Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 402ffdf..6a5ec3e 100644 (file)
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -20,6 +20,7 @@
  */
 package jalview.io.vamsas;
 
+import jalview.bin.Console;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -99,13 +100,13 @@ public class Sequencemapping extends Rangetype
     }
     if (from != null && sequenceMapping.getLoc() != from)
     {
-      jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
+      Console.warn("Probable IMPLEMENTATION ERROR: " + from
               + " doesn't match the local mapping sequence.");
     }
     if (ds != null && sequenceMapping.is__stored_in_document()
             && sequenceMapping.getV_parent() != ds)
     {
-      jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + ds
+      Console.warn("Probable IMPLEMENTATION ERROR: " + ds
               + " doesn't match the parent of the bound sequence mapping object.");
     }
   }
@@ -153,7 +154,7 @@ public class Sequencemapping extends Rangetype
     SequenceType to = (SequenceType) getjv2vObj(jvto);
     if (to == null)
     {
-      jalview.bin.Cache.log.warn(
+      Console.warn(
               "FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
       return;
     }
@@ -184,7 +185,7 @@ public class Sequencemapping extends Rangetype
 
     if (!dnaToProt)
     {
-      jalview.bin.Cache.log.warn(
+      Console.warn(
               "Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
       return;
     }
@@ -224,29 +225,26 @@ public class Sequencemapping extends Rangetype
     // mapping
     bindjvvobj(mjvmapping.getMap(), sequenceMapping);
 
-    jalview.bin.Cache.log.debug(
+    Console.debug(
             "Successfully created mapping " + sequenceMapping.getVorbaId());
   }
 
   // private void update(jalview.util.MapList mjvmapping,
   // SequenceMapping sequenceMapping)
   {
-    jalview.bin.Cache.log
-            .error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
+    Console.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
   }
 
   private void update(SequenceMapping sequenceMapping,
           jalview.datamodel.Mapping mjvmapping)
   {
-    jalview.bin.Cache.log
-            .error("Not implemented: Update DBRef Mapping from Jalview");
+    Console.error("Not implemented: Update DBRef Mapping from Jalview");
   }
 
   private void update(jalview.datamodel.Mapping mjvmapping,
           SequenceMapping sequenceMapping)
   {
-    jalview.bin.Cache.log.error(
-            "Not implemented: Jalview Update Sequence DBRef Mapping");
+    Console.error("Not implemented: Jalview Update Sequence DBRef Mapping");
   }
 
   /**
@@ -282,7 +280,7 @@ public class Sequencemapping extends Rangetype
     }
     if (sdloc == null || sdmap == null)
     {
-      jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
+      Console.info("Ignoring non sequence-sequence mapping");
       return;
     }
     mobj = this.getvObj2jv(sdloc);
@@ -298,7 +296,7 @@ public class Sequencemapping extends Rangetype
     if (from == null || to == null)
     {
 
-      jalview.bin.Cache.log.error(
+      Console.error(
               "Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
       return;
     }
@@ -389,30 +387,30 @@ public class Sequencemapping extends Rangetype
   {
     if (from.getDBRefs() == null && to.getDBRefs() == null)
     {
-      if (jalview.bin.Cache.log.isDebugEnabled())
+      if (Console.isDebugEnabled())
       {
-        jalview.bin.Cache.log.debug("Not matching conjugate refs for "
-                + from.getName() + " and " + to.getName());
+        Console.debug("Not matching conjugate refs for " + from.getName()
+                + " and " + to.getName());
       }
       return;
     }
-    if (jalview.bin.Cache.log.isDebugEnabled())
+    if (Console.isDebugEnabled())
     {
-      jalview.bin.Cache.log.debug("Matching conjugate refs for "
-              + from.getName() + " and " + to.getName());
+      Console.debug("Matching conjugate refs for " + from.getName()
+              + " and " + to.getName());
     }
     List<DBRefEntry> fdb = from.getDBRefs();
     List<DBRefEntry> tdb = new ArrayList<DBRefEntry>(to.getDBRefs());
     int tdblen = to.getDBRefs().size();
-//    
-//    
-//    YOWSER
-//    
-//    System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
-//    
-//    
-//    
-//    
+    //
+    //
+    // YOWSER
+    //
+    // System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
+    //
+    //
+    //
+    //
     Vector matched = new Vector();
     jalview.util.MapList smapI = smap.getInverse();
     for (int f = 0, fn = fdb.size(); f < fn; f++)
@@ -422,7 +420,7 @@ public class Sequencemapping extends Rangetype
       boolean fmpnnl = (fmp != null);
       // if (fmpnnl && fmp.getTo()!=null)
       // {
-      // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
+      // Cache.debug("Not overwriting existing To reference in
       // "+fe);
       // continue;
       // }