inprogress

[jalview.git] / forester / java / src / org / forester / ws / seqdb / UniProtEntry.java

diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
index 05e2e59..2565339 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
+++ b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
@@ -26,15 +26,22 @@
 package org.forester.ws.seqdb;
 
 import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
+import org.forester.go.BasicGoTerm;
+import org.forester.go.GoTerm;
 import org.forester.util.ForesterUtil;
 
 public final class UniProtEntry implements SequenceDatabaseEntry {
 
-    private String _ac;
-    private String _name;
-    private String _os_scientific_name;
-    private String _tax_id;
+    public final static Pattern GO_PATTERN = Pattern.compile( "GO;\\s+GO:(\\d+);\\s+([PF]):([^;]+);" );
+    private String              _ac;
+    private String              _name;
+    private String              _symbol;
+    private String              _gene_name;
+    private String              _os_scientific_name;
+    private String              _tax_id;
 
     private UniProtEntry() {
     }
@@ -47,6 +54,7 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
     public static SequenceDatabaseEntry createInstanceFromPlainText( final List<String> lines ) {
         final UniProtEntry e = new UniProtEntry();
         for( final String line : lines ) {
+            //System.out.println( line );
             if ( line.startsWith( "AC" ) ) {
                 e.setAc( DatabaseTools.extract( line, "AC", ";" ) );
             }
@@ -58,6 +66,31 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
                     e.setSequenceName( DatabaseTools.extract( line, "Full=", ";" ) );
                 }
             }
+            else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceSymbol() ) ) {
+                if ( line.indexOf( "Short=" ) > 0 ) {
+                    e.setSequenceSymbol( DatabaseTools.extract( line, "Short=", ";" ) );
+                }
+            }
+            else if ( line.startsWith( "GN" ) && ForesterUtil.isEmpty( e.getGeneName() ) ) {
+                if ( line.indexOf( "Name=" ) > 0 ) {
+                    e.setGeneName( DatabaseTools.extract( line, "Name=", ";" ) );
+                }
+            }
+            else if ( line.startsWith( "DR" ) ) {
+                if ( line.indexOf( "GO;" ) > 0 ) {
+                    Matcher m = GO_PATTERN.matcher( line );
+                    if ( m.find() ) {
+                        String n = m.group( 1 );
+                        String ns_str = m.group( 2 );
+                        String desc = m.group( 3 );
+                        if ( ns_str.equals( "F" ) ) { 
+                        
+                        System.out.println( "GO:" + n + " " + desc + " " + ns );
+                        GoTerm go = new BasicGoTerm( n, desc, ns, false );
+                        //  e.setGeneName( DatabaseTools.extract( line, "Name=", ";" ) );
+                    }
+                }
+            }
             else if ( line.startsWith( "OS" ) ) {
                 if ( line.indexOf( "(" ) > 0 ) {
                     e.setOsScientificName( DatabaseTools.extract( line, "OS", "(" ) );
@@ -75,6 +108,10 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
         return e;
     }
 
+    private void setSequenceSymbol( String symbol ) {
+        _symbol = symbol;
+    }
+
     @Override
     public String getAccession() {
         return _ac;
@@ -119,20 +156,32 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
         }
     }
 
+    private void setGeneName( final String gene_name ) {
+        if ( _gene_name == null ) {
+            _gene_name = gene_name;
+        }
+    }
+
     @Override
     public String getSequenceSymbol() {
-        return "";
+        return _symbol;
     }
 
     @Override
     public boolean isEmpty() {
         return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
-                && ForesterUtil.isEmpty( getTaxonomyScientificName() )
-                && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) );
+                && ForesterUtil.isEmpty( getTaxonomyScientificName() ) && ForesterUtil.isEmpty( getSequenceSymbol() )
+                && ForesterUtil.isEmpty( getGeneName() ) && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil
+                .isEmpty( getSequenceSymbol() ) );
     }
 
     @Override
     public String getProvider() {
         return "uniprot";
     }
+
+    @Override
+    public String getGeneName() {
+        return _gene_name;
+    }
 }