inprogress

diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java
index 68639ff..7f65269 100644 (file)
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -134,7 +134,7 @@ public class msa_compactor {
             final DescriptiveStatistics initial_msa_stats = MsaMethods.calculateEffectiveLengthStatistics( msa );
             final boolean chart_only = ( !cla.isOptionSet( LENGTH_OPTION ) )
                     && ( !cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) )
-                    && ( !cla.isOptionSet( AV_GAPINESS_OPTION ) ) && ( !cla.isOptionSet( MIN_LENGTH_OPTION ) );
+                    && ( !cla.isOptionSet( AV_GAPINESS_OPTION ) );
             if ( !chart_only && ( out == null ) ) {
                 ForesterUtil.fatalError( PRG_NAME, "outfile file missing" );
             }
@@ -230,17 +230,20 @@ public class msa_compactor {
                 if ( cla.isOptionSet( MAFFT_OPTIONS ) ) {
                     mafft_options = cla.getOptionValueAsCleanString( MAFFT_OPTIONS );
                     if ( ForesterUtil.isEmpty( mafft_options ) || ( mafft_options.length() < 3 ) ) {
-                        ForesterUtil.fatalError( PRG_NAME, "gap ratio is out of range: " + gap_ratio );
+                        ForesterUtil.fatalError( PRG_NAME, "illegal or empty MAFFT options: " + mafft_options );
                     }
                 }
             }
+            else if ( cla.isOptionSet( MAFFT_OPTIONS ) ) {
+                ForesterUtil.fatalError( PRG_NAME, "no need to indicate MAFFT options without realigning" );
+            }
             if ( chart_only ) {
                 if ( ( out != null ) || ( removed_seqs_out_base != null ) ) {
                     ForesterUtil
                             .fatalError( PRG_NAME,
                                          "chart only, no outfile(s) produced, thus no need to indicate output file(s)" );
                 }
-                if ( !realign && ( step > 1 ) ) {
+                if ( !realign && cla.isOptionSet( STEP_OPTION ) ) {
                     ForesterUtil.fatalError( PRG_NAME,
                                              "chart only, no re-aligning, thus no need to use step for output and re-aligning; use -"
                                                      + STEP_FOR_DIAGNOSTICS_OPTION + " instead" );
@@ -261,7 +264,7 @@ public class msa_compactor {
                     + NF_1.format( initial_msa_stats.arithmeticMean() ) );
             System.out.println( "  Max sequence length                : " + ( ( int ) initial_msa_stats.getMax() ) );
             System.out.println( "  Min sequence length                : " + ( ( int ) initial_msa_stats.getMin() ) );
-            if ( out != null ) {
+            if ( !chart_only ) {
                 System.out.println( "Output                               : " + out );
             }
             else {
@@ -273,20 +276,33 @@ public class msa_compactor {
             if ( worst_remove > 0 ) {
                 System.out.println( "Number of worst offenders to remove  : " + worst_remove );
             }
-            else if ( av_gap > 0 ) {
+            if ( av_gap > 0 ) {
                 System.out.println( "Target gap-ratio                     : " + av_gap );
             }
-            else if ( length > 0 ) {
+            if ( length > 0 ) {
                 System.out.println( "Target MSA length                    : " + length );
             }
-            else {
-                System.out.println( "Chart and diagnostics only           : true" );
+            if ( min_length > 1 ) {
+                System.out.println( "Minimal effective sequence length    : " + min_length );
+            }
+            if ( gap_ratio > -1 ) {
+                System.out.println( "Maximum allowed gap ratio per column : " + gap_ratio );
             }
             if ( ( out != null ) || ( removed_seqs_out_base != null ) ) {
                 System.out.println( "Output format                        : "
                         + ( output_format == MSA_FORMAT.FASTA ? "fasta" : "phylip" ) );
             }
-            System.out.println( "Step for output and re-aligning      : " + step );
+            if ( chart_only && !realign ) {
+                System.out.println( "Step for output and re-aligning      : n/a" );
+            }
+            else {
+                if ( chart_only ) {
+                    System.out.println( "Step for re-aligning                 : " + step );
+                }
+                else {
+                    System.out.println( "Step for output and re-aligning      : " + step );
+                }
+            }
             System.out.println( "Step for diagnostics reports         : " + step_for_diagnostics );
             System.out.println( "Calculate mean identity              : " + report_aln_mean_identity );
             if ( !norm ) {
@@ -296,15 +312,7 @@ public class msa_compactor {
             if ( realign ) {
                 System.out.println( "MAFFT options                        : " + mafft_options );
             }
-            if ( min_length > 1 ) {
-                System.out.println( "Minimal effective sequence length    : " + min_length );
-            }
-            if ( gap_ratio > -1 ) {
-                System.out.println( "Maximum allowed gap ratio per column : " + gap_ratio );
-            }
             System.out.println();
-            //
-            //
             final int initial_number_of_seqs = msa.getNumberOfSequences();
             List<MsaProperties> msa_props = null;
             final MsaCompactor mc = new MsaCompactor( msa );

diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index 4a07813..366d5bd 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -99,8 +99,10 @@ public class MsaCompactor {
         for( final GapContribution gap_gontribution : stats ) {
             to_remove_ids.add( gap_gontribution.getId() );
         }
-        final boolean print_id = ( _step < 2 ) && ( _step_for_diagnostics < 2 );
-        printTableHeader( print_id );
+        if ( !_realign ) {
+            _step = -1;
+        }
+        printTableHeader();
         int x = ForesterUtil.roundToInt( _msa.getNumberOfSequences() / 20.0 );
         if ( x < 1 ) {
             x = 1;
@@ -134,6 +136,10 @@ public class MsaCompactor {
         return msa_props;
     }
 
