cleanup

diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java
index 8e71f5e..11b6ac8 100644 (file)
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -200,7 +200,7 @@ public class msa_compactor {
                 output_format = MSA_FORMAT.PHYLIP;
             }
             if ( cla.isOptionSet( OUTPUT_REMOVED_SEQS_OPTION ) ) {
-                String s = cla.getOptionValueAsCleanString( OUTPUT_REMOVED_SEQS_OPTION );
+                final String s = cla.getOptionValueAsCleanString( OUTPUT_REMOVED_SEQS_OPTION );
                 removed_seqs_out_base = new File( s );
             }
             if ( realign ) {
@@ -210,7 +210,7 @@ public class msa_compactor {
                 checkPathToMafft( path_to_mafft );
                 if ( cla.isOptionSet( MAFFT_OPTIONS ) ) {
                     mafft_options = cla.getOptionValueAsCleanString( MAFFT_OPTIONS );
-                    if ( ForesterUtil.isEmpty( mafft_options ) || mafft_options.length() < 3 ) {
+                    if ( ForesterUtil.isEmpty( mafft_options ) || ( mafft_options.length() < 3 ) ) {
                         ForesterUtil.fatalError( PRG_NAME, "gap ratio is out of range: " + gap_ratio );
                     }
                 }
@@ -245,7 +245,7 @@ public class msa_compactor {
             else {
                 System.out.println( "Chart and diagnostics only           : true" );
             }
-            if ( out != null || removed_seqs_out_base != null ) {
+            if ( ( out != null ) || ( removed_seqs_out_base != null ) ) {
                 System.out.println( "Output format                        : "
                         + ( output_format == MSA_FORMAT.FASTA ? "fasta" : "phylip" ) );
             }

diff --git a/forester/java/src/org/forester/msa/MsaMethods.java b/forester/java/src/org/forester/msa/MsaMethods.java
index 25330e0..1a94b74 100644 (file)
--- a/forester/java/src/org/forester/msa/MsaMethods.java
+++ b/forester/java/src/org/forester/msa/MsaMethods.java
@@ -168,9 +168,9 @@ public final class MsaMethods {
     }
 
     final public static DescriptiveStatistics calculateEffectiveLengthStatistics( final Msa msa ) {
-        DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( int row = 0; row < msa.getNumberOfSequences(); ++row ) {
-            Sequence s = msa.getSequence( row );
+            final Sequence s = msa.getSequence( row );
             stats.addValue( s.getLength() - s.getNumberOfGapResidues() );
         }
         return stats;

diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index b8332bb..56cc729 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -428,31 +428,31 @@ public class MsaCompactor {
         return null;
     }
 
-    public final void setStep( int step ) {
+    public final void setStep( final int step ) {
         _step = step;
     }
 
-    public final void setNorm( boolean norm ) {
+    public final void setNorm( final boolean norm ) {
         _norm = norm;
     }
 
-    public final void setStepForDiagnostics( int step_for_diagnostics ) {
+    public final void setStepForDiagnostics( final int step_for_diagnostics ) {
         _step_for_diagnostics = step_for_diagnostics;
     }
 
-    public final void setMinLength( int min_length ) {
+    public final void setMinLength( final int min_length ) {
         _min_length = min_length;
     }
 
-    public final void setGapRatio( double gap_ratio ) {
+    public final void setGapRatio( final double gap_ratio ) {
         _gap_ratio = gap_ratio;
     }
 
-    public final void setOutputFormat( MSA_FORMAT output_format ) {
+    public final void setOutputFormat( final MSA_FORMAT output_format ) {
         _output_format = output_format;
     }
 
-    public final void setRealign( boolean realign ) {
+    public final void setRealign( final boolean realign ) {
         _realign = realign;
     }