cleanup

diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index 56cc729..17e4397 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -58,23 +58,23 @@ public class MsaCompactor {
 
     final private static NumberFormat NF_3                      = new DecimalFormat( "#.###" );
     final private static NumberFormat NF_4                      = new DecimalFormat( "#.####" );
+    private double                    _gap_ratio                = -1;
     //
     private final String              _maffts_opts              = "--auto";
-    private int                       _step                     = 1;
-    //
-    private boolean                   _realign                  = false;
-    private boolean                   _norm                     = true;
-    private int                       _step_for_diagnostics     = 1;
     private int                       _min_length               = -1;
-    private double                    _gap_ratio                = -1;
-    private final boolean             _report_aln_mean_identity = false;
-    private MSA_FORMAT                _output_format            = MSA_FORMAT.FASTA;
-    private final File                _removed_seqs_out_base    = null;
     //
     private DeleteableMsa             _msa;
+    private boolean                   _norm                     = true;
     private File                      _out_file_base;
+    private MSA_FORMAT                _output_format            = MSA_FORMAT.FASTA;
     private String                    _path_to_mafft;
+    //
+    private boolean                   _realign                  = false;
     private final SortedSet<String>   _removed_seq_ids;
+    private final File                _removed_seqs_out_base    = null;
+    private final boolean             _report_aln_mean_identity = false;
+    private int                       _step                     = 1;
+    private int                       _step_for_diagnostics     = 1;
     static {
         NF_4.setRoundingMode( RoundingMode.HALF_UP );
         NF_3.setRoundingMode( RoundingMode.HALF_UP );
@@ -85,6 +85,53 @@ public class MsaCompactor {
         _removed_seq_ids = new TreeSet<String>();
     }
 
+    public final List<MsaProperties> chart( final int step,
+                                            final boolean realign,
+                                            final boolean norm,
+                                            final boolean verbose ) throws IOException, InterruptedException {
+        final GapContribution stats[] = calcGapContribtionsStats( norm );
+        final List<String> to_remove_ids = new ArrayList<String>();
+        final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
+        for( final GapContribution gap_gontribution : stats ) {
+            to_remove_ids.add( gap_gontribution.getId() );
+        }
+        if ( verbose ) {
+            printTableHeader();
+        }
+        int i = 0;
+        final int s = _msa.getNumberOfSequences();
+        final int x = ForesterUtil.roundToInt( s / 20.0 );
+        while ( _msa.getNumberOfSequences() > x ) {
+            final String id = to_remove_ids.get( i );
+            //~_msa = MsaMethods.removeSequence( _msa, id );
+            _msa.deleteRow( id );
+            if ( ( s < 500 ) || ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) ) {
+                removeGapColumns();
+                if ( realign && ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) ) {
+                    realignWithMafft();
+                    msa_props.add( new MsaProperties( _msa ) );
+                    if ( verbose ) {
+                        printMsaStats( id );
+                    }
+                    if ( verbose ) {
+                        System.out.print( "(realigned)" );
+                    }
+                }
+                else {
+                    msa_props.add( new MsaProperties( _msa ) );
+                    if ( verbose ) {
+                        printMsaStats( id );
+                    }
+                }
+                if ( verbose ) {
+                    System.out.println();
+                }
+            }
+            ++i;
+        }
+        return msa_props;
+    }
+
     final public Msa getMsa() {
         return _msa;
     }
@@ -93,10 +140,125 @@ public class MsaCompactor {
         return _removed_seq_ids;
     }
 