+    final public void deleteGapColumns( final double max_allowed_gap_ratio ) {
+        _msa.deleteGapColumns( max_allowed_gap_ratio );
+    }
+
     final public Msa getMsa() {
         return _msa;
     }
@@ -142,6 +148,15 @@ public class MsaCompactor {
         return _removed_seq_ids;
     }
 
+    public final void removeSequencesByMinimalLength( final int min_effective_length ) {
+        printMsaProperties( "", new MsaProperties( _msa, _report_aln_mean_identity ) );
+        System.out.println();
+        _msa = DeleteableMsa.createInstance( MsaMethods.removeSequencesByMinimalLength( _msa, min_effective_length ) );
+        removeGapColumns();
+        printMsaProperties( "", new MsaProperties( _msa, _report_aln_mean_identity ) );
+        System.out.println();
+    }
+
     public final List<MsaProperties> removeViaGapAverage( final double mean_gapiness ) throws IOException,
             InterruptedException {
         final GapContribution stats[] = calcGapContribtionsStats( _norm );
@@ -150,8 +165,7 @@ public class MsaCompactor {
         for( final GapContribution gap_gontribution : stats ) {
             to_remove_ids.add( gap_gontribution.getId() );
         }
-        final boolean print_id = ( _step < 2 ) || ( _step_for_diagnostics < 2 );
-        printTableHeader( print_id );
+        printTableHeader();
         MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
         msa_props.add( msa_prop );
         printMsaProperties( "", msa_prop );
@@ -191,8 +205,7 @@ public class MsaCompactor {
         for( final GapContribution gap_gontribution : stats ) {
             to_remove_ids.add( gap_gontribution.getId() );
         }
-        final boolean print_id = ( _step < 2 ) || ( _step_for_diagnostics < 2 );
-        printTableHeader( print_id );
+        printTableHeader();
         MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
         msa_props.add( msa_prop );
         printMsaProperties( "", msa_prop );
@@ -225,15 +238,6 @@ public class MsaCompactor {
         return msa_props;
     }
 
-    public final void removeSequencesByMinimalLength( final int min_effective_length ) {
-        printMsaProperties( "", new MsaProperties( _msa, _report_aln_mean_identity ) );
-        System.out.println();
-        _msa = DeleteableMsa.createInstance( MsaMethods.removeSequencesByMinimalLength( _msa, min_effective_length ) );
-        removeGapColumns();
-        printMsaProperties( "", new MsaProperties( _msa, _report_aln_mean_identity ) );
-        System.out.println();
-    }
-
     public final List<MsaProperties> removeWorstOffenders( final int to_remove ) throws IOException,
             InterruptedException {
         final GapContribution stats[] = calcGapContribtionsStats( _norm );
@@ -243,8 +247,7 @@ public class MsaCompactor {
             to_remove_ids.add( stats[ j ].getId() );
             _removed_seq_ids.add( stats[ j ].getId() );
         }
-        final boolean print_id = ( _step < 2 ) || ( _step_for_diagnostics < 2 );
-        printTableHeader( print_id );
+        printTableHeader();
         MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity );
         msa_props.add( msa_prop );
         printMsaProperties( "", msa_prop );
@@ -275,10 +278,6 @@ public class MsaCompactor {
         return msa_props;
     }
 
-    final public void deleteGapColumns( final double max_allowed_gap_ratio ) {
-        _msa.deleteGapColumns( max_allowed_gap_ratio );
-    }
-
     public final void setGapRatio( final double gap_ratio ) {
         _gap_ratio = gap_ratio;
     }
@@ -436,11 +435,11 @@ public class MsaCompactor {
     }
 
     private final boolean isPrintMsaStats( final int i ) {
-        return ( ( ( _step < 2 ) && ( _step_for_diagnostics < 2 ) ) || ( ( _step_for_diagnostics > 0 ) && ( ( ( i + 1 ) % _step_for_diagnostics ) == 0 ) ) );
+        return ( ( ( _step == 1 ) && ( _step_for_diagnostics == 1 ) ) || ( ( _step_for_diagnostics > 0 ) && ( ( ( i + 1 ) % _step_for_diagnostics ) == 0 ) ) );
     }
 
     private final boolean isPrintMsaStatsWriteOutfileAndRealign( final int i ) {
-        return ( ( ( _step < 2 ) && ( _step_for_diagnostics < 2 ) ) || ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) );
+        return ( ( ( _step == 1 ) && ( _step_for_diagnostics == 1 ) ) || ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) );
     }
 
     private final StringBuilder msaPropertiesAsSB( final MsaProperties msa_properties ) {
@@ -486,7 +485,7 @@ public class MsaCompactor {
     }
 
     private final void printMsaProperties( final String id, final MsaProperties msa_properties ) {
-        if ( ( _step < 2 ) || ( _step_for_diagnostics < 2 ) ) {
+        if ( ( _step == 1 ) || ( _step_for_diagnostics == 1 ) ) {
             System.out.print( ForesterUtil.pad( id, _longest_id_length, ' ', false ) );
             System.out.print( "\t" );
         }
@@ -506,8 +505,8 @@ public class MsaCompactor {
         return msa_prop;
     }
 
-    private final void printTableHeader( final boolean print_id ) {
-        if ( print_id ) {
+    private final void printTableHeader() {
+        if ( ( _step == 1 ) || ( _step_for_diagnostics == 1 ) ) {
             System.out.print( ForesterUtil.pad( "Id", _longest_id_length, ' ', false ) );
             System.out.print( "\t" );
         }