in progress

diff --git a/forester/java/src/org/forester/application/aa.java b/forester/java/src/org/forester/application/aa.java
index 1ae5dfb..899120c 100644 (file)
--- a/forester/java/src/org/forester/application/aa.java
+++ b/forester/java/src/org/forester/application/aa.java
@@ -3,6 +3,7 @@ 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;
@@ -10,6 +11,7 @@ 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;
 
@@ -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 ) {
@@ -63,10 +66,19 @@ public class aa {
                     System.exit( -1 );
                 }
             }
+            String fasta_ary[] = new String[ all_found_seqs.size() ];
             int i = 0;
             for( Sequence sequence : all_found_seqs ) {
-                System.out.println( i++ + ": " + sequence );
+                fasta_ary[ i ] = ">" + sequence.getIdentifier() + "\n" + sequence.getMolecularSequenceAsString();
+                System.out.println( sequence );
+                i++;
             }
+            Arrays.sort( fasta_ary );
+            
+            for( int j = 0; j < fasta_ary.length; ++j ) {
+                System.out.println(  fasta_ary[ j ] );
+            }
+            
             System.out.println( "DONE." );
         }
         catch ( final Exception e ) {

diff --git a/forester/java/src/org/forester/application/aaa.java b/forester/java/src/org/forester/application/aaa.java
new file mode 100644 (file)
index 0000000..b42ba7b
--- /dev/null
+++ b/forester/java/src/org/forester/application/aaa.java
@@ -0,0 +1,101 @@
+
+package org.forester.application;
+
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.forester.io.parsers.FastaParser;
+import org.forester.sequence.Sequence;
+import org.forester.util.ForesterUtil;
+
+public class aaa {
+
+    public final static Pattern GN_PATTERN    = Pattern.compile( "GN=(\\S+)\\s" );     //use w+ instead of S+ for more stringent setting.
+    public final static Pattern RANGE_PATTERN = Pattern.compile( "\\[(\\d+-\\d+)\\]" ); //use w+ instead of S+ for more stringent setting.
+
+    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_2.fasta" ) );
+            final List<String> new_seqs = new ArrayList<String>();
+            for( final Sequence seq : orig ) {
+                final Matcher matcher = GN_PATTERN.matcher( seq.getIdentifier() );
+                String gn = "";
+                if ( matcher.find() ) {
+                    gn = matcher.group( 1 );
+                }
+                else {
+                    System.out.println( "ERROR: no gene for: " + seq.getIdentifier() );
+                    System.exit( -1 );
+                }
+                new_seqs.add( ">" + gn + "|" + seq.getIdentifier() + "\n" + seq.getMolecularSequenceAsString() );
+            }
+            final Set<String> gn_ra_set = new HashSet<String>();
+            final Set<String> mol_seq_set = new HashSet<String>();
+            Collections.sort( new_seqs );
+            int unique_counter = 0;
+            int duplicate_counter_gn_ra = 0;
+            int duplicate_counter_mol_seq = 0;
+            String prev_gn = "____";
+            for( final String seq : new_seqs ) {
+                final Matcher matcher_ra = RANGE_PATTERN.matcher( seq );
+                final Matcher matcher_gn = GN_PATTERN.matcher( seq );
+                String range = "";
+                if ( matcher_ra.find() ) {
+                    range = matcher_ra.group( 1 );
+                }
+                else {
+                    System.out.println( "ERROR: no range for: " + seq );
+                    System.exit( -1 );
+                }
+                matcher_gn.find();
+                final String gn = matcher_gn.group( 1 );
+                final String gn_ra = gn + "_" + range;
+                if ( !gn_ra_set.contains( gn_ra ) ) {
+                    gn_ra_set.add( gn_ra );
+                    final String mol_seq = seq.split( "\n" )[ 1 ];
+                    if ( !mol_seq_set.contains( mol_seq ) ) {
+                        mol_seq_set.add( mol_seq );
+                        if ( prev_gn.equals( gn ) ) {
+                            int count = same_protein_seqs.size();
+                            if ( count == 1 ) {
+                                System.out.println( seq );
+                            }
+                            else {
+                                int c = 1;
+                                for( final String s : same_protein_seqs ) {
+                                    System.out.println( new StringBuffer( s ).insert( s.indexOf( "|" ),
+                                                                                      "__" + c + "_OF_" + count )
+                                            .toString() );
+                                    c++;
+                                }
+                            }
+                        }
+                        prev_gn = gn;
+                        System.out.println( seq );
+                        unique_counter++;
+                    }
+                    else {
+                        duplicate_counter_mol_seq++;
+                    }
+                }
+                else {
+                    duplicate_counter_gn_ra++;
+                }
+            }
+            System.out.println( "unique   : " + unique_counter );
+            System.out.println( "duplicate because gn and range same: " + duplicate_counter_gn_ra );
+            System.out.println( "duplicate because mol seq same     : " + duplicate_counter_mol_seq );
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace();
+        }
+    }
+}