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 b9e88a7..b835e52 100644 (file)
--- a/forester/java/src/org/forester/application/aa.java
+++ b/forester/java/src/org/forester/application/aa.java
@@ -1,12 +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 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;
 
@@ -18,6 +23,7 @@ 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( "_" ) );
@@ -35,12 +41,18 @@ 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 );
                     }
                 }
                 if ( found > 0 ) {
+                    for( final Sequence found_seq : found_seqs ) {
+                        if ( found_seq.getLength() >= 85 ) {
+                            all_found_seqs.add( BasicSequence.createAaSequence( id, found_seq
+                                    .getMolecularSequenceAsString() ) );
+                        }
+                    }
                     if ( found > 1 ) {
                         System.out.println( i + ": " + id + "=>" + id_ + " " + range );
                         System.out.println( "  found: " + found );
@@ -54,6 +66,17 @@ public class aa {
                     System.exit( -1 );
                 }
             }
+            final String fasta_ary[] = new String[ all_found_seqs.size() ];
+            int i = 0;
+            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." );
         }
         catch ( final Exception e ) {