inprogress

diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java
index 19d5caf..4e51675 100644 (file)
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -48,9 +48,11 @@ import org.forester.util.ForesterUtil;
 
 public class msa_compactor {
 
-    final private static NumberFormat NF_1                                   = new DecimalFormat( "#.0" );
+    final private static NumberFormat NF_1                                   = new DecimalFormat( "0.#" );
+    final private static NumberFormat NF_4                                   = new DecimalFormat( "0.####" );
     static {
         NF_1.setRoundingMode( RoundingMode.HALF_UP );
+        NF_4.setRoundingMode( RoundingMode.HALF_UP );
     }
     final static private String       HELP_OPTION_1                          = "help";
     final static private String       HELP_OPTION_2                          = "h";
@@ -64,7 +66,7 @@ public class msa_compactor {
     final static private String       MIN_LENGTH_OPTION                      = "ml";
     final static private String       GAP_RATIO_LENGTH_OPTION                = "gr";
     final static private String       REPORT_ENTROPY                         = "e";
-    final static private String       OUTPUT_FORMAT_PHYLIP_OPTION            = "p";
+    final static private String       OUTPUT_FORMAT_OPTION                   = "f";
     final static private String       OUTPUT_REMOVED_SEQS_OPTION             = "ro";
     final static private String       MAFFT_OPTIONS                          = "mo";
     final static private String       PERFORM_PHYLOGENETIC_INFERENCE         = "t";
@@ -118,7 +120,7 @@ public class msa_compactor {
             allowed_options.add( MIN_LENGTH_OPTION );
             allowed_options.add( GAP_RATIO_LENGTH_OPTION );
             allowed_options.add( REPORT_ENTROPY );
-            allowed_options.add( OUTPUT_FORMAT_PHYLIP_OPTION );
+            allowed_options.add( OUTPUT_FORMAT_OPTION );
             allowed_options.add( OUTPUT_REMOVED_SEQS_OPTION );
             allowed_options.add( MAFFT_OPTIONS );
             allowed_options.add( PERFORM_PHYLOGENETIC_INFERENCE );
@@ -137,7 +139,7 @@ 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( AV_GAPINESS_OPTION ) && ( !cla.isOptionSet( MIN_LENGTH_OPTION ) ) );
             if ( !chart_only && ( out == null ) ) {
                 ForesterUtil.fatalError( PRG_NAME, "outfile file missing" );
             }
@@ -175,6 +177,22 @@ public class msa_compactor {
                                                      + initial_msa_stats.getMin() + ") ]: " + length );
                 }
             }
+            if ( cla.isOptionSet( MIN_LENGTH_OPTION ) ) {
+                if ( cla.isOptionSet( LENGTH_OPTION ) || cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION )
+                        || cla.isOptionSet( AV_GAPINESS_OPTION ) || cla.isOptionSet( STEP_OPTION )
+                        || cla.isOptionSet( REALIGN_OPTION ) || cla.isOptionSet( PATH_TO_MAFFT_OPTION )
+                        || cla.isOptionSet( STEP_FOR_DIAGNOSTICS_OPTION ) || cla.isOptionSet( REPORT_ENTROPY )
+                        || cla.isOptionSet( OUTPUT_REMOVED_SEQS_OPTION )
+                        || cla.isOptionSet( PERFORM_PHYLOGENETIC_INFERENCE ) ) {
+                    printHelp();
+                    System.exit( 0 );
+                }
+                min_length = cla.getOptionValueAsInt( MIN_LENGTH_OPTION );
+                if ( ( min_length < 2 ) || ( min_length > initial_msa_stats.getMax() ) ) {
+                    ForesterUtil.fatalError( PRG_NAME, "value for minimal sequence length is out of range: "
+                            + min_length );
+                }
+            }
             if ( cla.isOptionSet( STEP_OPTION ) ) {
                 step = cla.getOptionValueAsInt( STEP_OPTION );
                 if ( ( step < 1 )
@@ -202,13 +220,6 @@ public class msa_compactor {
                             + step_for_diagnostics );
                 }
             }
-            if ( cla.isOptionSet( MIN_LENGTH_OPTION ) ) {
-                min_length = cla.getOptionValueAsInt( MIN_LENGTH_OPTION );
-                if ( ( min_length < 2 ) || ( min_length > initial_msa_stats.getMax() ) ) {
-                    ForesterUtil.fatalError( PRG_NAME, "value for minimal sequence length is out of range: "
