inprogress

diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java
index b030d74..765648f 100644 (file)
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -9,9 +9,8 @@ import java.util.List;
 import org.forester.io.parsers.FastaParser;
 import org.forester.io.parsers.GeneralMsaParser;
 import org.forester.msa.Msa;
-import org.forester.msa.MsaInferrer;
 import org.forester.msa.Msa.MSA_FORMAT;
-import org.forester.msa.MsaMethods;
+import org.forester.msa.MsaInferrer;
 import org.forester.msa_compactor.MsaCompactor;
 import org.forester.util.CommandLineArguments;
 import org.forester.util.ForesterUtil;
@@ -20,11 +19,11 @@ public class msa_compactor {
 
     final static private String HELP_OPTION_1                          = "help";
     final static private String HELP_OPTION_2                          = "h";
-    final static private String REMOVE_WORST_OFFENDERS_OPTION          = "w";
-    final static private String AV_GAPINESS_OPTION                     = "a";
+    final static private String REMOVE_WORST_OFFENDERS_OPTION          = "r";
+    final static private String AV_GAPINESS_OPTION                     = "g";
     final static private String STEP_OPTION                            = "s";
     final static private String LENGTH_OPTION                          = "l";
-    final static private String REALIGN_OPTION                         = "r";
+    final static private String REALIGN_OPTION                         = "a";
     final static private String PATH_TO_MAFFT_OPTION                   = "mafft";
     final static private String DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn";
     final static private String PRG_NAME                               = "msa_compactor";
@@ -94,15 +93,12 @@ public class msa_compactor {
             //                printHelp();
             //                System.exit( 0 );
             //            }
-            
             if ( realign ) {
                 if ( ForesterUtil.isEmpty( path_to_mafft ) ) {
                     path_to_mafft = MsaCompactor.guessPathToMafft();
                 }
                 checkPathToMafft( path_to_mafft );
             }
-            
-            
             Msa msa = null;
             final FileInputStream is = new FileInputStream( in );
             if ( FastaParser.isLikelyFasta( in ) ) {
@@ -111,9 +107,6 @@ public class msa_compactor {
             else {
                 msa = GeneralMsaParser.parse( is );
             }
-            
-          
-            
             MsaCompactor mc = null;
             if ( worst_remove > 0 ) {
                 mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign, norm, path_to_mafft );
@@ -124,10 +117,10 @@ public class msa_compactor {
             else if ( length > 0 ) {
                 mc = MsaCompactor.reduceLength( msa, length, step, realign, path_to_mafft );
             }
-            System.out.println( MsaMethods.calcGapRatio( mc.getMsa() ) );
-            for( final String id : mc.getRemovedSeqIds() ) {
-                System.out.println( id );
-            }
+            //System.out.println( MsaMethods.calcGapRatio( mc.getMsa() ) );
+            // for( final String id : mc.getRemovedSeqIds() ) {
+            //     System.out.println( id );
+            //}
             mc.writeMsa( out, MSA_FORMAT.PHYLIP, ".aln" );
         }
         catch ( final Exception e ) {
@@ -136,16 +129,17 @@ public class msa_compactor {
         }
     }
 
-    private static void checkPathToMafft( String path_to_mafft ) {
+    private static void checkPathToMafft( final String path_to_mafft ) {
         if ( !ForesterUtil.isEmpty( path_to_mafft ) && MsaInferrer.isInstalled( path_to_mafft ) ) {
-            ForesterUtil.programMessage( PRG_NAME, "using MAFFT at \"" + path_to_mafft + "\""  );
+            ForesterUtil.programMessage( PRG_NAME, "using MAFFT at \"" + path_to_mafft + "\"" );
         }
         else {
             if ( ForesterUtil.isEmpty( path_to_mafft ) ) {
-                ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable found, use -\"" + PATH_TO_MAFFT_OPTION + "=<path to MAFFT>\" option" );
+                ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable found, use -\"" + PATH_TO_MAFFT_OPTION
+                        + "=<path to MAFFT>\" option" );
             }
             else {
-                ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable at \""  + path_to_mafft + "\""  );
+                ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable at \"" + path_to_mafft + "\"" );
             }
         }
     }
@@ -161,20 +155,20 @@ public class msa_compactor {
         final String path_to_mafft = MsaCompactor.guessPathToMafft();
         String mafft_comment;
         if ( !ForesterUtil.isEmpty( path_to_mafft ) ) {
-            mafft_comment = " (" + path_to_mafft + ")";
+            mafft_comment = " (using " + path_to_mafft + ")";
         }
         else {
             mafft_comment = " (no path to MAFFT found, use -\"" + PATH_TO_MAFFT_OPTION + "=<path to MAFFT>\" option";
         }
-        
         System.out.println( "Usage:" );
         System.out.println();
-        System.out.println( PRG_NAME + " <options> <msa input file>" );
+        System.out.println( PRG_NAME + " <options> <msa input file> <output file>" );
         System.out.println();
         System.out.println( " options: " );
         System.out.println();
-        System.out.println( "   -" + REMOVE_WORST_OFFENDERS_OPTION + "=<integer>  number of sequences to remove" );
-        System.out.println( "   -" + REALIGN_OPTION + " to realign using MAFFT" + mafft_comment );
+        System.out.println( "   -" + REMOVE_WORST_OFFENDERS_OPTION
+                + "=<integer>  number of worst offender sequences to remove" );
+        System.out.println( "   -" + REALIGN_OPTION + "            to realign using MAFFT" + mafft_comment );
         System.out.println();
         System.out.println();
         System.out.println();

