inprogress

diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java
index 7947bdd..1cd94d6 100644 (file)
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -42,9 +42,9 @@ public class msa_compactor {
             final File in = cla.getFile( 0 );
             final File out = cla.getFile( 1 );
             int worst_remove = -1;
-            double av = -1;
+            double av_gap = -1;
             int length = -1;
-            int step = 1;
+            int step = -1;
             boolean realign = false;
             boolean norm = true;
             String path_to_mafft = null;
@@ -60,15 +60,30 @@ public class msa_compactor {
             if ( dissallowed_options.length() > 0 ) {
                 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
             }
+            Msa msa = null;
+            final FileInputStream is = new FileInputStream( in );
+            if ( FastaParser.isLikelyFasta( in ) ) {
+                msa = FastaParser.parseMsa( is );
+            }
+            else {
+                msa = GeneralMsaParser.parse( is );
+            }
             if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) ) {
                 worst_remove = cla.getOptionValueAsInt( REMOVE_WORST_OFFENDERS_OPTION );
+                if ( ( worst_remove < 1 ) || ( worst_remove >= msa.getNumberOfSequences() - 1 ) ) {
+                    ForesterUtil.fatalError( PRG_NAME, "number of worst offender sequences to remove is out of range: "
+                            + worst_remove );
+                }
             }
             if ( cla.isOptionSet( AV_GAPINESS_OPTION ) ) {
                 if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) ) {
                     printHelp();
                     System.exit( 0 );
                 }
-                av = cla.getOptionValueAsDouble( AV_GAPINESS_OPTION );
+                av_gap = cla.getOptionValueAsDouble( AV_GAPINESS_OPTION );
+                if ( ( av_gap < 0 ) || ( av_gap >= 1 ) ) {
+                    ForesterUtil.fatalError( PRG_NAME, "target gap-ratio is out of range: " + av_gap );
+                }
             }
             if ( cla.isOptionSet( LENGTH_OPTION ) ) {
                 if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) || cla.isOptionSet( AV_GAPINESS_OPTION ) ) {
@@ -76,9 +91,16 @@ public class msa_compactor {
                     System.exit( 0 );
                 }
                 length = cla.getOptionValueAsInt( LENGTH_OPTION );
+                if ( ( length < 2 ) || ( length >= msa.getLength() ) ) {
+                    ForesterUtil.fatalError( PRG_NAME, "target length is out of range: " + length );
+                }
             }
             if ( cla.isOptionSet( STEP_OPTION ) ) {
                 step = cla.getOptionValueAsInt( STEP_OPTION );
+                if ( ( step < 1 )
+                        || ( ( step > msa.getNumberOfSequences() ) || ( ( worst_remove > 0 ) && ( step > worst_remove ) ) ) ) {
+                    ForesterUtil.fatalError( PRG_NAME, "value for step is out of range: " + step );
+                }
             }
             if ( cla.isOptionSet( REALIGN_OPTION ) ) {
                 realign = true;
@@ -98,25 +120,13 @@ public class msa_compactor {
                 }
                 checkPathToMafft( path_to_mafft );
             }
-            Msa msa = null;
-            final FileInputStream is = new FileInputStream( in );
-            if ( FastaParser.isLikelyFasta( in ) ) {
-                msa = FastaParser.parseMsa( is );
-            }
-            else {
-                msa = GeneralMsaParser.parse( is );
-            }
             if ( worst_remove > 0 ) {
                 MsaCompactor.removeWorstOffenders( msa, worst_remove, step, realign, norm, path_to_mafft, out );
             }
-            else if ( av > 0 ) {
-                MsaCompactor.reduceGapAverage( msa, av, step, realign, norm, path_to_mafft, out );
+            else if ( av_gap > 0 ) {
+                MsaCompactor.reduceGapAverage( msa, av_gap, step, realign, norm, path_to_mafft, out );
             }
             else if ( length > 0 ) {
-                if ( length >= msa.getLength() ) {
-                    ForesterUtil.fatalError( PRG_NAME, "target MSA length (" + length
-                            + ") is greater than or equal to MSA original length (" + msa.getLength() + ")" );
-                }
                 // TODO if < shortest seq -> error
                 MsaCompactor.reduceLength( msa, length, step, realign, norm, path_to_mafft, out );
             }

diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index 88deac8..47e1b9c 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -37,11 +37,11 @@ public class MsaCompactor {
 
     final private static NumberFormat NF_3         = new DecimalFormat( "#.###" );
     final private static NumberFormat NF_4         = new DecimalFormat( "#.####" );
+    private final String              _maffts_opts = "--retree 1";
     private Msa                       _msa;
     private File                      _out_file_base;
     private String                    _path_to_mafft;
     private final SortedSet<String>   _removed_seq_ids;
-    private final String              _maffts_opts = "--retree 1";
     static {
         NF_4.setRoundingMode( RoundingMode.HALF_UP );
         NF_3.setRoundingMode( RoundingMode.HALF_UP );
@@ -179,6 +179,14 @@ public class MsaCompactor {
         return sb;
     }
 
