JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

[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 2bcef3a..5a172fe 100644 (file)
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -20,13 +20,17 @@
  */
 package jalview.io.vamsas;
 
+import jalview.bin.Console;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
 import jalview.gui.Desktop;
 import jalview.io.VamsasAppDatastore;
 
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Vector;
 
 import uk.ac.vamsas.objects.core.AlignmentSequence;
@@ -96,13 +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.");
     }
   }
@@ -150,7 +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;
     }
@@ -181,7 +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;
     }
@@ -221,28 +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(
+    Console.error(
             "Not implemented: Jalview Update Sequence DBRef Mapping");
   }
 
@@ -279,7 +281,7 @@ 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);
@@ -295,7 +297,7 @@ 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;
     }
@@ -386,33 +388,40 @@ 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 "
+        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 "
+      Console.debug("Matching conjugate refs for "
               + from.getName() + " and " + to.getName());
     }
-    jalview.datamodel.DBRefEntry[] fdb = from.getDBRefs();
-    jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to
-            .getDBRefs().length];
-    int tdblen = to.getDBRefs().length;
-    System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
+    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);
+//    
+//    
+//    
+//    
     Vector matched = new Vector();
     jalview.util.MapList smapI = smap.getInverse();
-    for (int f = 0; f < fdb.length; f++)
+    for (int f = 0, fn = fdb.size(); f < fn; f++)
     {
-      jalview.datamodel.DBRefEntry fe = fdb[f];
+      jalview.datamodel.DBRefEntry fe = fdb.get(f);
       jalview.datamodel.Mapping fmp = fe.getMap();
-      boolean fmpnnl = fmp != null;
+      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;
       // }
@@ -424,7 +433,7 @@ public class Sequencemapping extends Rangetype
               : false;
       for (int t = 0; t < tdblen; t++)
       {
-        jalview.datamodel.DBRefEntry te = tdb[t];
+        jalview.datamodel.DBRefEntry te = tdb.get(t);
         if (te != null)
         {
           if (fe.getSource().equals(te.getSource())