inprogress

diff --git a/forester/java/src/org/forester/msa/DeleteableMsa.java b/forester/java/src/org/forester/msa/DeleteableMsa.java
index a781bf6..350aae2 100644 (file)
--- a/forester/java/src/org/forester/msa/DeleteableMsa.java
+++ b/forester/java/src/org/forester/msa/DeleteableMsa.java
@@ -81,7 +81,7 @@ public final class DeleteableMsa extends BasicMsa {
         }
     }
 
-    final public Sequence deleteRow( final String id ) {
+    final public Sequence deleteRow( final String id, final boolean return_removed_seq ) {
         int row = -1;
         for( int r = 0; r < getNumberOfSequences(); ++r ) {
             if ( getIdentifier( r ).equals( id ) ) {
@@ -92,9 +92,25 @@ public final class DeleteableMsa extends BasicMsa {
         if ( row < 0 ) {
             throw new IllegalArgumentException( "id [" + id + "] not found" );
         }
-        final Sequence s = getSequence( row );
+        Sequence s = null;
+        StringBuilder sb = null;
+        if ( return_removed_seq ) {
+            s = getSequence( row );
+            final char[] x = s.getMolecularSequence();
+            sb = new StringBuilder( x.length );
+            for( int i = 0; i < x.length; ++i ) {
+                if ( x[ i ] != Sequence.GAP ) {
+                    sb.append( x[ i ] );
+                }
+            }
+        }
         deleteRow( row );
-        return s;
+        if ( return_removed_seq ) {
+            return new BasicSequence( new String( s.getIdentifier() ), sb.toString(), s.getType() );
+        }
+        else {
+            return null;
+        }
     }
 
     @Override

diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index 374d3bb..3ade90f 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -114,7 +114,7 @@ public class MsaCompactor {
         while ( MsaMethods.calcGapRatio( _msa ) > mean_gapiness ) {
             final String id = to_remove_ids.get( i );
             _removed_seq_ids.add( id );
-            final Sequence deleted = _msa.deleteRow( id );
+            final Sequence deleted = _msa.deleteRow( id, true );
             _removed_seqs.add( deleted );
             removeGapColumns();
             if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) )
@@ -145,7 +145,7 @@ public class MsaCompactor {
         while ( _msa.getLength() > length ) {
             final String id = to_remove_ids.get( i );
             _removed_seq_ids.add( id );
-            final Sequence deleted = _msa.deleteRow( id );
+            final Sequence deleted = _msa.deleteRow( id, true );
             _removed_seqs.add( deleted );
             removeGapColumns();
             if ( ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) || ( _msa.getLength() <= length ) ) {
@@ -173,7 +173,7 @@ public class MsaCompactor {
         for( int i = 0; i < to_remove_ids.size(); ++i ) {
             final String id = to_remove_ids.get( i );
             _removed_seq_ids.add( id );
-            final Sequence deleted = _msa.deleteRow( id );
+            final Sequence deleted = _msa.deleteRow( id, true );
             _removed_seqs.add( deleted );
             removeGapColumns();
             if ( isPrintMsaStatsWriteOutfileAndRealign( i ) || ( i == ( to_remove_ids.size() - 1 ) ) ) {
@@ -209,7 +209,7 @@ public class MsaCompactor {
         System.out.println();
         while ( _msa.getNumberOfSequences() > x ) {
             final String id = to_remove_ids.get( i );
-            _msa.deleteRow( id );
+            _msa.deleteRow( id, false );
             if ( realign && isPrintMsaStatsWriteOutfileAndRealign( i ) ) {
                 removeGapColumns();
                 realignWithMafft();
@@ -291,7 +291,7 @@ public class MsaCompactor {
         final StringBuilder msg = new StringBuilder();
         final String n = _removed_seqs_out_base + "_" + _removed_seqs.size() + ".fasta";
         SequenceWriter.writeSeqs( _removed_seqs, new File( n ), SEQ_FORMAT.FASTA, 100 );
-        msg.append( "wrote " + _removed_seqs.size() + " removed sequences to " + n );
+        msg.append( "wrote " + _removed_seqs.size() + " removed sequences to " + " to \"" + n + "\"" );
         if ( _realign ) {
             final MsaInferrer mafft = Mafft.createInstance( _path_to_mafft );
             final List<String> opts = new ArrayList<String>();
@@ -311,7 +311,7 @@ public class MsaCompactor {
             }
             s += suffix;
             writeMsa( removed_msa, s, _output_format );
-            msg.append( ", and as MSA of length " + removed_msa.getLength() + " to " + s );
+            msg.append( ", and as MSA of length " + removed_msa.getLength() + " to \"" + s + "\"" );
         }
         return msg.toString();
     }

