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

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

diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java
index 6e93f45..e6302fc 100644 (file)
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -20,13 +20,14 @@
  */
 package jalview.io.vamsas;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.VamsasAppDatastore;
 import jalview.util.UrlLink;
 
 import java.util.Enumeration;
+import java.util.Iterator;
 import java.util.Vector;
 
 import uk.ac.vamsas.objects.core.DataSetAnnotations;
@@ -71,6 +72,7 @@ public class Sequencefeature extends Rangetype
     doJvUpdate();
   }
 
+  @Override
   public void addToDocument()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -89,15 +91,14 @@ public class Sequencefeature extends Rangetype
     dataset.addDataSetAnnotations(dsa);
   }
 
+  @Override
   public void addFromDocument()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
     if (dsa.getSeqRefCount() != 1)
     {
-      Cache.log
-              .warn("Not binding "
-                      + dsa.getVorbaId()
-                      + " to Sequence Feature - has multiple dataset sequence references.");
+      Console.warn("Not binding " + dsa.getVorbaId()
+              + " to Sequence Feature - has multiple dataset sequence references.");
       return;
     }
     jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
@@ -106,6 +107,7 @@ public class Sequencefeature extends Rangetype
     bindjvvobj(sf, dsa);
   }
 
+  @Override
   public void conflict()
   {
     log.warn("Untested sequencefeature conflict code");
@@ -118,6 +120,7 @@ public class Sequencefeature extends Rangetype
     addToDocument(); // and create a new feature in the document
   }
 
+  @Override
   public void updateToDoc()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -125,8 +128,8 @@ public class Sequencefeature extends Rangetype
     if (dsa.getSeqRefCount() != 1)
     {
       replaceJvObjMapping(feature, null);
-      Cache.log
-              .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
+      Console.warn(
+              "Binding of annotation to jalview feature has changed. Removing binding and recreating.");
       doSync(); // re-verify bindings.
     }
     else
@@ -136,14 +139,14 @@ public class Sequencefeature extends Rangetype
       getDSAnnotationFromJalview(dsa, feature);
       if (oldref != dsa.hashCode())
       {
-        Cache.log
-                .debug("Updated dataset sequence annotation from feature.");
+        Console.debug("Updated dataset sequence annotation from feature.");
         addProvenance(dsa.getProvenance(), "modified");
       }
     }
 
   }
 
+  @Override
   public void updateFromDoc()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -152,10 +155,8 @@ public class Sequencefeature extends Rangetype
     {
       // conflicting update from document - we cannot map this feature anymore.
       replaceJvObjMapping(feature, null);
-      Cache.log
-              .warn("annotation ("
-                      + dsa.getVorbaId()
-                      + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
+      Console.warn("annotation (" + dsa.getVorbaId()
+              + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
       // - consider deleting the feature ?
       dsSeq.deleteFeature(feature);
       // doSync();
@@ -196,8 +197,8 @@ public class Sequencefeature extends Rangetype
     vSeg.setInclusive(true);
     if (dsa.getSegCount() > 1)
     {
-      Cache.log
-              .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
+      Console.debug(
+              "About to destroy complex annotation in vamsas document mapped to sequence feature ("
                       + dsa.getVorbaId() + ")");
     }
     dsa.setSeg(new Seg[] { vSeg });
@@ -229,11 +230,11 @@ public class Sequencefeature extends Rangetype
     }
     if (feature.otherDetails != null)
     {
-      Enumeration iter = feature.otherDetails.keys();
+      Iterator<String> iter = feature.otherDetails.keySet().iterator();
       Vector props = dsa.getPropertyAsReference();
-      while (iter.hasMoreElements())
+      while (iter.hasNext())
       {
-        String key = (String) iter.nextElement();
+        String key = iter.next();
         if (!key.equalsIgnoreCase("score")
                 && !key.equalsIgnoreCase("status"))
         {
@@ -250,7 +251,8 @@ public class Sequencefeature extends Rangetype
           else if (vlu instanceof Integer)
           {
             valid = true;
-            nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
+            nprop.setType(
+                    uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
           }
           else if (vlu instanceof Float)
           {
@@ -278,9 +280,39 @@ public class Sequencefeature extends Rangetype
   private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
   {
     int[] se = getBounds(dseta);
-    SequenceFeature sf = new jalview.datamodel.SequenceFeature(
-            dseta.getType(), dseta.getDescription(), dseta.getStatus(),
-            se[0], se[1], dseta.getGroup());
+
+    /*
+     * try to identify feature score
+     */
+    boolean scoreFound = false;
+    float theScore = 0f;
+    String featureType = dseta.getType();
+    if (dseta.getScoreCount() > 0)
+    {
+      Enumeration scr = dseta.enumerateScore();
+      while (scr.hasMoreElements())
+      {
+        Score score = (Score) scr.nextElement();
+        if (score.getName().equals(featureType))
+        {
+          theScore = score.getContent();
+          scoreFound = true;
+        }
+      }
+    }
+
+    SequenceFeature sf = null;
+    if (scoreFound)
+    {
+      sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
+              se[1], theScore, dseta.getGroup());
+    }
+    else
+    {
+      sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
+              se[1], dseta.getGroup());
+    }
+    sf.setStatus(dseta.getStatus());
     if (dseta.getLinkCount() > 0)
     {
       Link[] links = dseta.getLink();
@@ -296,11 +328,7 @@ public class Sequencefeature extends Rangetype
       while (scr.hasMoreElements())
       {
         Score score = (Score) scr.nextElement();
-        if (score.getName().equals(sf.getType()))
-        {
-          sf.setScore(score.getContent());
-        }
-        else
+        if (!score.getName().equals(sf.getType()))
         {
           sf.setValue(score.getName(), "" + score.getContent());
         }
@@ -322,7 +350,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Boolean(p.getContent());
+            val = Boolean.valueOf(p.getContent());
           } catch (Exception e)
           {
           }
@@ -331,7 +359,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Float(p.getContent());
+            val = Float.valueOf(p.getContent());
 
           } catch (Exception e)
           {
@@ -341,7 +369,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Integer(p.getContent());
+            val = Integer.valueOf(p.getContent());
           } catch (Exception e)
           {
           }