gff3

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2420 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/io/GFFEntryInformation.java

@@ -20,18 +20,169 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFEntryInformation.java,v 1.1 2004-06-09 09:49:31 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFEntryInformation.java,v 1.2 2005-04-26 14:31:44 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.io;
 
+import java.io.InputStream;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Properties;
+
+import uk.ac.sanger.artemis.util.StringVector;
+import uk.ac.sanger.artemis.Options;
+
 /**
  *  An EntryInformation object for GFFDocumentEntry objects.
  *
  *  @author Kim Rutherford <kmr@sanger.ac.uk>
- *  @version $Id: GFFEntryInformation.java,v 1.1 2004-06-09 09:49:31 tjc Exp $
+ *  @version $Id: GFFEntryInformation.java,v 1.2 2005-04-26 14:31:44 tjc Exp $
+ **/
+
+public class GFFEntryInformation extends SimpleEntryInformation 
+{
+
+  public GFFEntryInformation()
+  {
+    super(); 
+
+    try
+    {
+      makeEntryInformation();
+    }
+    catch(QualifierInfoException e)
+    {
+      System.err.println("could not initialise the embl package: " +
+                          e.getMessage());
+      System.exit(1);
+    }
+    catch(IOException e)
+    {
+      System.err.println("could not initialise the embl package: " +
+                          e.getMessage());
+      System.exit(1);
+    }
+  }
+
+ 
+  /**
+   *  Return an EntryInformation object that is suitable for EMBL and GENBANK
+   *  entries.
    **/
+  private void makeEntryInformation()
+      throws IOException, QualifierInfoException
+  {
+    final InputStream feature_keys_stream =
+      Options.class.getResourceAsStream("/etc/feature_keys_gff");
+
+    final InputStream qualifier_types_stream =
+      Options.class.getResourceAsStream("/etc/qualifier_types_gff");
+
+
+    QualifierInfoVector qualifier_info_vector =
+      readQualifierInfo(qualifier_types_stream, feature_keys_stream);
+
+    for(int i = 0 ; i < qualifier_info_vector.size() ; ++i)
+    {
+      final QualifierInfo qualifier_info =
+        qualifier_info_vector.elementAt(i);
+
+      addQualifierInfo(qualifier_info);
+    }
+
+//  entry_information.setEMBLFormat(true);
+  }
+
+  /**
+   *  Read the possible feature key and qualifier names and types from the two
+   *  given streams (see etc/feature_keys and etc/qualifier_types for details
+   *  on the formats).
+   **/
+  private static QualifierInfoVector
+    readQualifierInfo(final InputStream qualifier_types_stream,
+                      final InputStream feature_keys_stream)
+      throws IOException 
+  {
+
+    final QualifierInfoVector return_vector = new QualifierInfoVector();
+
+    Properties feature_properties = new Properties();
+    final Properties qualifier_properties = new Properties();
+
+    feature_properties.load(feature_keys_stream);
+    qualifier_properties.load(qualifier_types_stream);
 
-public class GFFEntryInformation extends SimpleEntryInformation {
+    // parse the feature_properties
 
