"rio" work

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

diff --git a/forester/java/src/org/forester/application/aaa.java b/forester/java/src/org/forester/application/aaa.java
index b42ba7b..ac643c4 100644 (file)
--- a/forester/java/src/org/forester/application/aaa.java
+++ b/forester/java/src/org/forester/application/aaa.java
@@ -2,6 +2,7 @@
 package org.forester.application;
 
 import java.io.FileInputStream;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashSet;
@@ -12,20 +13,29 @@ import java.util.regex.Pattern;
 
 import org.forester.io.parsers.FastaParser;
 import org.forester.sequence.Sequence;
+import org.forester.util.EasyWriter;
 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 final static int     MIN_LENGTH    = 85;
 
     public static void main( final String args[] ) {
         try {
+            final EasyWriter out = ( EasyWriter ) ForesterUtil.createEasyWriter( "aaa_out" );
             System.out.println( "STARTING..." );
+            final List<Sequence> too_short = new ArrayList<Sequence>();
             final List<Sequence> orig = FastaParser
                     .parse( new FileInputStream( "C:\\Users\\zma\\Desktop\\RRMa_domains_ext_20_2.fasta" ) );
+            final int initial_number = orig.size();
             final List<String> new_seqs = new ArrayList<String>();
             for( final Sequence seq : orig ) {
+                if ( seq.getLength() < MIN_LENGTH ) {
+                    too_short.add( seq );
+                    continue;
+                }
                 final Matcher matcher = GN_PATTERN.matcher( seq.getIdentifier() );
                 String gn = "";
                 if ( matcher.find() ) {
@@ -41,9 +51,9 @@ public class aaa {
             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 = "____";
+            final List<String> duplicate_gn_ra = new ArrayList<String>();
+            final List<String> duplicate_mol_seq = new ArrayList<String>();
+            final List<String> new_seqs_unique = new ArrayList<String>();
             for( final String seq : new_seqs ) {
                 final Matcher matcher_ra = RANGE_PATTERN.matcher( seq );
                 final Matcher matcher_gn = GN_PATTERN.matcher( seq );
@@ -63,39 +73,79 @@ public class aaa {
                     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 );
+                        new_seqs_unique.add( seq );
                         unique_counter++;
                     }
                     else {
-                        duplicate_counter_mol_seq++;
+                        duplicate_mol_seq.add( seq );
                     }
                 }
                 else {
-                    duplicate_counter_gn_ra++;
+                    duplicate_gn_ra.add( seq );
                 }
             }
-            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 );
+            String prev_gn = "___";
+            boolean is_first = true;
+            List<String> seqs_from_same_protein = new ArrayList<String>();
+            for( final String seq : new_seqs_unique ) {
+                final Matcher matcher_gn = GN_PATTERN.matcher( seq );
+                matcher_gn.find();
+                final String gn = matcher_gn.group( 1 );
+                if ( !prev_gn.equals( gn ) && !is_first ) {
+                    doit( seqs_from_same_protein, out );
+                    seqs_from_same_protein = new ArrayList<String>();
+                }
+                prev_gn = gn;
+                is_first = false;
+                seqs_from_same_protein.add( seq );
+            }
+            doit( seqs_from_same_protein, out );
+            out.println( "" );
+            out.println( "" );
+            out.println( "Removed because same GN and region:" );
+            for( final String s : duplicate_gn_ra ) {
+                out.println( s );
+            }
+            out.println( "" );
+            out.println( "" );
+            out.println( "Removed because identical mol sequence:" );
+            for( final String s : duplicate_mol_seq ) {
+                out.println( s );
+            }
+            out.println( "" );
+            out.println( "" );
+            out.println( "Removed because too short:" );
+            for( final Sequence s : too_short ) {
+                out.println( s.toString() );
+            }
+            out.println( "" );
+            out.println( "" );
+            out.println( "initial:" + initial_number );
+            out.println( "ignored because shorter than " + MIN_LENGTH + "aa: " + too_short.size() );
+            out.println( "unique   : " + unique_counter );
+            out.println( "unique   : " + new_seqs_unique.size() );
+            out.println( "duplicate because gn and range same: " + duplicate_gn_ra.size() );
+            out.println( "duplicate because mol seq same     : " + duplicate_mol_seq.size() );
+            out.flush();
+            out.close();
+            System.out.println( "DONE " );
         }
         catch ( final Exception e ) {
             e.printStackTrace();
         }
     }
+
+    private static void doit( final List<String> same_protein_seqs, final EasyWriter out ) throws IOException {
+        final int count = same_protein_seqs.size();
+        if ( count == 1 ) {
+            out.println( same_protein_seqs.get( 0 ) );
+        }
+        else {
+            int c = 1;
+            for( final String s : same_protein_seqs ) {
+                out.println( new StringBuffer( s ).insert( s.indexOf( "|" ), "__" + c + "_OF_" + count ).toString() );
+                c++;
+            }
+        }
+    }
 }