Merge pull request #175 from satta/filter_qualifiers

allow to exclude attributes from GFF3 output

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

@@ -27,8 +27,10 @@ package uk.ac.sanger.artemis.io;
 
 
 import java.util.Hashtable;
+import java.util.HashSet;
 import java.util.Enumeration;
 import java.util.List;
+import java.util.Set;
 import java.util.StringTokenizer;
 import java.util.Vector;
 import java.io.IOException;
@@ -113,6 +115,28 @@ public class GFFStreamFeature extends SimpleDocumentFeature
     { "\n", "%5C" }   // new-line
   };
 
+  private static Set<String> attrs_to_filter = new HashSet<String>();
+
+  /**
+   *  Registers an attribute not to be included in the GFF3 output for
+   *  GFFStreamFeatures
+   *  @param attr The GFF3 attribute to remove
+   **/
+  public static void removeAttribute(String attr)
+  {
+    attrs_to_filter.add(attr);
+  }
+
+  /**
+   *  Registers an attribute to be included in the GFF3 output for
+   *  GFFStreamFeatures
+   *  @param attr The GFF3 attribute to include
+   **/
+  public static void includeAttribute(String attr)
+  {
+    attrs_to_filter.remove(attr);
+  }
+
   /**
    *  Create a new GFFStreamFeature object.  The feature should be added
    *  to an Entry (with Entry.add()).
@@ -893,6 +917,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature
       if(lname)
         continue;
 
+      if(attrs_to_filter.contains(this_qualifier.getName()))
+        continue;
+
       if( (this_qualifier.getName().equals("private") && System.getProperty("noprivate") != null) ||
           (this_qualifier.getName().equals("history") && System.getProperty("nohistory") != null) )
         continue;

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

@@ -294,6 +294,7 @@ public class ReadAndWriteEntry
         System.out.println("-h\tshow help");
 
         System.out.println("-f\t[y|n] flatten the gene model, default is y");
+        System.out.println("-flt\tspace separated list of qualifiers to ignore (GFF only)");
         System.out.println("-i\t[y|n] ignore obsolete features, default is y");
         System.out.println("-s\tspace separated list of sequences to read and write out");
         System.out.println("-o\t[EMBL|GFF] output format, default is EMBL");
@@ -407,6 +408,18 @@ public class ReadAndWriteEntry
             if(args[j].startsWith("-"))
               break;
             files.add(args[j]);
+            i++;
+          }
+        }
+        else if(args[i].toLowerCase().equals("-flt"))
+        {
+          for(int j = i + 1; j < args.length; j++)
+          {
+            if(args[j].startsWith("-")) {
+              break;
+            }
+            GFFStreamFeature.removeAttribute(args[j]);
+            i++;
           }
         }
         else if(args[i].startsWith("-"))