JAL-3594 New Jalview Test logos and .icns/.ico creation helper script

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 64b3a9c..9b6741b 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -20,6 +20,8 @@
  */
 package jalview.project;
 
+import java.util.Locale;
+
 import static jalview.math.RotatableMatrix.Axis.X;
 import static jalview.math.RotatableMatrix.Axis.Y;
 import static jalview.math.RotatableMatrix.Axis.Z;
@@ -2076,8 +2078,8 @@ public class Jalview2XML
       final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
       final String pdbId = pdbentry.getId();
       if (!pdbId.equals(entry.getId())
-              && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
-                      .startsWith(pdbId.toLowerCase())))
+              && !(entry.getId().length() > 4 && entry.getId().toLowerCase(Locale.ROOT)
+                      .startsWith(pdbId.toLowerCase(Locale.ROOT))))
       {
         /*
          * not interested in a binding to a different PDB entry here
@@ -2529,6 +2531,7 @@ public class Jalview2XML
         dbref.setSource(ref.getSource());
         dbref.setVersion(ref.getVersion());
         dbref.setAccessionId(ref.getAccessionId());
+        dbref.setCanonical(ref.isCanonical());
         if (ref instanceof GeneLocus)
         {
           dbref.setLocus(true);
@@ -2644,7 +2647,7 @@ public class Jalview2XML
         for (int i = 0; i < colours.length; i++)
         {
           Colour col = new Colour();
-          col.setName(ResidueProperties.aa[i].toLowerCase());
+          col.setName(ResidueProperties.aa[i].toLowerCase(Locale.ROOT));
           col.setRGB(jalview.util.Format.getHexString(colours[i]));
           // jbucs.addColour(col);
           jbucs.getColour().add(col);
@@ -5622,6 +5625,7 @@ public class Jalview2XML
       {
         entry.setMap(addMapping(dr.getMapping()));
       }
+      entry.setCanonical(dr.isCanonical());
       datasetSequence.addDBRef(entry);
     }
   }