changes for writing out EMBL from database entry

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6421 ee4ac58c-ac51-4696-9907-e4b3aa274f04

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

@@ -69,8 +69,8 @@ public class DatabaseDocumentEntry extends GFFDocumentEntry
    *  it, otherwise create and return a new feature of the appropriate type.
    *  @param copy if true then always new a new copy of the Feature.
    **/
-  protected SimpleDocumentFeature makeNativeFeature(final Feature feature,
-                                                    final boolean copy)
+  protected Object makeNativeFeature(final Feature feature,
+                                     final boolean copy)
   {
     if (!copy)
     {

uk/ac/sanger/artemis/io/GFFDocumentEntry.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/GFFDocumentEntry.java,v 1.48 2007-09-11 11:00:37 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFDocumentEntry.java,v 1.49 2007-09-25 09:59:57 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.io;
@@ -42,7 +42,7 @@ import java.sql.Timestamp;
  *  A DocumentEntry that can read an GFF entry from a Document.
  *
  *  @author Kim Rutherford
- *  @version $Id: GFFDocumentEntry.java,v 1.48 2007-09-11 11:00:37 tjc Exp $
+ *  @version $Id: GFFDocumentEntry.java,v 1.49 2007-09-25 09:59:57 tjc Exp $
  **/
 
 public class GFFDocumentEntry extends SimpleDocumentEntry
@@ -126,8 +126,8 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
    *  it, otherwise create and return a new feature of the appropriate type.
    *  @param copy if true then always new a new copy of the Feature.
    **/
-  protected SimpleDocumentFeature makeNativeFeature(final Feature feature,
-                                                    final boolean copy) 
+  protected Object makeNativeFeature(final Feature feature,
+                                     final boolean copy) 
   {
     if(!copy && feature instanceof GFFStreamFeature) 
       return (GFFStreamFeature)feature;

uk/ac/sanger/artemis/io/MSPcrunchDocumentEntry.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/MSPcrunchDocumentEntry.java,v 1.1 2004-06-09 09:49:57 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/MSPcrunchDocumentEntry.java,v 1.2 2007-09-25 09:59:57 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.io;
@@ -34,7 +34,7 @@ import java.io.*;
  *  MSPcrunch -d or -x output.
  *
  *  @author Kim Rutherford
- *  @version $Id: MSPcrunchDocumentEntry.java,v 1.1 2004-06-09 09:49:57 tjc Exp $
+ *  @version $Id: MSPcrunchDocumentEntry.java,v 1.2 2007-09-25 09:59:57 tjc Exp $
  **/
 
 public class MSPcrunchDocumentEntry extends SimpleDocumentEntry
@@ -95,7 +95,7 @@ public class MSPcrunchDocumentEntry extends SimpleDocumentEntry
    *  it, otherwise create and return a new feature of the appropriate type.
    *  @param copy if true then always new a new copy of the Feature.
    **/
-  protected SimpleDocumentFeature makeNativeFeature (final Feature feature,
+  protected Object makeNativeFeature (final Feature feature,
                                                      final boolean copy) {
     if (!copy && feature instanceof MSPcrunchStreamFeature) {
       return (MSPcrunchStreamFeature) feature;

uk/ac/sanger/artemis/io/PublicDBDocumentEntry.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/PublicDBDocumentEntry.java,v 1.3 2007-09-21 15:26:22 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java,v 1.4 2007-09-25 09:59:57 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.io;
@@ -35,7 +35,7 @@ import java.io.IOException;
  *  entry.
  *
  *  @author Kim Rutherford
- *  @version $Id: PublicDBDocumentEntry.java,v 1.3 2007-09-21 15:26:22 tjc Exp $
+ *  @version $Id: PublicDBDocumentEntry.java,v 1.4 2007-09-25 09:59:57 tjc Exp $
  **/
 
 public class PublicDBDocumentEntry extends SimpleDocumentEntry
@@ -103,7 +103,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
    *  it, otherwise create and return a new feature of the appropriate type.
    *  @param copy if true then always new a new copy of the Feature.
    **/
-  protected SimpleDocumentFeature makeNativeFeature(final Feature feature,
+  protected Object makeNativeFeature(final Feature feature,
                                                     final boolean copy) 
   {
     if (!copy && (feature instanceof EmblStreamFeature &&
@@ -115,16 +115,12 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
     } 
     else 
     {
-      final PublicDBStreamFeature feature_copy;
-
       if(feature instanceof GFFStreamFeature)
-        feature_copy = mapGffToNativeFeature(feature);
+        return mapGffToNativeFeature(feature);
       else if (this instanceof EmblDocumentEntry)
-        feature_copy = new EmblStreamFeature (feature);
+        return new EmblStreamFeature(feature);
       else
-        feature_copy = new GenbankStreamFeature (feature);
-      
-      return feature_copy;
+        return new GenbankStreamFeature(feature);
     }
   }
 