+    {
+      final Properties new_feature_properties = new Properties();
+      final Enumeration feature_enum = feature_properties.propertyNames();
+
+      while(feature_enum.hasMoreElements()) 
+      {
+        String current_feature_name = (String) feature_enum.nextElement();
+
+        final StringVector property_values =
+          Options.getPropertyValues(feature_properties, current_feature_name);
+
+        new_feature_properties.put(current_feature_name, property_values);
+      }
+
+      feature_properties = new_feature_properties;
+    }
+
+    final Enumeration qualifier_enum = qualifier_properties.propertyNames();
+
+    while(qualifier_enum.hasMoreElements()) 
+    {
+      String current_qualifier_name = (String) qualifier_enum.nextElement();
+
+      final StringVector current_qualifier_values =
+        Options.getPropertyValues(qualifier_properties,
+                                  current_qualifier_name);
+
+      final boolean once_only =
+        current_qualifier_values.elementAt(0).equals("yes");
+
+      final String type_string = current_qualifier_values.elementAt(1);
+
+      // find the keys for which this qualifier name is valid or required
+
+      final KeyVector valid_keys = new KeyVector();
+      final KeyVector required_keys = new KeyVector();
+
+      final Enumeration features_enum = feature_properties.propertyNames();
+
+      while(features_enum.hasMoreElements()) 
+      {
+        final String current_key_string = (String)features_enum.nextElement();
+
+        final Key current_key = new Key(current_key_string);
+
+        final StringVector current_feature_qualifiers =
+          (StringVector) feature_properties.get(current_key_string);
+
+        if(current_feature_qualifiers.contains(current_qualifier_name)) 
+          valid_keys.add(current_key);
+        else
+          if(current_feature_qualifiers.contains("@" +
+                                                   current_qualifier_name)) 
+          {
+            valid_keys.add(current_key);
+            required_keys.add(current_key);
+          }
+      }
+
+      final int type = QualifierInfo.getQualifierTypeID(type_string);
+
+      final QualifierInfo qualifier_info =
+        new QualifierInfo(current_qualifier_name, type, valid_keys,
+                           required_keys, once_only);
+
+      return_vector.add(qualifier_info);
+    }
+
+    return return_vector;
+  }
 }

uk/ac/sanger/artemis/io/GFFStreamFeature.java

@@ -20,7 +20,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.7 2005-04-22 15:26:47 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.8 2005-04-26 14:31:44 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.io;
@@ -35,7 +35,7 @@ import java.util.StringTokenizer;
  *  A StreamFeature that thinks it is a GFF feature.
  *
  *  @author Kim Rutherford
- *  @version $Id: GFFStreamFeature.java,v 1.7 2005-04-22 15:26:47 tjc Exp $
+ *  @version $Id: GFFStreamFeature.java,v 1.8 2005-04-26 14:31:44 tjc Exp $
  **/
 
 public class GFFStreamFeature extends SimpleDocumentFeature
@@ -525,6 +525,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
       count++;
     }
 
+    boolean lname;
     for(int i = 0 ; i < qualifiers.size() ; ++i) 
     {
       this_qualifier = (Qualifier)qualifiers.elementAt(i);
@@ -533,8 +534,12 @@ public class GFFStreamFeature extends SimpleDocumentFeature
       if(this_qualifier_str == null)
         continue;
 
+      lname = false;
       for(int j=0; j<names.length; j++)
-        if(this_qualifier_str.equals(names[j]))
+        if(this_qualifier_str.startsWith(names[j]))
+          lname = true;
+
+      if(lname)
         continue;
 
       if(count != 0)
@@ -579,7 +584,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
           catch (NumberFormatException __)
           {
             // not a double or integer so quote it
-            buffer.append('"' + encode(this_value) + '"');
+            buffer.append(encode(this_value));
           }
         }
       }
@@ -609,7 +614,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
       final String this_token = tokeniser.nextToken().trim();
       int index_of_first_space = this_token.indexOf(" ");
        
-      final String att_name;
+      String att_name;
       final StringVector att_values = new StringVector();
 
       if( this_token.indexOf("=") > -1 &&

uk/ac/sanger/artemis/sequence/Bases.java

@@ -20,7 +20,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Bases.java,v 1.11 2005-01-11 13:24:38 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Bases.java,v 1.12 2005-04-26 14:31:44 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.sequence;
@@ -45,7 +45,7 @@ import java.util.Iterator;
  *  non-base letter returns '@'.
  *
  *  @author Kim Rutherford
- *  @version $Id: Bases.java,v 1.11 2005-01-11 13:24:38 tjc Exp $ */
+ *  @version $Id: Bases.java,v 1.12 2005-04-26 14:31:44 tjc Exp $ */
 
 public class Bases 
 {