     private String                             _maffts_opts               = "--auto";
     private DeleteableMsa                      _msa                       = null;
-    private boolean                            _norm                      = true;
+    private boolean                            _normalize_for_effective_seq_length                      = true;
     private File                               _out_file_base             = null;
     private MSA_FORMAT                         _output_format             = MSA_FORMAT.FASTA;
     private String                             _path_to_mafft             = null;
@@ -130,9 +130,9 @@ public class MsaCompactor {
         return phy;
     }
 
-    public final List<MsaProperties> chart( final int step, final boolean realign, final boolean norm )
+    public final List<MsaProperties> chart( final int step, final boolean realign, final boolean normalize_for_effective_seq_length )
             throws IOException, InterruptedException {
-        final GapContribution stats[] = calcGapContribtionsStats( norm );
+        final GapContribution stats[] = calcGapContribtionsStats( normalize_for_effective_seq_length );
         final List<String> to_remove_ids = new ArrayList<String>();
         final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
         for( final GapContribution gap_gontribution : stats ) {
@@ -179,6 +179,7 @@ public class MsaCompactor {
             }
             ++i;
         }
+        
         if ( _phylogentic_inference ) {
             decorateTree( phy, msa_props, true );
             displayTree( phy );
@@ -304,7 +305,7 @@ public class MsaCompactor {
 
     public final List<MsaProperties> removeViaGapAverage( final double mean_gapiness ) throws IOException,
     InterruptedException {
-        final GapContribution stats[] = calcGapContribtionsStats( _norm );
+        final GapContribution stats[] = calcGapContribtionsStats( _normalize_for_effective_seq_length );
         final List<String> to_remove_ids = new ArrayList<String>();
         final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
         for( final GapContribution gap_gontribution : stats ) {
@@ -350,12 +351,19 @@ 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;
     }
 
     public List<MsaProperties> removeViaLength( final int length ) throws IOException, InterruptedException {
-        final GapContribution stats[] = calcGapContribtionsStats( _norm );
+        final GapContribution stats[] = calcGapContribtionsStats( _normalize_for_effective_seq_length );
         final List<String> to_remove_ids = new ArrayList<String>();
         final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
         for( final GapContribution gap_gontribution : stats ) {
@@ -401,13 +409,19 @@ 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;
     }
 
     public final List<MsaProperties> removeWorstOffenders( final int to_remove ) throws IOException,
     InterruptedException {
-        final GapContribution stats[] = calcGapContribtionsStats( _norm );
+        final GapContribution stats[] = calcGapContribtionsStats( _normalize_for_effective_seq_length );
         final List<String> to_remove_ids = new ArrayList<String>();
         final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
         for( int j = 0; j < to_remove; ++j ) {
@@ -456,7 +470,8 @@ public class MsaCompactor {
             final Phylogeny phy2 = calcTree();
             addSeqs2Tree( _msa, phy2 );
             displayTree( phy2 );
-        }
+        }   
+       
         return msa_props;
     }
 
@@ -472,8 +487,8 @@ public class MsaCompactor {
         _maffts_opts = maffts_opts;
     }
 
-    public final void setNorm( final boolean norm ) {
-        _norm = norm;
+    public final void setNorm( final boolean normalize_for_effective_seq_length ) {
+        _normalize_for_effective_seq_length = normalize_for_effective_seq_length;
     }
 
     final public void setOutFileBase( final File out_file_base ) {
@@ -569,8 +584,8 @@ public class MsaCompactor {
         return stats;
     }
 
-    final private GapContribution[] calcGapContribtionsStats( final boolean norm ) {
-        final GapContribution stats[] = calcGapContribtions( norm );
+    final private GapContribution[] calcGapContribtionsStats( final boolean normalize_for_effective_seq_length ) {
+        final GapContribution stats[] = calcGapContribtions( normalize_for_effective_seq_length );
         Arrays.sort( stats );
         return stats;
     }