Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / src / jalview / io / vamsas / Dbref.java

diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index bdef00f..e9f44d0 100644 (file)
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -20,6 +20,7 @@
  */
 package jalview.io.vamsas;
 
+import jalview.bin.Console;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.VamsasAppDatastore;
@@ -92,7 +93,7 @@ public class Dbref extends Rangetype
     }
     else
     {
-      jalview.bin.Cache.log.debug(
+      Console.debug(
               "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
     }
 
@@ -158,9 +159,8 @@ public class Dbref extends Rangetype
       // TODO: Jalview ignores all the other maps
       if (vobj.getMapCount() > 1)
       {
-        jalview.bin.Cache.log
-                .debug("Ignoring additional mappings on DbRef: "
-                        + jvobj.getSource() + ":" + jvobj.getAccessionId());
+        Console.debug("Ignoring additional mappings on DbRef: "
+                + jvobj.getSource() + ":" + jvobj.getAccessionId());
       }
       jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
               parsemapType(vobj.getMap(0)));
@@ -175,9 +175,8 @@ public class Dbref extends Rangetype
   {
     DbRef vobj = (DbRef) this.vobj;
     DBRefEntry jvobj = (DBRefEntry) this.jvobj;
-    jalview.bin.Cache.log
-            .debug("Conflict in dbentry update for " + vobj.getAccessionId()
-                    + vobj.getSource() + " " + vobj.getVorbaId());
+    Console.debug("Conflict in dbentry update for " + vobj.getAccessionId()
+            + vobj.getSource() + " " + vobj.getVorbaId());
     // TODO Auto-generated method stub
 
   }
@@ -195,9 +194,8 @@ public class Dbref extends Rangetype
       // TODO: Jalview ignores all the other maps
       if (vobj.getMapCount() > 1)
       {
-        jalview.bin.Cache.log
-                .debug("Ignoring additional mappings on DbRef: "
-                        + jvobj.getSource() + ":" + jvobj.getAccessionId());
+        Console.debug("Ignoring additional mappings on DbRef: "
+                + jvobj.getSource() + ":" + jvobj.getAccessionId());
       }
       jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
               parsemapType(vobj.getMap(0)));
@@ -230,7 +228,7 @@ public class Dbref extends Rangetype
       }
       else
       {
-        jalview.bin.Cache.log.debug(
+        Console.debug(
                 "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
       }
     }