+    public final void removeViaGapAverage( final double mean_gapiness, final boolean verbose ) throws IOException,
+            InterruptedException {
+        final GapContribution stats[] = calcGapContribtionsStats( _norm );
+        final List<String> to_remove_ids = new ArrayList<String>();
+        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 );
+            _msa.deleteRow( id );
+            removeGapColumns();
+            if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) )
+                    || ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) {
+                printMsaStatsWriteOutfileAndRealign( _realign, verbose, id );
+            }
+            else if ( verbose ) {
+                printMsaStats( id );
+            }
+            if ( verbose ) {
+                System.out.println();
+            }
+            ++i;
+        }
+    }
+
+    public void removeViaLength( final int length, final boolean verbose ) throws IOException, InterruptedException {
+        final GapContribution stats[] = calcGapContribtionsStats( _norm );
+        final List<String> to_remove_ids = new ArrayList<String>();
+        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 );
+            _msa.deleteRow( id );
+            removeGapColumns();
+            if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) || ( _msa.getLength() <= length ) ) {
+                printMsaStatsWriteOutfileAndRealign( _realign, verbose, id );
+            }
+            else if ( verbose ) {
+                printMsaStats( id );
+            }
+            if ( verbose ) {
+                System.out.println();
+            }
+            ++i;
+        }
+    }
+
+    public final void removeWorstOffenders( final int to_remove, final boolean verbose ) throws IOException,
+            InterruptedException {
+        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() );
+        }
+        if ( verbose ) {
+            printTableHeader();
+        }
+        for( int i = 0; i < to_remove_ids.size(); ++i ) {
+            final String id = to_remove_ids.get( i );
+            _msa.deleteRow( id );
+            removeGapColumns();
+            if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) || ( i == ( to_remove_ids.size() - 1 ) ) ) {
+                printMsaStatsWriteOutfileAndRealign( _realign, verbose, id );
+            }
+            else if ( verbose ) {
+                printMsaStats( id );
+            }
+            if ( verbose ) {
+                System.out.println();
+            }
+        }
+    }
+
+    public final void setGapRatio( final double gap_ratio ) {
+        _gap_ratio = gap_ratio;
+    }
+
+    public final void setMinLength( final int min_length ) {
+        _min_length = min_length;
+    }
+
+    public final void setNorm( final boolean norm ) {
+        _norm = norm;
+    }
+
     final public void setOutFileBase( final File out_file_base ) {
         _out_file_base = out_file_base;
     }
 
+    public final void setOutputFormat( final MSA_FORMAT output_format ) {
+        _output_format = output_format;
+    }
+
+    public void setPathToMafft( final String path_to_mafft ) {
+        _path_to_mafft = path_to_mafft;
+    }
+
+    public final void setRealign( final boolean realign ) {
+        _realign = realign;
+    }
+
+    public final void setStep( final int step ) {
+        _step = step;
+    }
+
+    public final void setStepForDiagnostics( final int step_for_diagnostics ) {
+        _step_for_diagnostics = step_for_diagnostics;
+    }
+
     final public String writeMsa( final File outfile, final MSA_FORMAT format, final String suffix ) throws IOException {
         final Double gr = MsaMethods.calcGapRatio( _msa );
         final String s = outfile + "_" + _msa.getNumberOfSequences() + "_" + _msa.getLength() + "_"
@@ -169,53 +331,6 @@ public class MsaCompactor {
         return gappiness;
     }
 
-    public final List<MsaProperties> chart( final int step,
-                                            final boolean realign,
-                                            final boolean norm,
-                                            final boolean verbose ) throws IOException, InterruptedException {
-        final GapContribution stats[] = calcGapContribtionsStats( norm );
-        final List<String> to_remove_ids = new ArrayList<String>();
-        final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
-        for( final GapContribution gap_gontribution : stats ) {
-            to_remove_ids.add( gap_gontribution.getId() );
-        }
-        if ( verbose ) {
-            printTableHeader();
-        }
-        int i = 0;
-        final int s = _msa.getNumberOfSequences();
-        final int x = ForesterUtil.roundToInt( s / 20.0 );
-        while ( _msa.getNumberOfSequences() > x ) {
-            final String id = to_remove_ids.get( i );
-            //~_msa = MsaMethods.removeSequence( _msa, id );
-            _msa.deleteRow( id );
-            if ( ( s < 500 ) || ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) ) {
-                removeGapColumns();
-                if ( realign && ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) ) {
-                    realignWithMafft();
-                    msa_props.add( new MsaProperties( _msa ) );
-                    if ( verbose ) {
-                        printMsaStats( id );
-                    }
-                    if ( verbose ) {
-                        System.out.print( "(realigned)" );
-                    }
-                }
-                else {
-                    msa_props.add( new MsaProperties( _msa ) );
-                    if ( verbose ) {
-                        printMsaStats( id );
-                    }
-                }
-                if ( verbose ) {
-                    System.out.println();
-                }
-            }
-            ++i;
-        }
-        return msa_props;
-    }
-
     private Phylogeny inferNJphylogeny( final PWD_DISTANCE_METHOD pwd_distance_method,
                                         final Msa msa,
                                         final boolean write_matrix,
@@ -297,93 +412,6 @@ public class MsaCompactor {
         _msa.deleteGapOnlyColumns();
     }
 
