X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsequence%2FBasicSequence.java;h=6d339cae25790d8538deed1f8efbd04527729d75;hb=c0439ed8b088887ffea2faf11bc7897333287cb3;hp=4cc03a712eb8e445277aa640631936a15688efd3;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/sequence/BasicSequence.java b/forester/java/src/org/forester/sequence/BasicSequence.java
index 4cc03a7..6d339ca 100644
--- a/forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/forester/java/src/org/forester/sequence/BasicSequence.java
@@ -6,7 +6,7 @@
 // Copyright (C) 2010 Christian M Zmasek
 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -16,76 +16,162 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.sequence;
 
-public class BasicSequence implements Sequence {
+import org.forester.util.ForesterUtil;
+
+public class BasicSequence implements MolecularSequence {
 
     private final char[] _mol_sequence;
-    private final Object _identifier;
+    private String       _identifier;
     private final TYPE   _type;
 
-    private BasicSequence( final Object identifier, final String mol_sequence, final TYPE type ) {
+    /**
+     * Only use if you know what you are doing!
+     *
+     */
+    public BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
+        check( identifier, mol_sequence );
         _mol_sequence = mol_sequence.toCharArray();
         _identifier = identifier;
         _type = type;
     }
 
-    // Only use if you know what you are doing!
-    public BasicSequence( final Object identifier, final char[] mol_sequence, final TYPE type ) {
+    private static final void check( final String identifier, final String mol_sequence ) {
+        if ( ForesterUtil.isEmpty( identifier ) ) {
+            throw new IllegalArgumentException( "identifier of sequence cannot be empty" );
+        }
+        if ( ForesterUtil.isEmpty( mol_sequence ) ) {
+            throw new IllegalArgumentException( "molecular sequence cannot be empty" );
+        }
+    }
+
+    /**
+     * Only use if you know what you are doing!
+     *
+     */
+    public BasicSequence( final String identifier, final char[] mol_sequence, final TYPE type ) {
+        if ( ForesterUtil.isEmpty( identifier ) ) {
+            throw new IllegalArgumentException( "identifier of sequence cannot be empty" );
+        }
+        if ( ( mol_sequence == null ) || ( mol_sequence.length < 1 ) ) {
+            throw new IllegalArgumentException( "molecular sequence cannot be empty" );
+        }
         _mol_sequence = mol_sequence;
         _identifier = identifier;
         _type = type;
     }
 
-    public Object getIdentifier() {
+    public void setIdentifier( final String id ) {
+        _identifier = id;
+    }
+
+    @Override
+    public String getIdentifier() {
         return _identifier;
     }
 
+    @Override
     public int getLength() {
         return _mol_sequence.length;
     }
 
+    @Override
     public char[] getMolecularSequence() {
         return _mol_sequence;
     }
 
+    @Override
     public char getResidueAt( final int position ) {
         return _mol_sequence[ position ];
     }
 
+    @Override
     public TYPE getType() {
         return _type;
     }
 
     @Override
+    public int getNumberOfGapResidues() {
+        int gaps = 0;
+        for( final char element : _mol_sequence ) {
+            if ( element == GAP ) {
+                ++gaps;
+            }
+        }
+        return gaps;
+    }
+
+    @Override
+    public boolean equals( final Object obj ) {
+        if ( obj == null ) {
+            return false;
+        }
+        if ( obj.getClass() != getClass() ) {
+            return false;
+        }
+        final MolecularSequence other = ( MolecularSequence ) obj;
+        if ( getMolecularSequenceAsString().equals( other.getMolecularSequenceAsString() ) ) {
+            return true;
+        }
+        return false;
+    }
+
+    @Override
+    public int hashCode() {
+        return getMolecularSequenceAsString().hashCode();
+    }
+
+    @Override
     public String toString() {
         final StringBuffer sb = new StringBuffer();
         sb.append( _identifier.toString() );
-        sb.append( " " );
-        sb.append( new String( _mol_sequence ) );
+        sb.append( ": " );
+        sb.append( getMolecularSequenceAsString() );
         return sb.toString();
     }
 
-    public static Sequence createAaSequence( final Object identifier, final String mol_sequence ) {
+    public static MolecularSequence copySequence( final MolecularSequence seq ) {
+        final char[] s = new char[ seq.getMolecularSequence().length ];
+        for( int i = 0; i < seq.getMolecularSequence().length; i++ ) {
+            s[ i ] = seq.getMolecularSequence()[ i ];
+        }
+        return new BasicSequence( new String( seq.getIdentifier() ), s, seq.getType() );
+    }
+
+    public static MolecularSequence createAaSequence( final String identifier, final String mol_sequence ) {
+        check( identifier, mol_sequence );
         return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
-                .replaceAll( AA_REGEXP, Character.toString( UNSPECIFIED_AA ) ), TYPE.AA );
+                                  .replaceAll( AA_REGEXP, Character.toString( UNSPECIFIED_AA ) ), TYPE.AA );
     }
 
-    public static Sequence createDnaSequence( final Object identifier, final String mol_sequence ) {
+    public static MolecularSequence createDnaSequence( final String identifier, final String mol_sequence ) {
+        check( identifier, mol_sequence );
         return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
-                .replaceAll( DNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.DNA );
+                                  .replaceAll( DNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.DNA );
     }
 
-    public static Sequence createRnaSequence( final Object identifier, final String mol_sequence ) {
+    public static MolecularSequence createRnaSequence( final String identifier, final String mol_sequence ) {
+        check( identifier, mol_sequence );
         return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
-                .replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA );
+                                  .replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA );
+    }
+
+    @Override
+    public String getMolecularSequenceAsString() {
+        return new String( getMolecularSequence() );
+    }
+
+    @Override
+    public boolean isGapAt( final int position ) {
+        return getResidueAt( position ) == GAP;
     }
 }