in progress

diff --git a/forester/java/src/org/forester/msa/BasicMsa.java b/forester/java/src/org/forester/msa/BasicMsa.java
index a7367a2..7d90c3c 100644 (file)
--- a/forester/java/src/org/forester/msa/BasicMsa.java
+++ b/forester/java/src/org/forester/msa/BasicMsa.java
@@ -71,8 +71,8 @@ public class BasicMsa implements Msa {
 
     private int determineMaxIdLength() {
         int max = 0;
-        for( int row = 0; row < _data.length; ++row ) {
-            final int l = _identifiers[ row ].toString().length();
+        for( int row = 0; row < getNumberOfSequences(); ++row ) {
+            final int l = getIdentifier(row).length();
             if ( l > max ) {
                 max = l;
             }
@@ -112,17 +112,22 @@ public class BasicMsa implements Msa {
 
     @Override
     public Sequence getSequence( final int row ) {
-        return new BasicSequence( getIdentifier( row ), _data[ row ], getType() );
+        return new BasicSequence( getIdentifier( row ),  getSequenceAsArray( row ), getType() );
     }
 
     @Override
     public StringBuffer getSequenceAsString( final int row ) {
-        final StringBuffer sb = new StringBuffer( _data[ 0 ].length );
-        for( int col = 0; col < _data[ 0 ].length; ++col ) {
+        final StringBuffer sb = new StringBuffer(getLength() );
+        for( int col = 0; col < getLength(); ++col ) {
             sb.append( getResidueAt( row, col ) );
         }
         return sb;
     }
+    
+    @Override
+    public char[] getSequenceAsArray( final int row ) {
+        return  _data[ row ];
+    }
 
     @Override
     public TYPE getType() {
@@ -143,9 +148,9 @@ public class BasicMsa implements Msa {
     public String toString() {
         final int max = determineMaxIdLength() + 1;
         final StringBuffer sb = new StringBuffer();
-        for( int row = 0; row < _data.length; ++row ) {
-            sb.append( ForesterUtil.pad( _identifiers[ row ].toString(), max, ' ', false ) );
-            for( int col = 0; col < _data[ 0 ].length; ++col ) {
+        for( int row = 0; row < getNumberOfSequences(); ++row ) {
+            sb.append( ForesterUtil.pad( getIdentifier( row ).toString(), max, ' ', false ) );
+            for( int col = 0; col < getLength(); ++col ) {
                 sb.append( getResidueAt( row, col ) );
             }
             sb.append( ForesterUtil.LINE_SEPARATOR );
@@ -173,9 +178,9 @@ public class BasicMsa implements Msa {
 
     private void writeToPhylip( final Writer w ) throws IOException {
         final int max = determineMaxIdLength() + 1;
-        for( int row = 0; row < _data.length; ++row ) {
-            w.write( ForesterUtil.pad( _identifiers[ row ].toString(), max, ' ', false ).toString() );
-            for( int col = 0; col < _data[ 0 ].length; ++col ) {
+        for( int row = 0; row < getNumberOfSequences(); ++row ) {
+            w.write( ForesterUtil.pad( getIdentifier( row ), max, ' ', false ).toString() );
+            for( int col = 0; col < getLength(); ++col ) {
                 w.write( getResidueAt( row, col ) );
             }
             w.write( ForesterUtil.LINE_SEPARATOR );

diff --git a/forester/java/src/org/forester/msa/DeleteableMsa.java b/forester/java/src/org/forester/msa/DeleteableMsa.java
index 3041994..392f239 100644 (file)
--- a/forester/java/src/org/forester/msa/DeleteableMsa.java
+++ b/forester/java/src/org/forester/msa/DeleteableMsa.java
@@ -26,6 +26,8 @@ package org.forester.msa;
 
 import java.util.HashMap;
 
+import org.forester.util.ForesterUtil;
+
 public final class DeleteableMsa extends BasicMsa {
 
     private int                      _length                 = 0;
@@ -51,6 +53,12 @@ public final class DeleteableMsa extends BasicMsa {
         _length = msa.getLength();
         _seqs = msa.getNumberOfSequences();
     }
+    
+    
+    @Override
+    public char[] getSequenceAsArray( final int row ) {
+        return  super.getSequenceAsArray( _mapped_row_positions[ row ] );
+    }
 
     public void deleteColumn( final int col ) {
         if ( col >= _length || col < 0 ) {
@@ -62,7 +70,9 @@ public final class DeleteableMsa extends BasicMsa {
         --_length;
     }
 
-    public void deleteRow( final int row ) {
+    
+  
+    private void deleteRow( final int row ) {
         if ( row >= _seqs || row < 0 ) {
             throw new IllegalArgumentException( "row " + row + " is out of range" );
         }
@@ -101,9 +111,10 @@ public final class DeleteableMsa extends BasicMsa {
         return _seqs;
     }
 
+    
     @Override
     public char getResidueAt( final int row, final int col ) {
-        return super.getResidueAt( _mapped_row_positions[ row ], _mapped_col_positions[ col ] );
+         return super.getResidueAt( _mapped_row_positions[ row ], _mapped_col_positions[ col ] );
     }
 