diff --git a/forester/java/src/org/forester/msa/MsaMethods.java b/forester/java/src/org/forester/msa/MsaMethods.java
index b05e837..ac6cb1f 100644 (file)
--- a/forester/java/src/org/forester/msa/MsaMethods.java
+++ b/forester/java/src/org/forester/msa/MsaMethods.java
@@ -175,11 +175,13 @@ public final class MsaMethods {
     public static SortedMap<Character, Integer> calculateResidueDestributionPerColumn( final Msa msa, final int column ) {
         final SortedMap<Character, Integer> map = new TreeMap<Character, Integer>();
         for( final Character r : msa.getColumnAt( column ) ) {
-            if ( !map.containsKey( r ) ) {
-                map.put( r, 1 );
-            }
-            else {
-                map.put( r, map.get( r ) + 1 );
+            if ( r != Sequence.GAP ) {
+                if ( !map.containsKey( r ) ) {
+                    map.put( r, 1 );
+                }
+                else {
+                    map.put( r, map.get( r ) + 1 );
+                }
             }
         }
         return map;

diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index d6ece5d..5d3a55c 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -13,7 +13,6 @@ import java.util.List;
 import java.util.SortedSet;
 import java.util.TreeSet;
 
-import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.evoinference.distance.NeighborJoiningF;
 import org.forester.evoinference.distance.PairwiseDistanceCalculator;
 import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
@@ -30,6 +29,8 @@ import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.sequence.Sequence;
 import org.forester.tools.ConfidenceAssessor;
+import org.forester.util.BasicDescriptiveStatistics;
+import org.forester.util.DescriptiveStatistics;
 import org.forester.util.ForesterUtil;
 
 public class MsaCompactor {
@@ -39,7 +40,7 @@ public class MsaCompactor {
     private static final boolean      VERBOSE = true;
     private Msa                       _msa;
     private final SortedSet<String>   _removed_seq_ids;
-    private String _path_to_mafft;
+    private String                    _path_to_mafft;
     static {
         NF_4.setRoundingMode( RoundingMode.HALF_UP );
         NF_3.setRoundingMode( RoundingMode.HALF_UP );
@@ -98,19 +99,27 @@ public class MsaCompactor {
     final private GapContribution[] calcGapContribtionsStats( final boolean norm ) {
         final GapContribution stats[] = calcGapContribtions( norm );
         Arrays.sort( stats );
-        for( final GapContribution stat : stats ) {
-            final StringBuilder sb = new StringBuilder();
-            sb.append( stat.getId() );
-            sb.append( "\t" );
-            sb.append( NF_4.format( stat.getValue() ) );
-            sb.append( "\t" );
-            //            sb.append( NF_4.format( stat.median() ) );
-            //            sb.append( "\t" );
-            //            sb.append( NF_4.format( stat.getMin() ) );
-            //            sb.append( "\t" );
-            //            sb.append( NF_4.format( stat.getMax() ) );
-            //sb.append( "\t" );
-            System.out.println( sb );
+        // for( final GapContribution stat : stats ) {
+        //  final StringBuilder sb = new StringBuilder();
+        //  sb.append( stat.getId() );
+        //  sb.append( "\t" );
+        //  sb.append( NF_4.format( stat.getValue() ) );
+        //  sb.append( "\t" );
+        //            sb.append( NF_4.format( stat.median() ) );
+        //            sb.append( "\t" );
+        //            sb.append( NF_4.format( stat.getMin() ) );
+        //            sb.append( "\t" );
+        //            sb.append( NF_4.format( stat.getMax() ) );
+        //sb.append( "\t" );
+        //System.out.println( sb );
+        // }
+        return stats;
+    }
+
+    private static DescriptiveStatistics calculateIdentityRatio( final int from, final int to, final Msa msa ) {
+        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+        for( int c = from; c <= to; ++c ) {
+            stats.addValue( MsaMethods.calculateIdentityRatio( msa, c ) );
         }
         return stats;
     }
@@ -124,7 +133,7 @@ public class MsaCompactor {
         }
         return gappiness;
     }
-    
+
     // Returns null if not path found.
     final public static String guessPathToMafft() {
         String path;
@@ -133,7 +142,6 @@ public class MsaCompactor {
             if ( MsaInferrer.isInstalled( path ) ) {
                 return path;
             }
-            
         }
         path = "/usr/local/bin/mafft";
         if ( MsaInferrer.isInstalled( path ) ) {
@@ -153,16 +161,11 @@ public class MsaCompactor {
         }
         return null;
     }
-    
 
