Changeset 519 for trunk

Timestamp:

06/05/11 13:04:06 (12 months ago)

Author:

martijn

Message:

Allow concurrent modification of IDMapperStack;
Thanks to Leon Mei from BioAssist? for suggesting this fix.

Location:

trunk

Files:

• org.bridgedb.rdb/src/org/bridgedb/rdb/GdbProvider.java (modified) (4 diffs)
• org.bridgedb/src/org/bridgedb/IDMapperStack.java (modified) (3 diffs)

trunk/org.bridgedb.rdb/src/org/bridgedb/rdb/GdbProvider.java

@@ -56 +56 @@
                         organism2gdb.put(organism, l = new IDMapperStack());
                         l.setTransitive(transitive);
+                        for (IDMapper globalGdb : globalGdbs)
+                        {
+                                l.addIDMapper(globalGdb);
+                        }
                 }
                 l.addIDMapper(gdb);
@@ -68 +72 @@
         
         public void addGlobalGdb(IDMapper gdb) {
-                if(!globalGdbs.contains(gdb)) globalGdbs.add(gdb);
+                if(!globalGdbs.contains(gdb)) 
+                {
+                        globalGdbs.add(gdb);
+                        for (Organism org : organism2gdb.keySet())
+                        {
+                                organism2gdb.get(org).addIDMapper(gdb);
+                        }
+                }
         }
         
         public void removeGlobalGdb(IDMapper gdb) {
-                globalGdbs.remove(gdb);
+                if (globalGdbs.contains(gdb))
+                {
+                        globalGdbs.remove(gdb);
+                        for (Organism org : organism2gdb.keySet())
+                        {
+                                organism2gdb.get(org).removeIDMapper(gdb);
+                        }
+                }
         }
         
@@ -86 +104 @@
                         gdbs = new IDMapperStack();
                         gdbs.setTransitive(transitive);
-                }
-                for (IDMapper globalGdb : globalGdbs)
-                {
-                        gdbs.addIDMapper(globalGdb);
+                        for (IDMapper globalGdb : globalGdbs)
+                        {
+                                gdbs.addIDMapper(globalGdb);
+                        }
                 }
                 return gdbs;
@@ -97 +115 @@
         
         private final boolean transitive;
-        GdbProvider() { this(false); }
-        GdbProvider(boolean transitive)
+        public GdbProvider() { this(false); }
+        public GdbProvider(boolean transitive)
         {
                 this.transitive = transitive;

trunk/org.bridgedb/src/org/bridgedb/IDMapperStack.java

@@ -17 +17 @@
 package org.bridgedb;
 
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -26 +25 @@
 import java.util.Map;
 import java.util.Set;
+import java.util.concurrent.CopyOnWriteArrayList;
 
 /**
@@ -42 +42 @@
 public class IDMapperStack implements IDMapper, AttributeMapper
 {
-        private List<IDMapper> gdbs = new ArrayList<IDMapper>();
+        private List<IDMapper> gdbs = new CopyOnWriteArrayList<IDMapper>();
 
         /**