X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2FFastaParser.java;h=5f42df83344f1d6ccbf0c7ffde3da4e1e8afe13b;hb=7019346e7e8cecf22a06ffb59ea86daf0d28189d;hp=b04e25426b9042f8aec3ec852722313c3daa5dbb;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/io/parsers/FastaParser.java b/forester/java/src/org/forester/io/parsers/FastaParser.java
index b04e254..5f42df8 100644
--- a/forester/java/src/org/forester/io/parsers/FastaParser.java
+++ b/forester/java/src/org/forester/io/parsers/FastaParser.java
@@ -28,6 +28,8 @@ package org.forester.io.parsers;
 
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
@@ -39,13 +41,8 @@ import java.util.regex.Pattern;
 import org.forester.msa.BasicMsa;
 import org.forester.msa.Msa;
 import org.forester.msa.MsaFormatException;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Accession;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.sequence.BasicSequence;
 import org.forester.sequence.Sequence;
-import org.forester.util.ForesterUtil;
 
 public class FastaParser {
 
@@ -53,7 +50,7 @@ public class FastaParser {
     private static final Pattern SEQ_REGEX       = Pattern.compile( "^\\s*(.+)" );
     private static final Pattern ANYTHING_REGEX  = Pattern.compile( "[\\d\\s]+" );
     //>gi|71834668|ref|NP_001025424.1| Bcl2 [Danio rerio]
-    private static final Pattern FASTA_DESC_LINE = Pattern
+    public static final Pattern  FASTA_DESC_LINE = Pattern
                                                          .compile( ">?\\s*([^|]+)\\|([^|]+)\\S*\\s+(.+)\\s+\\[(.+)\\]" );
 
     public static void main( final String[] args ) {
@@ -92,6 +89,10 @@ public class FastaParser {
         return false;
     }
 
+    static public Msa parseMsa( final File f ) throws IOException {
+        return parseMsa( new FileInputStream( f ) );
+    }
+
     static public Msa parseMsa( final InputStream is ) throws IOException {
         return BasicMsa.createInstance( parse( is ) );
     }
@@ -104,6 +105,10 @@ public class FastaParser {
         return parseMsa( new ByteArrayInputStream( bytes ) );
     }
 
+    static public List<Sequence> parse( final File f ) throws IOException {
+        return parse( new FileInputStream( f ) );
+    }
+
     static public List<Sequence> parse( final InputStream is ) throws IOException {
         final BufferedReader reader = new BufferedReader( new InputStreamReader( is, "UTF-8" ) );
         String line = null;
@@ -175,36 +180,4 @@ public class FastaParser {
         }
         return line;
     }
-
-    public static void extractFastaInformation( final Phylogeny phy ) {
-        for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
-            final PhylogenyNode node = iter.next();
-            if ( !ForesterUtil.isEmpty( node.getName() ) ) {
-                final Matcher name_m = FASTA_DESC_LINE.matcher( node.getName() );
-                if ( name_m.lookingAt() ) {
-                    System.out.println();
-                    // System.out.println( name_m.group( 1 ) );
-                    // System.out.println( name_m.group( 2 ) );
-                    // System.out.println( name_m.group( 3 ) );
-                    // System.out.println( name_m.group( 4 ) );
-                    final String acc_source = name_m.group( 1 );
-                    final String acc = name_m.group( 2 );
-                    final String seq_name = name_m.group( 3 );
-                    final String tax_sn = name_m.group( 4 );
-                    if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
-                        ForesterUtil.ensurePresenceOfSequence( node );
-                        node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
-                    }
-                    if ( !ForesterUtil.isEmpty( seq_name ) ) {
-                        ForesterUtil.ensurePresenceOfSequence( node );
-                        node.getNodeData().getSequence( 0 ).setName( seq_name );
-                    }
-                    if ( !ForesterUtil.isEmpty( tax_sn ) ) {
-                        ForesterUtil.ensurePresenceOfTaxonomy( node );
-                        node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
-                    }
-                }
-            }
-        }
-    }
 }