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 3753c8b..df8fce2 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -6104,13 +6104,13 @@ public final class Test {
             l0.add( s4 );
             l0.add( s5 );
             final DeleteableMsa dmsa0 = DeleteableMsa.createInstance( l0 );
-            dmsa0.deleteRow( "b" );
+            dmsa0.deleteRow( "b", false );
             if ( !dmsa0.getIdentifier( 1 ).equals( "c" ) ) {
                 return false;
             }
-            dmsa0.deleteRow( "e" );
-            dmsa0.deleteRow( "a" );
-            dmsa0.deleteRow( "f" );
+            dmsa0.deleteRow( "e", false );
+            dmsa0.deleteRow( "a", false );
+            dmsa0.deleteRow( "f", false );
             if ( dmsa0.getLength() != 4 ) {
                 return false;
             }
@@ -6132,8 +6132,8 @@ public final class Test {
             if ( dmsa0.getColumnAt( 0 ).size() != 2 ) {
                 return false;
             }
-            dmsa0.deleteRow( "c" );
-            dmsa0.deleteRow( "d" );
+            dmsa0.deleteRow( "c", false );
+            dmsa0.deleteRow( "d", false );
             if ( dmsa0.getNumberOfSequences() != 0 ) {
                 return false;
             }
@@ -6153,9 +6153,9 @@ public final class Test {
             l1.add( s_5 );
             final DeleteableMsa dmsa1 = DeleteableMsa.createInstance( l1 );
             dmsa1.deleteGapOnlyColumns();
-            dmsa1.deleteRow( "a" );
-            dmsa1.deleteRow( "f" );
-            dmsa1.deleteRow( "d" );
+            dmsa1.deleteRow( "a", false );
+            dmsa1.deleteRow( "f", false );
+            dmsa1.deleteRow( "d", false );
             dmsa1.deleteGapOnlyColumns();
             if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C-" ) ) {
                 return false;
@@ -6166,7 +6166,7 @@ public final class Test {
             if ( !dmsa1.getSequenceAsString( 2 ).toString().equals( "EAAC-" ) ) {
                 return false;
             }
-            dmsa1.deleteRow( "c" );
+            dmsa1.deleteRow( "c", false );
             dmsa1.deleteGapOnlyColumns();
             final Writer w0 = new StringWriter();
             dmsa1.write( w0, MSA_FORMAT.FASTA );
@@ -6214,14 +6214,17 @@ public final class Test {
                 return false;
             }
             dmsa2.deleteGapColumns( 0 );
-            dmsa2.deleteRow( "a" );
-            dmsa2.deleteRow( "b" );
-            dmsa2.deleteRow( "f" );
-            dmsa2.deleteRow( "e" );
+            dmsa2.deleteRow( "a", false );
+            dmsa2.deleteRow( "b", false );
+            dmsa2.deleteRow( "f", false );
+            dmsa2.deleteRow( "e", false );
             dmsa2.setIdentifier( 0, "new_c" );
             dmsa2.setIdentifier( 1, "new_d" );
             dmsa2.setResidueAt( 0, 0, 'x' );
-            dmsa2.deleteRow( "new_d" );
+            final Sequence s = dmsa2.deleteRow( "new_d", true );
+            if ( !s.getMolecularSequenceAsString().equals( "D" ) ) {
+                return false;
+            }
             final Writer w = new StringWriter();
             dmsa2.write( w, MSA_FORMAT.PHYLIP );
             final String phylip = w.toString();