moved

[jalview.git] / forester / java / src / org / forester / application / aa.java

diff --git a/forester/java/src/org/forester/application/aa.java b/forester/java/src/org/forester/application/aa.java
index 1ae5dfb..b835e52 100644 (file)
--- a/forester/java/src/org/forester/application/aa.java
+++ b/forester/java/src/org/forester/application/aa.java
@@ -1,15 +1,17 @@
+//
 
 package org.forester.application;
 
 import java.io.FileInputStream;
 import java.util.ArrayList;
+import java.util.Arrays;
 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;
+import org.forester.sequence.BasicSequence;
 import org.forester.sequence.Sequence;
 import org.forester.util.ForesterUtil;
 
@@ -39,7 +41,7 @@ public class aa {
                 final List<Sequence> found_seqs = new ArrayList<Sequence>();
                 for( final Sequence orig_seq : orig ) {
                     final String orig_seq_id = orig_seq.getIdentifier();
-                    if ( orig_seq_id.indexOf( id_ ) >= 0 && orig_seq_id.indexOf( "[" + range + "]" ) >= 0 ) {
+                    if ( ( orig_seq_id.indexOf( id_ ) >= 0 ) && ( orig_seq_id.indexOf( "[" + range + "]" ) >= 0 ) ) {
                         found++;
                         found_seqs.add( orig_seq );
                     }
@@ -47,7 +49,8 @@ public class aa {
                 if ( found > 0 ) {
                     for( final Sequence found_seq : found_seqs ) {
                         if ( found_seq.getLength() >= 85 ) {
-                            all_found_seqs.add( found_seq );
+                            all_found_seqs.add( BasicSequence.createAaSequence( id, found_seq
+                                    .getMolecularSequenceAsString() ) );
                         }
                     }
                     if ( found > 1 ) {
@@ -63,9 +66,16 @@ public class aa {
                     System.exit( -1 );
                 }
             }
+            final String fasta_ary[] = new String[ all_found_seqs.size() ];
             int i = 0;
-            for( Sequence sequence : all_found_seqs ) {
-                System.out.println( i++ + ": " + sequence );
+            for( final Sequence sequence : all_found_seqs ) {
+                fasta_ary[ i ] = ">" + sequence.getIdentifier() + "\n" + sequence.getMolecularSequenceAsString();
+                System.out.println( sequence );
+                i++;
+            }
+            Arrays.sort( fasta_ary );
+            for( final String element : fasta_ary ) {
+                System.out.println( element );
             }
             System.out.println( "DONE." );
         }