     final private void mafft() throws IOException, InterruptedException {
-      //  final MsaInferrer mafft = Mafft
+        //  final MsaInferrer mafft = Mafft
         //       .createInstance( "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft" );
-      
-        final MsaInferrer mafft = Mafft
-                .createInstance( _path_to_mafft );
-      
-        
+        final MsaInferrer mafft = Mafft.createInstance( _path_to_mafft );
         final List<String> opts = new ArrayList<String>();
         opts.add( "--maxiterate" );
         opts.add( "1000" );
@@ -178,6 +181,8 @@ public class MsaCompactor {
         sb.append( _msa.getLength() );
         sb.append( "\t" );
         sb.append( NF_3.format( MsaMethods.calcGapRatio( _msa ) ) );
+        sb.append( "\t" );
+        sb.append( NF_3.format( calculateIdentityRatio( 0, _msa.getLength() - 1, _msa ).arithmeticMean() ) );
         return sb;
     }
 
@@ -303,19 +308,20 @@ public class MsaCompactor {
                                              final int step,
                                              final boolean realign,
                                              final boolean norm ) throws IOException, InterruptedException {
-        final Phylogeny a = pi( "a.pwd" );
-        Archaeopteryx.createApplication( a );
+        //final Phylogeny a = pi( "a.pwd" );
+        //Archaeopteryx.createApplication( a );
         final GapContribution stats[] = calcGapContribtionsStats( norm );
         final List<String> to_remove_ids = new ArrayList<String>();
         for( int j = 0; j < to_remove; ++j ) {
             to_remove_ids.add( stats[ j ].getId() );
             _removed_seq_ids.add( stats[ j ].getId() );
         }
-        //TODO if verbose/interactve
+        //TODO if verbose/interactive
         for( final String id : to_remove_ids ) {
             _msa = MsaMethods.removeSequence( _msa, id );
             removeGapColumns();
-            System.out.print( id );
+            //System.out.print( id );
+            System.out.print( ForesterUtil.pad( id, 20, ' ', false ) );
             System.out.print( "\t" );
             final StringBuilder sb = msaStatsAsSB();
             System.out.println( sb );
@@ -326,8 +332,8 @@ public class MsaCompactor {
         if ( realign ) {
             mafft();
         }
-        final Phylogeny b = pi( "b.pwd" );
-        Archaeopteryx.createApplication( b );
+        //final Phylogeny b = pi( "b.pwd" );
+        //Archaeopteryx.createApplication( b );
     }
 
     final private void writeMsa( final String outfile, final MSA_FORMAT format ) throws IOException {
@@ -345,7 +351,7 @@ public class MsaCompactor {
                                                        final String path_to_mafft ) throws IOException,
             InterruptedException {
         final MsaCompactor mc = new MsaCompactor( msa );
-        if ( realign) {
+        if ( realign ) {
             mc.setPathToMafft( path_to_mafft );
         }
         mc.removeViaGapAverage( max_gap_average, step, realign, out, minimal_effective_length );
@@ -356,9 +362,10 @@ public class MsaCompactor {
                                                    final int length,
                                                    final int step,
                                                    final boolean realign,
-                                                   final String path_to_mafft ) throws IOException, InterruptedException {
+                                                   final String path_to_mafft ) throws IOException,
+            InterruptedException {
         final MsaCompactor mc = new MsaCompactor( msa );
-        if ( realign) {
+        if ( realign ) {
             mc.setPathToMafft( path_to_mafft );
         }
         mc.removeViaLength( length, step, realign );
@@ -372,7 +379,7 @@ public class MsaCompactor {
                                                            final String path_to_mafft ) throws IOException,
             InterruptedException {
         final MsaCompactor mc = new MsaCompactor( msa );
-        if ( realign) {
+        if ( realign ) {
             mc.setPathToMafft( path_to_mafft );
         }
         mc.removeWorstOffenders( worst_offenders_to_remove, 1, realign, norm );
@@ -381,6 +388,5 @@ public class MsaCompactor {
 
     private void setPathToMafft( final String path_to_mafft ) {
         _path_to_mafft = path_to_mafft;
-        
     }
 }

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 1fcf900..80a20b6 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -5698,10 +5698,10 @@ public final class Test {
 
     private static boolean testMsaQualityMethod() {
         try {
-            final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
-            final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
-            final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
-            final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
+            final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
+            final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
+            final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
+            final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
             final List<Sequence> l = new ArrayList<Sequence>();
             l.add( s0 );
             l.add( s1 );
@@ -5720,6 +5720,15 @@ public final class Test {
             if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
                 return false;
             }
+            if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) {
+                return false;
+            }
+            if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) {
+                return false;
+            }
+            if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) {
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );