inprogress (not working)

diff --git a/forester/java/src/org/forester/msa/BasicMsa.java b/forester/java/src/org/forester/msa/BasicMsa.java
index 4c00a30..395a16d 100644 (file)
--- a/forester/java/src/org/forester/msa/BasicMsa.java
+++ b/forester/java/src/org/forester/msa/BasicMsa.java
@@ -42,9 +42,10 @@ import org.forester.util.ForesterUtil;
 
 public class BasicMsa implements Msa {
 
-    private final char[][] _data;
-    private final String[] _identifiers;
-    private final TYPE     _type;
+    private final char[][]    _data;
+    private final String[]    _identifiers;
+    private final Set<String> _identifiers_set;
+    private final TYPE        _type;
 
     public BasicMsa( final int rows, final int columns, final TYPE type ) {
         if ( ( rows < 1 ) || ( columns < 1 ) ) {
@@ -52,6 +53,7 @@ public class BasicMsa implements Msa {
         }
         _data = new char[ rows ][ columns ];
         _identifiers = new String[ rows ];
+        _identifiers_set = new HashSet<String>();
         _type = type;
     }
 
@@ -59,6 +61,7 @@ public class BasicMsa implements Msa {
         _data = msa._data;
         _identifiers = msa._identifiers;
         _type = msa._type;
+        _identifiers_set = msa._identifiers_set;
     }
 
     @Override
@@ -70,15 +73,13 @@ public class BasicMsa implements Msa {
         return seqs;
     }
 
-    private int determineMaxIdLength() {
-        int max = 0;
+    @Override
+    public List<Character> getColumnAt( final int col ) {
+        final List<Character> column = new ArrayList<Character>();
         for( int row = 0; row < getNumberOfSequences(); ++row ) {
-            final int l = getIdentifier( row ).length();
-            if ( l > max ) {
-                max = l;
-            }
+            column.add( getResidueAt( row, col ) );
         }
-        return max;
+        return column;
     }
 
     @Override
@@ -102,6 +103,11 @@ public class BasicMsa implements Msa {
     }
 
     @Override
+    public Sequence getSequence( final int row ) {
+        return new BasicSequence( getIdentifier( row ), _data[ row ], getType() );
+    }
+
+    @Override
     public Sequence getSequence( final String id ) {
         for( int i = 0; i < getNumberOfSequences(); ++i ) {
             if ( getIdentifier( i ).equals( id ) ) {
@@ -112,11 +118,6 @@ public class BasicMsa implements Msa {
     }
 
     @Override
-    public Sequence getSequence( final int row ) {
-        return new BasicSequence( getIdentifier( row ), _data[ row ], getType() );
-    }
-
-    @Override
     public StringBuffer getSequenceAsString( final int row ) {
         final StringBuffer sb = new StringBuffer( getLength() );
         for( int col = 0; col < getLength(); ++col ) {
@@ -131,7 +132,20 @@ public class BasicMsa implements Msa {
     }
 
     @Override
+    public boolean isGapAt( final int row, final int col ) {
+        return getResidueAt( row, col ) == Sequence.GAP;
+    }
+
+    @Override
     public void setIdentifier( final int row, final String id ) {
+        if ( ForesterUtil.isEmpty( id ) ) {
+            throw new IllegalArgumentException( "illegal attempt to create msa with empty identifier" );
+        }
+        if ( _identifiers_set.contains( id ) ) {
+            throw new IllegalArgumentException( "illegal attempt to create msa with non-unique identifiers [" + id
+                    + "]" );
+        }
+        _identifiers_set.add( id );
         _identifiers[ row ] = id;
     }
 
@@ -166,6 +180,17 @@ public class BasicMsa implements Msa {
         }
     }
 
+    private int determineMaxIdLength() {
+        int max = 0;
+        for( int row = 0; row < getNumberOfSequences(); ++row ) {
+            final int l = getIdentifier( row ).length();
+            if ( l > max ) {
+                max = l;
+            }
+        }
+        return max;
+    }
+
     private void writeToFasta( final Writer w ) throws IOException {
         SequenceWriter.writeSeqs( asSequenceList(), w, SEQ_FORMAT.FASTA, 100 );
     }
@@ -183,9 +208,8 @@ public class BasicMsa implements Msa {
 