-                            + min_length );
-                }
-            }
             if ( cla.isOptionSet( GAP_RATIO_LENGTH_OPTION ) ) {
                 gap_ratio = cla.getOptionValueAsDouble( GAP_RATIO_LENGTH_OPTION );
                 if ( ( gap_ratio < 0 ) || ( gap_ratio > 1 ) ) {
@@ -218,8 +229,20 @@ public class msa_compactor {
             if ( cla.isOptionSet( REPORT_ENTROPY ) ) {
                 report_entropy = true;
             }
-            if ( cla.isOptionSet( OUTPUT_FORMAT_PHYLIP_OPTION ) ) {
-                output_format = MSA_FORMAT.PHYLIP;
+            if ( cla.isOptionSet( OUTPUT_FORMAT_OPTION ) ) {
+                final String fs = cla.getOptionValueAsCleanString( OUTPUT_FORMAT_OPTION );
+                if ( fs.equalsIgnoreCase( "p" ) ) {
+                    output_format = MSA_FORMAT.PHYLIP;
+                }
+                else if ( fs.equalsIgnoreCase( "f" ) ) {
+                    output_format = MSA_FORMAT.FASTA;
+                }
+                else if ( fs.equalsIgnoreCase( "n" ) ) {
+                    output_format = MSA_FORMAT.NEXUS;
+                }
+                else {
+                    ForesterUtil.fatalError( PRG_NAME, "illegal or empty output format option: " + fs );
+                }
             }
             if ( cla.isOptionSet( OUTPUT_REMOVED_SEQS_OPTION ) ) {
                 final String s = cla.getOptionValueAsCleanString( OUTPUT_REMOVED_SEQS_OPTION );
@@ -276,6 +299,10 @@ 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() ) );
+            System.out.println( "  Gap ratio                          : "
+                    + NF_4.format( MsaMethods.calcGapRatio( msa ) ) );
+            System.out.println( "  Normalized Shannon Entropy (entn21): "
+                    + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, msa ) ) );
             if ( !chart_only ) {
                 System.out.println( "Output                               : " + out );
             }
@@ -301,69 +328,80 @@ public class msa_compactor {
                 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" ) );
-            }
-            if ( chart_only && !realign ) {
-                System.out.println( "Step for output and re-aligning      : n/a" );
+                System.out.print( "Output format                        : " );
+                if ( output_format == MSA_FORMAT.FASTA ) {
+                    System.out.println( "fasta" );
+                }
+                else if ( output_format == MSA_FORMAT.PHYLIP ) {
+                    System.out.println( "phylip" );
+                }
+                else if ( output_format == MSA_FORMAT.NEXUS ) {
+                    System.out.println( "nexus" );
+                }
             }
-            else {
-                if ( chart_only ) {
-                    System.out.println( "Step for re-aligning                 : " + step );
+            if ( min_length == -1 ) {
+                if ( chart_only && !realign ) {
+                    System.out.println( "Step for output and re-aligning      : n/a" );
                 }
                 else {
-                    System.out.println( "Step for output and re-aligning      : " + step );
+                    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 normalized Shannon Entropy : " + report_entropy );
+                if ( !norm ) {
+                    System.out.println( "Normalize                            : " + norm );
+                }
+                System.out.println( "Realign with MAFFT                   : " + realign );
+                if ( realign ) {
+                    System.out.println( "MAFFT options                        : " + mafft_options );
+                }
+                System.out.println( "Simple tree (Kimura distances, NJ)   : " + perform_phylogenetic_inference );
             }
-            System.out.println( "Step for diagnostics reports         : " + step_for_diagnostics );
-            System.out.println( "Calculate normalized Shannon Entropy : " + report_entropy );
-            if ( !norm ) {
-                System.out.println( "Normalize                            : " + norm );
-            }
-            System.out.println( "Realign with MAFFT                   : " + realign );
-            if ( realign ) {
-                System.out.println( "MAFFT options                        : " + mafft_options );