     @Override

diff --git a/forester/java/src/org/forester/msa/Msa.java b/forester/java/src/org/forester/msa/Msa.java
index 648006a..ff2b110 100644 (file)
--- a/forester/java/src/org/forester/msa/Msa.java
+++ b/forester/java/src/org/forester/msa/Msa.java
@@ -65,4 +65,6 @@ public interface Msa {
     public void setResidueAt( final int row, final int col, final char residue );
 
     public void write( Writer w, MSA_FORMAT format ) throws IOException;
+
+    char[] getSequenceAsArray( int row );
 }

diff --git a/forester/java/src/org/forester/msa/MsaMethods.java b/forester/java/src/org/forester/msa/MsaMethods.java
index 2280320..9975ab2 100644 (file)
--- a/forester/java/src/org/forester/msa/MsaMethods.java
+++ b/forester/java/src/org/forester/msa/MsaMethods.java
@@ -164,7 +164,7 @@ public final class MsaMethods {
             throw new IllegalArgumentException( "max allowed gap ration is out of range: " + max_allowed_gap_ratio );
         }
         //   final boolean ignore_too_short_seqs = min_allowed_length > 0;
-        for( int col = 0; col < msa.getLength(); ++col ) {
+        for( int col = msa.getLength() - 1; col >= 0 ; --col ) {
             final boolean delete = ( ( double ) calcGapSumPerColumn( msa, col ) / msa.getNumberOfSequences() ) >= max_allowed_gap_ratio;
             if ( delete ) {
                 msa.deleteColumn( col );

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 924b643..51024d5 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -61,6 +61,7 @@ import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.io.writers.SequenceWriter;
 import org.forester.msa.BasicMsa;
+import org.forester.msa.DeleteableMsa;
 import org.forester.msa.Mafft;
 import org.forester.msa.Msa;
 import org.forester.msa.MsaInferrer;
@@ -899,6 +900,16 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
+        System.out.print( "Deleteable MSA: " );
+        if ( Test.testDeleteableMsa() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
+        System.exit(  0 );
         if ( PERFORM_DB_TESTS ) {
             System.out.print( "Uniprot Entry Retrieval: " );
             if ( Test.testUniprotEntryRetrieval() ) {
@@ -6074,6 +6085,94 @@ public final class Test {
         }
         return true;
     }
+    
+    private static boolean testDeleteableMsa() {
+        try {
+            final Sequence s0 = BasicSequence.createAaSequence( "a", "AAAA" );
+            final Sequence s1 = BasicSequence.createAaSequence( "b", "BAAA" );
+            final Sequence s2 = BasicSequence.createAaSequence( "c", "CAAA" );
+            final Sequence s3 = BasicSequence.createAaSequence( "d", "DAAA" );
+            final Sequence s4 = BasicSequence.createAaSequence( "e", "EAAA" );
+            final Sequence s5 = BasicSequence.createAaSequence( "f", "FAAA" );
+            final List<Sequence> l0 = new ArrayList<Sequence>();
+            l0.add( s0 );
+            l0.add( s1 );
+            l0.add( s2 );
+            l0.add( s3 );
+            l0.add( s4 );
+            l0.add( s5 );
+            final Msa msa0 = BasicMsa.createInstance( l0 );
+            final DeleteableMsa dmsa0 = new DeleteableMsa( ( BasicMsa ) msa0 );
+            dmsa0.deleteRow( "b" );
+            if ( !dmsa0.getIdentifier( 1 ).equals( "c" ) ) {
+                return false;
+            }
+            System.out.println();
+            System.out.println(  dmsa0.toString() );
+            dmsa0.deleteRow( "e" );
+            System.out.println();
+            System.out.println(  dmsa0.toString() );
+            dmsa0.deleteRow( "a" );
+            System.out.println();
+            System.out.println(  dmsa0.toString() );
+            dmsa0.deleteRow( "f" );
+            System.out.println();
+            System.out.println(  dmsa0.toString() );
+            
+            if ( dmsa0.getLength() != 4 ) {
+                return false;
+            }
+            if ( dmsa0.getNumberOfSequences() != 2 ) {
+                return false;
+            }
+            
+            if ( !dmsa0.getIdentifier( 0 ).equals( "c" ) ) {
+                return false;
+            }
+            if ( !dmsa0.getIdentifier( 1 ).equals( "d" ) ) {
+                return false;
+            }
+            if ( dmsa0.getResidueAt( 0, 0 )  != 'C') {
+                return false;
+            }
+            if ( !dmsa0.getSequenceAsString( 0 ).toString().equals( "CAAA" )) {
+                return false;
+            }
+            if ( dmsa0.getColumnAt( 0 ).size() !=2 ) {
+                return false;
+            }
+            dmsa0.deleteRow( "c" );
+            dmsa0.deleteRow( "d" );
+            if ( dmsa0.getNumberOfSequences() != 0 ) {
+                return false;
+            }
+            //
+            final Sequence s_0 = BasicSequence.createAaSequence( "a", "--A---A-A---" );
+            final Sequence s_1 = BasicSequence.createAaSequence( "b", "--B-----A---" );
+            final Sequence s_2 = BasicSequence.createAaSequence( "c", "--C--AA-A---" );
+            final Sequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-A---" );
+            final Sequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-A---" );
+            final Sequence s_5 = BasicSequence.createAaSequence( "f", "--F--AA-AA--" );
+            final List<Sequence> l1 = new ArrayList<Sequence>();
+            l1.add( s_0 );
+            l1.add( s_1 );
+            l1.add( s_2 );
+            l1.add( s_3 );
+            l1.add( s_4 );
+            l1.add( s_5 );
+            final Msa msa1 = BasicMsa.createInstance( l1 );
+            final DeleteableMsa dmsa1 = new DeleteableMsa( ( BasicMsa ) msa1 );
+            System.out.println(  dmsa1.toString() );
+            MsaMethods.removeGapColumns( 1, dmsa1 );
+            System.out.println(  dmsa1.toString() );
+            
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
 
     private static boolean testNextNodeWithCollapsing() {
         try {