     public static Msa createInstance( final List<Sequence> seqs ) {
         if ( seqs.size() < 1 ) {
-            throw new IllegalArgumentException( "cannot create basic msa from less than one sequence" );
+            throw new IllegalArgumentException( "cannot create msa from less than one sequence" );
         }
-        final Set<String> ids = new HashSet<String>();
         final int length = seqs.get( 0 ).getLength();
         final BasicMsa msa = new BasicMsa( seqs.size(), length, seqs.get( 0 ).getType() );
         for( int row = 0; row < seqs.size(); ++row ) {
@@ -198,11 +222,6 @@ public class BasicMsa implements Msa {
                 throw new IllegalArgumentException( "illegal attempt to build msa from sequences of different type ["
                         + seq.getIdentifier() + "]" );
             }
-            if ( ids.contains( seq.getIdentifier() ) ) {
-                throw new IllegalArgumentException( "illegal attempt to create msa with non-unique identifiers ["
-                        + seq.getIdentifier() + "]" );
-            }
-            ids.add( seq.getIdentifier() );
             msa.setIdentifier( row, seq.getIdentifier() );
             for( int col = 0; col < length; ++col ) {
                 msa._data[ row ][ col ] = seq.getResidueAt( col );
@@ -210,18 +229,4 @@ public class BasicMsa implements Msa {
         }
         return msa;
     }
-
-    @Override
-    public List<Character> getColumnAt( final int col ) {
-        final List<Character> column = new ArrayList<Character>();
-        for( int row = 0; row < getNumberOfSequences(); ++row ) {
-            column.add( getResidueAt( row, col ) );
-        }
-        return column;
-    }
-
-    @Override
-    public boolean isGapAt( final int row, final int col ) {
-        return getResidueAt( row, col ) == Sequence.GAP;
-    }
 }

diff --git a/forester/java/src/org/forester/msa/DeleteableMsa.java b/forester/java/src/org/forester/msa/DeleteableMsa.java
index 17f72bb..da781b8 100644 (file)
--- a/forester/java/src/org/forester/msa/DeleteableMsa.java
+++ b/forester/java/src/org/forester/msa/DeleteableMsa.java
@@ -24,7 +24,6 @@
 
 package org.forester.msa;
 
-import java.util.HashMap;
 import java.util.List;
 
 import org.forester.sequence.BasicSequence;
@@ -32,11 +31,10 @@ import org.forester.sequence.Sequence;
 
 public final class DeleteableMsa extends BasicMsa {
 
-    private int                      _length                 = 0;
-    private int                      _mapped_col_positions[] = null;
-    private int                      _mapped_row_positions[] = null;
-    private HashMap<String, Integer> _seq_id_to_row_map      = null;
-    private int                      _seqs                   = 0;
+    private int _length                 = 0;
+    private int _mapped_col_positions[] = null;
+    private int _mapped_row_positions[] = null;
+    private int _seqs                   = 0;
 
     private DeleteableMsa( final BasicMsa msa ) {
         super( msa );
@@ -48,10 +46,6 @@ public final class DeleteableMsa extends BasicMsa {
         for( int i = 0; i < _mapped_row_positions.length; ++i ) {
             _mapped_row_positions[ i ] = i;
         }
-        _seq_id_to_row_map = new HashMap<String, Integer>();
-        for( int row = 0; row < msa.getNumberOfSequences(); ++row ) {
-            _seq_id_to_row_map.put( msa.getIdentifier( row ), row );
-        }
         _length = msa.getLength();
         _seqs = msa.getNumberOfSequences();
     }
@@ -92,6 +86,7 @@ public final class DeleteableMsa extends BasicMsa {
 
     @Override
     final public String getIdentifier( final int row ) {
+        checkRow( row );
         return super.getIdentifier( _mapped_row_positions[ row ] );
     }
 
@@ -107,28 +102,44 @@ public final class DeleteableMsa extends BasicMsa {
 
     @Override
     final public char getResidueAt( final int row, final int col ) {
+        checkRow( row );
+        checkColumn( col );
         return super.getResidueAt( _mapped_row_positions[ row ], _mapped_col_positions[ col ] );
     }
 
     @Override
     public Sequence getSequence( final int row ) {
+        checkRow( row );
         return new BasicSequence( getIdentifier( row ), getSequenceAsString( row ).toString(), getType() );
     }
 
     @Override
     final public void setIdentifier( final int row, final String id ) {
+        checkRow( row );
         super.setIdentifier( _mapped_row_positions[ row ], id );
     }
 
