X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencemapping.java;h=3183bf6dfe24c2121249855a946c23872bc6657d;hb=a9177efb4097815d9a8031aa22700c61a7d6260a;hp=3c2aa4c9dbc5957c977b7d269b95f3e13eff3d63;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;p=jalview.git

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 3c2aa4c..3183bf6 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -20,7 +20,7 @@
  */
 package jalview.io.vamsas;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -100,13 +100,13 @@ public class Sequencemapping extends Rangetype
     }
     if (from != null && sequenceMapping.getLoc() != from)
     {
-      Cache.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)
     {
-      Cache.warn("Probable IMPLEMENTATION ERROR: " + ds
+      Console.warn("Probable IMPLEMENTATION ERROR: " + ds
               + " doesn't match the parent of the bound sequence mapping object.");
     }
   }
@@ -139,7 +139,7 @@ public class Sequencemapping extends Rangetype
 
   private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
   {
-    System.err.println("Conflict in update of sequenceMapping "
+    jalview.bin.Console.errPrintln("Conflict in update of sequenceMapping "
             + sequenceMapping.getVorbaId());
   }
 
@@ -154,7 +154,7 @@ public class Sequencemapping extends Rangetype
     SequenceType to = (SequenceType) getjv2vObj(jvto);
     if (to == null)
     {
-      Cache.warn(
+      Console.warn(
               "FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
       return;
     }
@@ -185,7 +185,7 @@ public class Sequencemapping extends Rangetype
 
     if (!dnaToProt)
     {
-      Cache.warn(
+      Console.warn(
               "Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
       return;
     }
@@ -225,27 +225,26 @@ public class Sequencemapping extends Rangetype
     // mapping
     bindjvvobj(mjvmapping.getMap(), sequenceMapping);
 
-    Cache.debug(
+    Console.debug(
             "Successfully created mapping " + sequenceMapping.getVorbaId());
   }
 
   // private void update(jalview.util.MapList mjvmapping,
   // SequenceMapping sequenceMapping)
   {
-    Cache.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)
   {
-    Cache.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)
   {
-    Cache.error(
-            "Not implemented: Jalview Update Sequence DBRef Mapping");
+    Console.error("Not implemented: Jalview Update Sequence DBRef Mapping");
   }
 
   /**
@@ -281,7 +280,7 @@ public class Sequencemapping extends Rangetype
     }
     if (sdloc == null || sdmap == null)
     {
-      Cache.info("Ignoring non sequence-sequence mapping");
+      Console.info("Ignoring non sequence-sequence mapping");
       return;
     }
     mobj = this.getvObj2jv(sdloc);
@@ -297,7 +296,7 @@ public class Sequencemapping extends Rangetype
     if (from == null || to == null)
     {
 
-      Cache.error(
+      Console.error(
               "Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
       return;
     }
@@ -388,30 +387,30 @@ public class Sequencemapping extends Rangetype
   {
     if (from.getDBRefs() == null && to.getDBRefs() == null)
     {
-      if (Cache.isDebugEnabled())
+      if (Console.isDebugEnabled())
       {
-        Cache.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 (Cache.isDebugEnabled())
+    if (Console.isDebugEnabled())
     {
-      Cache.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++)