-    public final void removeViaGapAverage( final double mean_gapiness, final boolean verbose ) throws IOException,
-            InterruptedException {
-        final GapContribution stats[] = calcGapContribtionsStats( _norm );
-        final List<String> to_remove_ids = new ArrayList<String>();
-        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 );
-            _msa.deleteRow( id );
-            removeGapColumns();
-            if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) )
-                    || ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) {
-                printMsaStatsWriteOutfileAndRealign( _realign, verbose, id );
-            }
-            else if ( verbose ) {
-                printMsaStats( id );
-            }
-            if ( verbose ) {
-                System.out.println();
-            }
-            ++i;
-        }
-    }
-
-    public void removeViaLength( final int length, final boolean verbose ) throws IOException, InterruptedException {
-        final GapContribution stats[] = calcGapContribtionsStats( _norm );
-        final List<String> to_remove_ids = new ArrayList<String>();
-        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 );
-            _msa.deleteRow( id );
-            removeGapColumns();
-            if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) || ( _msa.getLength() <= length ) ) {
-                printMsaStatsWriteOutfileAndRealign( _realign, verbose, id );
-            }
-            else if ( verbose ) {
-                printMsaStats( id );
-            }
-            if ( verbose ) {
-                System.out.println();
-            }
-            ++i;
-        }
-    }
-
-    public final void removeWorstOffenders( final int to_remove, final boolean verbose ) throws IOException,
-            InterruptedException {
-        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() );
-        }
-        if ( verbose ) {
-            printTableHeader();
-        }
-        for( int i = 0; i < to_remove_ids.size(); ++i ) {
-            final String id = to_remove_ids.get( i );
-            _msa.deleteRow( id );
-            removeGapColumns();
-            if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) || ( i == ( to_remove_ids.size() - 1 ) ) ) {
-                printMsaStatsWriteOutfileAndRealign( _realign, verbose, id );
-            }
-            else if ( verbose ) {
-                printMsaStats( id );
-            }
-            if ( verbose ) {
-                System.out.println();
-            }
-        }
-    }
-
-    public void setPathToMafft( final String path_to_mafft ) {
-        _path_to_mafft = path_to_mafft;
-    }
-
     final private void writeMsa( final String outfile, final MSA_FORMAT format ) throws IOException {
         final Writer w = ForesterUtil.createBufferedWriter( outfile );
         _msa.write( w, format );
@@ -428,34 +456,6 @@ public class MsaCompactor {
         return null;
     }
 
-    public final void setStep( final int step ) {
-        _step = step;
-    }
-
-    public final void setNorm( final boolean norm ) {
-        _norm = norm;
-    }
-
-    public final void setStepForDiagnostics( final int step_for_diagnostics ) {
-        _step_for_diagnostics = step_for_diagnostics;
-    }
-
-    public final void setMinLength( final int min_length ) {
-        _min_length = min_length;
-    }
-
-    public final void setGapRatio( final double gap_ratio ) {
-        _gap_ratio = gap_ratio;
-    }
-
-    public final void setOutputFormat( final MSA_FORMAT output_format ) {
-        _output_format = output_format;
-    }
-
-    public final void setRealign( final boolean realign ) {
-        _realign = realign;
-    }
-
     private final static void printTableHeader() {
         System.out.print( ForesterUtil.pad( "Id", 20, ' ', false ) );
         System.out.print( "\t" );