     @Override
     final public void setResidueAt( final int row, final int col, final char residue ) {
+        checkRow( row );
+        checkColumn( col );
         super.setResidueAt( _mapped_row_positions[ row ], _mapped_col_positions[ col ], residue );
     }
 
-    final private void deleteColumn( final int col ) {
+    final private void checkColumn( final int col ) {
         if ( ( col >= _length ) || ( col < 0 ) ) {
             throw new IllegalArgumentException( "column " + col + " is out of range" );
         }
+    }
+
+    final private void checkRow( final int row ) {
+        if ( ( row >= _seqs ) || ( row < 0 ) ) {
+            throw new IllegalArgumentException( "row " + row + " is out of range" );
+        }
+    }
+
+    final private void deleteColumn( final int col ) {
+        checkColumn( col );
         for( int c = col; c < _length - 1; ++c ) {
             _mapped_col_positions[ c ] = _mapped_col_positions[ c + 1 ];
         }
@@ -136,9 +147,7 @@ public final class DeleteableMsa extends BasicMsa {
     }
 
     final private void deleteRow( final int row ) {
-        if ( ( row >= _seqs ) || ( row < 0 ) ) {
-            throw new IllegalArgumentException( "row " + row + " is out of range" );
-        }
+        checkRow( row );
         for( int r = row; r < _seqs - 1; ++r ) {
             _mapped_row_positions[ r ] = _mapped_row_positions[ r + 1 ];
         }

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 73c1c1f..3753c8b 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -912,7 +912,6 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        System.exit( 0 );
         if ( PERFORM_DB_TESTS ) {
             System.out.print( "Uniprot Entry Retrieval: " );
             if ( Test.testUniprotEntryRetrieval() ) {
@@ -6109,17 +6108,9 @@ public final class Test {
             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;
             }
@@ -6161,15 +6152,11 @@ public final class Test {
             l1.add( s_4 );
             l1.add( s_5 );
             final DeleteableMsa dmsa1 = DeleteableMsa.createInstance( l1 );
-            System.out.println( dmsa1.toString() );
             dmsa1.deleteGapOnlyColumns();
-            System.out.println( dmsa1.toString() );
             dmsa1.deleteRow( "a" );
             dmsa1.deleteRow( "f" );
             dmsa1.deleteRow( "d" );
-            System.out.println( dmsa1.toString() );
             dmsa1.deleteGapOnlyColumns();
-            System.out.println( dmsa1.toString() );
             if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C-" ) ) {
                 return false;
             }
@@ -6183,10 +6170,8 @@ public final class Test {
             dmsa1.deleteGapOnlyColumns();
             final Writer w0 = new StringWriter();
             dmsa1.write( w0, MSA_FORMAT.FASTA );
-            System.out.println( w0.toString() );
             final Writer w1 = new StringWriter();
             dmsa1.write( w1, MSA_FORMAT.PHYLIP );
-            System.out.println( w1.toString() );
             if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C" ) ) {
                 return false;
             }
@@ -6208,9 +6193,47 @@ public final class Test {
             l2.add( s__4 );
             l2.add( s__5 );
             final DeleteableMsa dmsa2 = DeleteableMsa.createInstance( l2 );
-            System.out.println( dmsa2.toString() );
             dmsa2.deleteGapColumns( 0.5 );
-            System.out.println( dmsa2.toString() );
+            if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A---" ) ) {
+                return false;
+            }
+            if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB--" ) ) {
+                return false;
+            }
+            if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CCC-" ) ) {
+                return false;
+            }
+            dmsa2.deleteGapColumns( 0.2 );
+            if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A-" ) ) {
+                return false;
+            }
+            if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB" ) ) {
+                return false;
+            }
+            if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CC" ) ) {
+                return false;
+            }
+            dmsa2.deleteGapColumns( 0 );
+            dmsa2.deleteRow( "a" );
+            dmsa2.deleteRow( "b" );
+            dmsa2.deleteRow( "f" );
+            dmsa2.deleteRow( "e" );
+            dmsa2.setIdentifier( 0, "new_c" );
+            dmsa2.setIdentifier( 1, "new_d" );
+            dmsa2.setResidueAt( 0, 0, 'x' );
+            dmsa2.deleteRow( "new_d" );
+            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 ) ) {
+                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 ) ) {
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );