Merge branch 'develop' into update/JAL-3949_abstracted_logging_for_jalviewjs_and_sanity

[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 74f73d4..a48f8c8 100644 (file)
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -97,7 +97,7 @@ public class Sequencefeature extends Rangetype
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
     if (dsa.getSeqRefCount() != 1)
     {
-      Cache.log.warn("Not binding " + dsa.getVorbaId()
+      Cache.warn("Not binding " + dsa.getVorbaId()
               + " to Sequence Feature - has multiple dataset sequence references.");
       return;
     }
@@ -128,7 +128,7 @@ public class Sequencefeature extends Rangetype
     if (dsa.getSeqRefCount() != 1)
     {
       replaceJvObjMapping(feature, null);
-      Cache.log.warn(
+      Cache.warn(
               "Binding of annotation to jalview feature has changed. Removing binding and recreating.");
       doSync(); // re-verify bindings.
     }
@@ -139,8 +139,7 @@ public class Sequencefeature extends Rangetype
       getDSAnnotationFromJalview(dsa, feature);
       if (oldref != dsa.hashCode())
       {
-        Cache.log
-                .debug("Updated dataset sequence annotation from feature.");
+        Cache.debug("Updated dataset sequence annotation from feature.");
         addProvenance(dsa.getProvenance(), "modified");
       }
     }
@@ -156,7 +155,7 @@ public class Sequencefeature extends Rangetype
     {
       // conflicting update from document - we cannot map this feature anymore.
       replaceJvObjMapping(feature, null);
-      Cache.log.warn("annotation (" + dsa.getVorbaId()
+      Cache.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);
@@ -198,7 +197,7 @@ public class Sequencefeature extends Rangetype
     vSeg.setInclusive(true);
     if (dsa.getSegCount() > 1)
     {
-      Cache.log.debug(
+      Cache.debug(
               "About to destroy complex annotation in vamsas document mapped to sequence feature ("
                       + dsa.getVorbaId() + ")");
     }
@@ -351,7 +350,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Boolean(p.getContent());
+            val = Boolean.valueOf(p.getContent());
           } catch (Exception e)
           {
           }
@@ -360,7 +359,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Float(p.getContent());
+            val = Float.valueOf(p.getContent());
 
           } catch (Exception e)
           {
@@ -370,7 +369,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Integer(p.getContent());
+            val = Integer.valueOf(p.getContent());
           } catch (Exception e)
           {
           }