in progress

diff --git a/forester/java/src/org/forester/application/aa.java b/forester/java/src/org/forester/application/aa.java
new file mode 100644 (file)
index 0000000..b9e88a7
--- /dev/null
+++ b/forester/java/src/org/forester/application/aa.java
@@ -0,0 +1,63 @@
+
+package org.forester.application;
+
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.forester.io.parsers.FastaParser;
+import org.forester.msa.Msa;
+import org.forester.sequence.Sequence;
+import org.forester.util.ForesterUtil;
+
+public class aa {
+
+    public static void main( final String args[] ) {
+        try {
+            System.out.println( "STARTING..." );
+            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" ) );
+            for( int i = 0; i < msa.getNumberOfSequences(); ++i ) {
+                final String id = msa.getIdentifier( i );
+                final String id_ = id.substring( 0, id.indexOf( "_" ) );
+                final String range = id.substring( id.indexOf( "[" ) + 1, id.indexOf( "]" ) );
+                //System.out.println( i + ": " + id + "=>" + id_ + " " + range );
+                if ( ForesterUtil.isEmpty( id_ ) ) {
+                    System.out.println( "ERROR: id is empty for: " + id );
+                    System.exit( -1 );
+                }
+                if ( ForesterUtil.isEmpty( range ) ) {
+                    System.out.println( "ERROR: range is empty for: " + id );
+                    System.exit( -1 );
+                }
+                int found = 0;
+                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 ) {
+                        found++;
+                        found_seqs.add( orig_seq );
+                    }
+                }
+                if ( found > 0 ) {
+                    if ( found > 1 ) {
+                        System.out.println( i + ": " + id + "=>" + id_ + " " + range );
+                        System.out.println( "  found: " + found );
+                        for( final Sequence found_seq : found_seqs ) {
+                            System.out.println( found_seq.toString() );
+                        }
+                    }
+                }
+                else {
+                    System.out.println( "ERROR: not found: " + id );
+                    System.exit( -1 );
+                }
+            }
+            System.out.println( "DONE." );
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace();
+        }
+    }
+}