X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FDeleteableMsa.java;h=350aae25cc4526b8907ca3fd93ec9b7fffd9dbf8;hb=0465b8ebe16d57902022bba6f90f25dd1a18e656;hp=17f72bb170f884e3c771306a46656f71f60e5d19;hpb=db8b10baefc3e1b5fee9b8192657ecc97ca5b86d;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/DeleteableMsa.java b/forester/java/src/org/forester/msa/DeleteableMsa.java
index 17f72bb..350aae2 100644
--- 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 );
@@ -48,14 +46,21 @@ 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();
     }
 
+    public short determineMaxIdLength() {
+        short max = 0;
+        for( int row = 0; row < getNumberOfSequences(); ++row ) {
+            final short l = ( short ) getIdentifier( row ).length();
+            if ( l > max ) {
+                max = l;
+            }
+        }
+        return max;
+    }
+
     final public void deleteGapColumns( final double max_allowed_gap_ratio ) {
         if ( ( max_allowed_gap_ratio < 0 ) || ( max_allowed_gap_ratio > 1 ) ) {
             throw new IllegalArgumentException( "max allowed gap ration is out of range: " + max_allowed_gap_ratio );
@@ -70,13 +75,13 @@ public final class DeleteableMsa extends BasicMsa {
 
     final public void deleteGapOnlyColumns() {
         for( int col = getLength() - 1; col >= 0; --col ) {
-            if ( MsaMethods.calcGapSumPerColumn( this, col ) == getNumberOfSequences() ) {
+            if ( isAllGap( col ) ) {
                 deleteColumn( col );
             }
         }
     }
 
-    final public void 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 ) ) {
@@ -87,11 +92,30 @@ public final class DeleteableMsa extends BasicMsa {
         if ( row < 0 ) {
             throw new IllegalArgumentException( "id [" + id + "] not found" );
         }
+        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 );
+        if ( return_removed_seq ) {
+            return new BasicSequence( new String( s.getIdentifier() ), sb.toString(), s.getType() );
+        }
+        else {
+            return null;
+        }
     }
 
     @Override
     final public String getIdentifier( final int row ) {
+        checkRow( row );
         return super.getIdentifier( _mapped_row_positions[ row ] );
     }
 
@@ -107,28 +131,54 @@ 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() );
     }
 
+    final public boolean isAllGap( final int col ) {
+        final int m_col = _mapped_col_positions[ col ];
+        for( int j = 0; j < getNumberOfSequences(); ++j ) {
+            if ( super.getResidueAt( _mapped_row_positions[ j ], m_col ) != Sequence.GAP ) {
+                return false;
+            }
+        }
+        return true;
+    }
+
     @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 +186,7 @@ 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 ];
         }