From cfda6a6b1a23304bdcdac75f629e9ce4beb9cd9a Mon Sep 17 00:00:00 2001
From: cmzmasek <cmzmasek@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 8 Aug 2012 13:23:55 +0000
Subject: [PATCH] work for rrm project (ComPhy 2012 Moscow)

---
 forester/java/src/org/forester/application/aa.java |    4 ++
 .../src/org/forester/sequence/BasicSequence.java   |   45 +++++++++++++++++++-
 .../java/src/org/forester/sequence/Sequence.java   |    2 +
 3 files changed, 49 insertions(+), 2 deletions(-)

diff --git a/forester/java/src/org/forester/application/aa.java b/forester/java/src/org/forester/application/aa.java
index b9e88a7..6d7be4f 100644
--- a/forester/java/src/org/forester/application/aa.java
+++ b/forester/java/src/org/forester/application/aa.java
@@ -3,7 +3,10 @@ package org.forester.application;
 
 import java.io.FileInputStream;
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
 
 import org.forester.io.parsers.FastaParser;
 import org.forester.msa.Msa;
@@ -18,6 +21,7 @@ public class aa {
             final List<Sequence> orig = FastaParser
                     .parse( new FileInputStream( "C:\\Users\\zma\\Desktop\\RRMa_domains_ext_20.fasta" ) );
             final Msa msa = FastaParser.parseMsa( new FileInputStream( "C:\\Users\\zma\\Desktop\\test3_sorted.fasta" ) );
+            final Set<Sequence> all_found_seqs = new HashSet<Sequence>();
             for( int i = 0; i < msa.getNumberOfSequences(); ++i ) {
                 final String id = msa.getIdentifier( i );
                 final String id_ = id.substring( 0, id.indexOf( "_" ) );
diff --git a/forester/java/src/org/forester/sequence/BasicSequence.java b/forester/java/src/org/forester/sequence/BasicSequence.java
index c14277c..e180481 100644
--- a/forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/forester/java/src/org/forester/sequence/BasicSequence.java
@@ -26,6 +26,8 @@
 
 package org.forester.sequence;
 
+import org.forester.util.ForesterUtil;
+
 public class BasicSequence implements Sequence {
 
     private final char[] _mol_sequence;
@@ -33,6 +35,12 @@ public class BasicSequence implements Sequence {
     private final TYPE   _type;
 
     private BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
+        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");
+        }
         _mol_sequence = mol_sequence.toCharArray();
         _identifier = identifier;
         _type = type;
@@ -40,6 +48,12 @@ public class BasicSequence implements Sequence {
 
     // 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;
@@ -82,11 +96,32 @@ public class BasicSequence implements Sequence {
     }
 
     @Override
+    public boolean equals(Object obj) {
+        if (obj == null) {
+            return false;
+        }
+        if (obj.getClass() != getClass()) {
+            return false;
+        }
+        Sequence other = ( Sequence) 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();
     }
 
@@ -112,4 +147,10 @@ public class BasicSequence implements Sequence {
         return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
                 .replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA );
     }
+
+    @Override
+    public String getMolecularSequenceAsString() {
+       
+        return new String( getMolecularSequence() );
+    }
 }
diff --git a/forester/java/src/org/forester/sequence/Sequence.java b/forester/java/src/org/forester/sequence/Sequence.java
index 9a92fbe..f4c17cf 100644
--- a/forester/java/src/org/forester/sequence/Sequence.java
+++ b/forester/java/src/org/forester/sequence/Sequence.java
@@ -44,6 +44,8 @@ public interface Sequence {
     public abstract int getNumberOfGapResidues();
 
     public abstract char[] getMolecularSequence();
+    
+    public abstract String getMolecularSequenceAsString();
 
     public abstract char getResidueAt( final int position );
 
-- 
1.7.10.2