@@ -133,18 +129,31 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
    * @param feature
    * @return
    */
-  private PublicDBStreamFeature mapGffToNativeFeature(final Feature feature)
+  private Object mapGffToNativeFeature(final Feature feature)
   {
     final String[] QUALIFIERS_TO_REMOVE = 
         { 
-          "timelastmodified", "ID", "feature_id", "Parent", "Derives_from", "feature_relationship_rank"
+          "timelastmodified", 
+          "ID", 
+          "comment",   // convert to note
+          "feature_id", 
+          "Parent", 
+          "Derives_from",
+          "feature_relationship_rank"
         };
     
     Key key = feature.getKey();
     QualifierVector qualifiers = feature.getQualifiers().copy();
     try
     {
-      int index;
+      int index = qualifiers.indexOfQualifierWithName("comment");
+      
+      if(index > -1)
+      {
+        StringVector comments = ((Qualifier)qualifiers.get(index)).getValues();
+        Qualifier noteQualifier = new Qualifier("note", comments);
+        qualifiers.setQualifier(noteQualifier);
+      }
       
       for(int i=0; i<QUALIFIERS_TO_REMOVE.length; i++)
       {
@@ -152,9 +161,10 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
         if(index > -1)
           qualifiers.removeElementAt(index);
       }
+
       
       if(key.getKeyString().equals(DatabaseDocument.EXONMODEL))
-        key = new Key("exon");
+        key = new Key("CDS");
       else if(key.getKeyString().startsWith("pseudo"))
       {
         if(key.getKeyString().equals("pseudogenic_transcript"))
@@ -178,6 +188,35 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
         }
       }
       
+      
+      //
+      // create separate exon features for each range in a CDS
+      // (returns an array of SimpleDocumentFeature)
+      if(key.getKeyString().equals("CDS"))
+      {
+        RangeVector ranges = feature.getLocation().getRanges();
+        SimpleDocumentFeature[] features = 
+          new SimpleDocumentFeature[ranges.size() + 1];
+        features[0] = new EmblStreamFeature(key, feature.getLocation(),
+            qualifiers);
+
+        for(int i = 0; i < ranges.size(); i++)
+        {
+          try
+          {
+            features[i + 1] = new EmblStreamFeature(new Key("exon"),
+                new Location((Range) ranges.get(i)), qualifiers);
+          }
+          catch(OutOfRangeException e)
+          {
+            e.printStackTrace();
+          }
+        }
+        return features;
+      }
+      
+      
+      
       if(this instanceof EmblDocumentEntry)
         return new EmblStreamFeature (
             key, 

uk/ac/sanger/artemis/io/SimpleDocumentEntry.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/SimpleDocumentEntry.java,v 1.20 2007-06-15 12:57:32 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java,v 1.21 2007-09-25 09:59:57 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.io;
@@ -38,7 +38,7 @@ import javax.swing.JOptionPane;
  *  This class contains the methods common to all DocumentEntry objects.
  *
  *  @author Kim Rutherford <kmr@sanger.ac.uk>
- *  @version $Id: SimpleDocumentEntry.java,v 1.20 2007-06-15 12:57:32 tjc Exp $
+ *  @version $Id: SimpleDocumentEntry.java,v 1.21 2007-09-25 09:59:57 tjc Exp $
  **/
 
 abstract public class SimpleDocumentEntry
@@ -340,13 +340,20 @@ abstract public class SimpleDocumentEntry
       {
         if(force) 
         {
-          if(forcedAdd(makeNativeFeature(new_feature, true)) == null)
+          if(forcedAdd((SimpleDocumentFeature)makeNativeFeature(new_feature, true)) == null)
             failed.append(new_feature.getKey().getKeyString()+"\n"); 
         }
         else
         {
-          
-          add(makeNativeFeature(new_feature, true));
+          final Object docFeature = makeNativeFeature(new_feature, true);
+          if(docFeature instanceof SimpleDocumentFeature[])
+          {
+            SimpleDocumentFeature[] docFeatures = (SimpleDocumentFeature[])docFeature;
+            for(int i=0; i<docFeatures.length; i++)
+              add((SimpleDocumentFeature)docFeatures[i]);
+          }
+          else
+            add((SimpleDocumentFeature)docFeature);
         }
       } 
       catch(ReadOnlyException e) 
@@ -583,7 +590,7 @@ abstract public class SimpleDocumentEntry
     }
 
     final SimpleDocumentFeature native_feature =
-      makeNativeFeature(feature, false);
+      (SimpleDocumentFeature)makeNativeFeature(feature, false);
 
     final FeatureTable feature_table = getFeatureTable();
     feature_table.add(native_feature);
@@ -679,7 +686,7 @@ abstract public class SimpleDocumentEntry
     }
 
     final SimpleDocumentFeature native_feature =
-      makeNativeFeature(feature, false);
+      (SimpleDocumentFeature)makeNativeFeature(feature, false);
 
     if(qualifiers_fixed) 
     {
@@ -1230,7 +1237,7 @@ abstract public class SimpleDocumentEntry
    *  The feature should not be in an Entry when this method is called.
    *  @param copy if true then always make a new copy of the Feature.
    **/
-  protected abstract SimpleDocumentFeature
+  protected abstract Object
     makeNativeFeature(final Feature feature,
                        final boolean copy);