-            }
-            System.out.println( "Simple tree (Kimura distances, NJ)   : " + perform_phylogenetic_inference );
             System.out.println();
             final int initial_number_of_seqs = msa.getNumberOfSequences();
             List<MsaProperties> msa_props = null;
             final MsaCompactor mc = new MsaCompactor( msa );
             mc.setInfileName( in.getName() );
-            mc.setNorm( norm );
-            mc.setRealign( realign );
-            if ( realign ) {
-                mc.setPathToMafft( path_to_mafft );
-                mc.setMafftOptions( mafft_options );
-            }
-            mc.setStep( step );
-            mc.setStepForDiagnostics( step_for_diagnostics );
-            mc.setCalculateNormalizedShannonEntropy( report_entropy );
-            mc.setPeformPhylogenticInference( perform_phylogenetic_inference );
-            if ( ( worst_remove > 0 ) || ( av_gap > 0 ) || ( length > 0 ) ) {
+            if ( ( worst_remove > 0 ) || ( av_gap > 0 ) || ( length > 0 ) || ( min_length != -1 ) ) {
                 mc.setOutputFormat( output_format );
                 mc.setOutFileBase( out );
-                if ( removed_seqs_out_base != null ) {
-                    mc.setRemovedSeqsOutBase( removed_seqs_out_base );
-                }
             }
-            if ( min_length > 1 ) {
+            if ( min_length != -1 ) {
                 mc.removeSequencesByMinimalLength( min_length );
-                mc.writeMsa( new File( "removed" ) );
-            }
-            if ( worst_remove > 0 ) {
-                msa_props = mc.removeWorstOffenders( worst_remove );
-            }
-            else if ( av_gap > 0 ) {
-                msa_props = mc.removeViaGapAverage( av_gap );
-            }
-            else if ( length > 0 ) {
-                msa_props = mc.removeViaLength( length );
             }
             else {
-                msa_props = mc.chart( step, realign, norm );
+                mc.setPeformPhylogenticInference( perform_phylogenetic_inference );
+                if ( removed_seqs_out_base != null ) {
+                    mc.setRemovedSeqsOutBase( removed_seqs_out_base );
+                }
+                mc.setNorm( norm );
+                mc.setRealign( realign );
+                if ( realign ) {
+                    mc.setPathToMafft( path_to_mafft );
+                    mc.setMafftOptions( mafft_options );
+                }
+                mc.setStep( step );
+                mc.setStepForDiagnostics( step_for_diagnostics );
+                mc.setCalculateNormalizedShannonEntropy( report_entropy );
+                if ( worst_remove > 0 ) {
+                    msa_props = mc.removeWorstOffenders( worst_remove );
+                }
+                else if ( av_gap > 0 ) {
+                    msa_props = mc.removeViaGapAverage( av_gap );
+                }
+                else if ( length > 0 ) {
+                    msa_props = mc.removeViaLength( length );
+                }
+                else {
+                    msa_props = mc.chart( step, realign, norm );
+                }
+                Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
             }
-            Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
         }
         catch ( final IllegalArgumentException iae ) {
             //  iae.printStackTrace(); //TODO remove me
@@ -425,8 +463,8 @@ public class msa_compactor {
                 + "=<integer>  step for diagnostics reports (default: 1)" );
         System.out.println( "   -" + REPORT_ENTROPY
                 + "             to calculate normalized Shannon Entropy (not recommended for very large alignments)" );
-        System.out.println( "   -" + OUTPUT_FORMAT_PHYLIP_OPTION
-                + "             to write output alignments in phylip format instead of fasta" );
+        System.out.println( "   -" + OUTPUT_FORMAT_OPTION
+                + "=<f|p|n>     format for output alignments: f for fasta (default), p for phylip, or n for nexus" );
         System.out.println( "   -" + OUTPUT_REMOVED_SEQS_OPTION + "=<file>     to output the removed sequences" );
         System.out.println( "   -" + MIN_LENGTH_OPTION
                 + "=<integer>  minimal effecive sequence length (for deleting of shorter sequences)" );

