inprogress

diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java
index fd035fe..7947bdd 100644 (file)
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -64,9 +64,17 @@ public class msa_compactor {
                 worst_remove = cla.getOptionValueAsInt( REMOVE_WORST_OFFENDERS_OPTION );
             }
             if ( cla.isOptionSet( AV_GAPINESS_OPTION ) ) {
+                if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) ) {
+                    printHelp();
+                    System.exit( 0 );
+                }
                 av = cla.getOptionValueAsDouble( AV_GAPINESS_OPTION );
             }
             if ( cla.isOptionSet( LENGTH_OPTION ) ) {
+                if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) || cla.isOptionSet( AV_GAPINESS_OPTION ) ) {
+                    printHelp();
+                    System.exit( 0 );
+                }
                 length = cla.getOptionValueAsInt( LENGTH_OPTION );
             }
             if ( cla.isOptionSet( STEP_OPTION ) ) {
@@ -98,12 +106,11 @@ public class msa_compactor {
             else {
                 msa = GeneralMsaParser.parse( is );
             }
-            MsaCompactor mc = null;
             if ( worst_remove > 0 ) {
-                mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, step, realign, norm, path_to_mafft, out );
+                MsaCompactor.removeWorstOffenders( msa, worst_remove, step, realign, norm, path_to_mafft, out );
             }
             else if ( av > 0 ) {
-                mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, norm, path_to_mafft, out );
+                MsaCompactor.reduceGapAverage( msa, av, step, realign, norm, path_to_mafft, out );
             }
             else if ( length > 0 ) {
                 if ( length >= msa.getLength() ) {
@@ -111,7 +118,7 @@ public class msa_compactor {
                             + ") is greater than or equal to MSA original length (" + msa.getLength() + ")" );
                 }
                 // TODO if < shortest seq -> error
-                mc = MsaCompactor.reduceLength( msa, length, step, realign, norm, path_to_mafft, out );
+                MsaCompactor.reduceLength( msa, length, step, realign, norm, path_to_mafft, out );
             }
         }
         catch ( final Exception e ) {

diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index 3092060..88deac8 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -35,12 +35,13 @@ import org.forester.util.ForesterUtil;
 
 public class MsaCompactor {
 
-    final private static NumberFormat NF_3 = new DecimalFormat( "#.###" );
-    final private static NumberFormat NF_4 = new DecimalFormat( "#.####" );
+    final private static NumberFormat NF_3         = new DecimalFormat( "#.###" );
+    final private static NumberFormat NF_4         = new DecimalFormat( "#.####" );
     private Msa                       _msa;
     private File                      _out_file_base;
     private String                    _path_to_mafft;
     private final SortedSet<String>   _removed_seq_ids;
+    private final String              _maffts_opts = "--retree 1";
     static {
         NF_4.setRoundingMode( RoundingMode.HALF_UP );
         NF_3.setRoundingMode( RoundingMode.HALF_UP );
@@ -158,7 +159,6 @@ public class MsaCompactor {
                 m.write( ForesterUtil.createBufferedWriter( matrix_name ) );
             }
             catch ( final IOException e ) {
-                // TODO Auto-generated catch block
                 e.printStackTrace();
             }
         }
@@ -173,9 +173,9 @@ public class MsaCompactor {
         sb.append( "\t" );
         sb.append( _msa.getLength() );
         sb.append( "\t" );
-        sb.append( NF_3.format( MsaMethods.calcGapRatio( _msa ) ) );
+        sb.append( NF_4.format( MsaMethods.calcGapRatio( _msa ) ) );
         sb.append( "\t" );
-        sb.append( NF_3.format( calculateIdentityRatio( 0, _msa.getLength() - 1, _msa ).arithmeticMean() ) );
+        sb.append( NF_4.format( calculateIdentityRatio( 0, _msa.getLength() - 1, _msa ).arithmeticMean() ) );
         return sb;
     }
 
@@ -184,10 +184,13 @@ public class MsaCompactor {
         //       .createInstance( "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft" );
         final MsaInferrer mafft = Mafft.createInstance( _path_to_mafft );
         final List<String> opts = new ArrayList<String>();
-        opts.add( "--maxiterate" );
-        opts.add( "1000" );
-        opts.add( "--localpair" );
-        opts.add( "--quiet" );
+        for( final String o : _maffts_opts.split( "\\s" ) ) {
+            opts.add( o );
+        }
+        //opts.add( "--maxiterate" );
+        //opts.add( "1000" );
+        //opts.add( "--localpair" );
+        //opts.add( "--quiet" );
         _msa = mafft.infer( _msa.asSequenceList(), opts );
     }
 
@@ -205,6 +208,9 @@ public class MsaCompactor {
         for( final GapContribution gap_gontribution : stats ) {
             to_remove_ids.add( gap_gontribution.getId() );
         }
+        if ( verbose ) {
+            printTableHeader();
+        }
         int i = 0;
         while ( MsaMethods.calcGapRatio( _msa ) > mean_gapiness ) {
             final String id = to_remove_ids.get( i );
@@ -233,6 +239,20 @@ public class MsaCompactor {
         }
     }
 
+    private final static void printTableHeader() {
+        System.out.print( ForesterUtil.pad( "Id", 20, ' ', false ) );
+        System.out.print( "\t" );
+        System.out.print( "Seqs" );
+        System.out.print( "\t" );
+        System.out.print( "Length" );
+        System.out.print( "\t" );
+        System.out.print( "Gaps" );
+        System.out.print( "\t" );
+        System.out.print( "MSA qual" );
+        System.out.print( "\t" );
+        System.out.println();
+    }
+
     final private void removeViaLength( final int length,
                                         final int step,
                                         final boolean realign,
@@ -243,6 +263,9 @@ public class MsaCompactor {
         for( final GapContribution gap_gontribution : stats ) {
             to_remove_ids.add( gap_gontribution.getId() );
         }
+        if ( verbose ) {
+            printTableHeader();
+        }
         int i = 0;
         while ( _msa.getLength() > length ) {
             final String id = to_remove_ids.get( i );
@@ -282,6 +305,9 @@ public class MsaCompactor {
             to_remove_ids.add( stats[ j ].getId() );
             _removed_seq_ids.add( stats[ j ].getId() );
         }
+        if ( verbose ) {
+            printTableHeader();
+        }
         for( int i = 0; i < to_remove_ids.size(); ++i ) {
             final String id = to_remove_ids.get( i );
             _msa = MsaMethods.removeSequence( _msa, id );
@@ -333,6 +359,10 @@ public class MsaCompactor {
                 return path;
             }
         }
+        path = "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft";
+        if ( MsaInferrer.isInstalled( path ) ) {
+            return path;
+        }
         path = "/usr/local/bin/mafft";
         if ( MsaInferrer.isInstalled( path ) ) {
             return path;