+    private final void printMsaStats( final String id ) {
+        System.out.print( ForesterUtil.pad( id, 20, ' ', false ) );
+        System.out.print( "\t" );
+        final StringBuilder sb = msaStatsAsSB();
+        System.out.print( sb );
+        System.out.print( "\t" );
+    }
+
     final private void realignWithMafft() throws IOException, InterruptedException {
         //  final MsaInferrer mafft = Mafft
         //       .createInstance( "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft" );
@@ -217,13 +225,10 @@ public class MsaCompactor {
             _msa = MsaMethods.removeSequence( _msa, id );
             removeGapColumns();
             if ( verbose ) {
-                System.out.print( ForesterUtil.pad( id, 20, ' ', false ) );
-                System.out.print( "\t" );
-                final StringBuilder sb = msaStatsAsSB();
-                System.out.print( sb );
-                System.out.print( "\t" );
+                printMsaStats( id );
             }
-            if ( ( ( ( i + 1 ) % step ) == 0 ) || ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) {
+            if ( ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) )
+                    || ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) {
                 if ( realign ) {
                     realignWithMafft();
                 }
@@ -239,20 +244,6 @@ public class MsaCompactor {
         }
     }
 
-    private final static void printTableHeader() {
-        System.out.print( ForesterUtil.pad( "Id", 20, ' ', false ) );
-        System.out.print( "\t" );
-        System.out.print( "Seqs" );
-        System.out.print( "\t" );
-        System.out.print( "Length" );
-        System.out.print( "\t" );
-        System.out.print( "Gaps" );
-        System.out.print( "\t" );
-        System.out.print( "MSA qual" );
-        System.out.print( "\t" );
-        System.out.println();
-    }
-
     final private void removeViaLength( final int length,
                                         final int step,
                                         final boolean realign,
@@ -272,13 +263,9 @@ public class MsaCompactor {
             _msa = MsaMethods.removeSequence( _msa, id );
             removeGapColumns();
             if ( verbose ) {
-                System.out.print( ForesterUtil.pad( id, 20, ' ', false ) );
-                System.out.print( "\t" );
-                final StringBuilder sb = msaStatsAsSB();
-                System.out.print( sb );
-                System.out.print( "\t" );
+                printMsaStats( id );
             }
-            if ( ( ( ( i + 1 ) % step ) == 0 ) || ( _msa.getLength() <= length ) ) {
+            if ( ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) || ( _msa.getLength() <= length ) ) {
                 if ( realign ) {
                     realignWithMafft();
                 }
@@ -313,13 +300,9 @@ public class MsaCompactor {
             _msa = MsaMethods.removeSequence( _msa, id );
             removeGapColumns();
             if ( verbose ) {
-                System.out.print( ForesterUtil.pad( id, 20, ' ', false ) );
-                System.out.print( "\t" );
-                final StringBuilder sb = msaStatsAsSB();
-                System.out.print( sb );
-                System.out.print( "\t" );
+                printMsaStats( id );
             }
-            if ( ( ( ( i + 1 ) % step ) == 0 ) || ( i == ( to_remove_ids.size() - 1 ) ) ) {
+            if ( ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) || ( i == ( to_remove_ids.size() - 1 ) ) ) {
                 if ( realign ) {
                     realignWithMafft();
                 }
@@ -437,4 +420,18 @@ public class MsaCompactor {
         }
         return stats;
     }
+
+    private final static void printTableHeader() {
+        System.out.print( ForesterUtil.pad( "Id", 20, ' ', false ) );
+        System.out.print( "\t" );
+        System.out.print( "Seqs" );
+        System.out.print( "\t" );
+        System.out.print( "Length" );
+        System.out.print( "\t" );
+        System.out.print( "Gaps" );
+        System.out.print( "\t" );
+        System.out.print( "MSA qual" );
+        System.out.print( "\t" );
+        System.out.println();
+    }
 }