diff --git a/forester/java/src/org/forester/msa/BasicMsa.java b/forester/java/src/org/forester/msa/BasicMsa.java
index d913531..dc383c9 100644 (file)
--- a/forester/java/src/org/forester/msa/BasicMsa.java
+++ b/forester/java/src/org/forester/msa/BasicMsa.java
@@ -175,6 +175,9 @@ public class BasicMsa implements Msa {
             case FASTA:
                 writeToFasta( w );
                 break;
+            case NEXUS:
+                writeToNexus( w );
+                break;
             default:
                 throw new RuntimeException( "unknown format " + format );
         }
@@ -195,10 +198,39 @@ public class BasicMsa implements Msa {
         SequenceWriter.writeSeqs( asSequenceList(), w, SEQ_FORMAT.FASTA, 100 );
     }
 
+    private void writeToNexus( final Writer w ) throws IOException {
+        final int max = determineMaxIdLength() + 1;
+        w.write( "Begin Data;" );
+        w.write( ForesterUtil.LINE_SEPARATOR );
+        w.write( "   Dimensions NTax=" + getNumberOfSequences() );
+        w.write( " NChar=" + getLength() );
+        w.write( ";" );
+        w.write( ForesterUtil.LINE_SEPARATOR );
+        w.write( "   Format DataType=Protein Interleave=No gap=-;" );
+        w.write( ForesterUtil.LINE_SEPARATOR );
+        w.write( "   Matrix" );
+        w.write( ForesterUtil.LINE_SEPARATOR );
+        for( int row = 0; row < getNumberOfSequences(); ++row ) {
+            final Sequence seq = getSequence( row );
+            final String s = seq.getMolecularSequenceAsString();
+            w.write( "      " );
+            w.write( ForesterUtil.pad( getIdentifier( row ).replace( ' ', '_' ), max, ' ', false ).toString() );
+            w.write( " " );
+            w.write( s );
+            w.write( ForesterUtil.LINE_SEPARATOR );
+        }
+        w.write( "   ;" );
+        w.write( ForesterUtil.LINE_SEPARATOR );
+        w.write( "End;" );
+        w.write( ForesterUtil.LINE_SEPARATOR );
+    }
+
     private void writeToPhylip( final Writer w ) throws IOException {
         final int max = determineMaxIdLength() + 1;
+        w.write( getNumberOfSequences() + " " + getLength() );
+        w.write( ForesterUtil.LINE_SEPARATOR );
         for( int row = 0; row < getNumberOfSequences(); ++row ) {
-            w.write( ForesterUtil.pad( getIdentifier( row ), max, ' ', false ).toString() );
+            w.write( ForesterUtil.pad( getIdentifier( row ).replace( ' ', '_' ), max, ' ', false ).toString() );
             for( int col = 0; col < getLength(); ++col ) {
                 w.write( getResidueAt( row, col ) );
             }

diff --git a/forester/java/src/org/forester/msa/Msa.java b/forester/java/src/org/forester/msa/Msa.java
index 648006a..ed73cd4 100644 (file)
--- a/forester/java/src/org/forester/msa/Msa.java
+++ b/forester/java/src/org/forester/msa/Msa.java
@@ -35,7 +35,7 @@ import org.forester.sequence.Sequence.TYPE;
 public interface Msa {
 
     public static enum MSA_FORMAT {
-        FASTA, PHYLIP;
+        FASTA, PHYLIP, NEXUS;
     }
 
     public String getIdentifier( int row );

diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index a1c61c1..81f22da 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -67,12 +67,14 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 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 {
 
-    final private static NumberFormat NF_3                       = new DecimalFormat( "#.###" );
-    final private static NumberFormat NF_4                       = new DecimalFormat( "#.####" );
+    final private static NumberFormat NF_1                       = new DecimalFormat( "0.#" );
+    final private static NumberFormat NF_3                       = new DecimalFormat( "0.###" );
+    final private static NumberFormat NF_4                       = new DecimalFormat( "0.####" );
     private boolean                   _calculate_shannon_entropy = false;
     //
     private String                    _infile_name               = null;
@@ -93,6 +95,7 @@ public class MsaCompactor {
     private int                       _step                      = -1;
     private int                       _step_for_diagnostics      = -1;
     static {
+        NF_1.setRoundingMode( RoundingMode.HALF_UP );
         NF_4.setRoundingMode( RoundingMode.HALF_UP );
         NF_3.setRoundingMode( RoundingMode.HALF_UP );
     }
@@ -260,12 +263,21 @@ public class MsaCompactor {
         return _msa;
     }
 
-    public final void removeSequencesByMinimalLength( final int min_effective_length ) {
-        printMsaProperties( new MsaProperties( _msa, "", _calculate_shannon_entropy ) );
-        System.out.println();
+    public final void removeSequencesByMinimalLength( final int min_effective_length ) throws IOException {
         _msa = DeleteableMsa.createInstance( MsaMethods.removeSequencesByMinimalLength( _msa, min_effective_length ) );
         removeGapColumns();
-        printMsaProperties( new MsaProperties( _msa, "", _calculate_shannon_entropy ) );
+        final String s = writeOutfile();
+        final DescriptiveStatistics msa_stats = MsaMethods.calculateEffectiveLengthStatistics( _msa );
+        System.out.println( "Output MSA                           : " + s );
+        System.out.println( "  MSA length                         : " + _msa.getLength() );
+        System.out.println( "  Number of sequences                : " + _msa.getNumberOfSequences() );
+        System.out.println( "  Median sequence length             : " + NF_1.format( msa_stats.median() ) );
+        System.out.println( "  Mean sequence length               : " + NF_1.format( msa_stats.arithmeticMean() ) );
+        System.out.println( "  Max sequence length                : " + ( ( int ) msa_stats.getMax() ) );
+        System.out.println( "  Min sequence length                : " + ( ( int ) msa_stats.getMin() ) );
+        System.out.println( "  Gap ratio                          : " + NF_4.format( MsaMethods.calcGapRatio( _msa ) ) );
+        System.out.println( "  Normalized Shannon Entropy (entn21): "
+                + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, _msa ) ) );
         System.out.println();
     }
 

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 59150d5..22253df 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -6376,13 +6376,15 @@ public final class Test {
             final Writer w = new StringWriter();
             dmsa2.write( w, MSA_FORMAT.PHYLIP );
             final String phylip = w.toString();
-            if ( !phylip.equals( "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) {
+            if ( !phylip.equals( "1 1" + ForesterUtil.LINE_SEPARATOR + "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) {
+                System.out.println( phylip );
                 return false;
             }
             final Writer w2 = new StringWriter();
             dmsa2.write( w2, MSA_FORMAT.FASTA );
             final String fasta = w2.toString();
             if ( !fasta.equals( ">new_c" + ForesterUtil.LINE_SEPARATOR + "x" + ForesterUtil.LINE_SEPARATOR ) ) {
+                System.out.println( fasta );
                 return false;
             }
         }