Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / schemes / FeatureColour.java

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index 0d36f4f..20b0796 100644 (file)
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -20,6 +20,8 @@
  */
 package jalview.schemes;
 
+import java.util.Locale;
+
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.features.FeatureMatcher;
@@ -46,8 +48,9 @@ import java.util.StringTokenizer;
  * <li>the range may be the full value range, or may be limited by the threshold
  * value</li>
  * </ul>
- * <li>colour by (text) value of a named attribute</li> <li>graduated colour by
- * (numeric) value of a named attribute</li> </ul>
+ * <li>colour by (text) value of a named attribute</li>
+ * <li>graduated colour by (numeric) value of a named attribute</li>
+ * </ul>
  */
 public class FeatureColour implements FeatureColourI
 {
@@ -194,19 +197,19 @@ public class FeatureColour implements FeatureColourI
               "Expected either 'label' or a colour specification in the line: "
                       + descriptor);
     }
-    if (nextToken.toLowerCase().startsWith(LABEL))
+    if (nextToken.toLowerCase(Locale.ROOT).startsWith(LABEL))
     {
       byLabel = true;
       // get the token after the next delimiter:
       mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
       mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
     }
-    else if (nextToken.toLowerCase().startsWith(SCORE))
+    else if (nextToken.toLowerCase(Locale.ROOT).startsWith(SCORE))
     {
       mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
       mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
     }
-    else if (nextToken.toLowerCase().startsWith(ATTRIBUTE))
+    else if (nextToken.toLowerCase(Locale.ROOT).startsWith(ATTRIBUTE))
     {
       byAttribute = true;
       attName = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
@@ -304,7 +307,7 @@ public class FeatureColour implements FeatureColourI
       }
 
       gcol.nextToken(); // skip next '|'
-      if (tok.toLowerCase().startsWith(ABSOLUTE))
+      if (tok.toLowerCase(Locale.ROOT).startsWith(ABSOLUTE))
       {
         minval = gcol.nextToken();
         gcol.nextToken(); // skip next '|'
@@ -380,19 +383,19 @@ public class FeatureColour implements FeatureColourI
       {
         // threshold type and possibly a threshold value
         ttype = gcol.nextToken();
-        if (ttype.toLowerCase().startsWith(BELOW))
+        if (ttype.toLowerCase(Locale.ROOT).startsWith(BELOW))
         {
           featureColour.setBelowThreshold(true);
         }
-        else if (ttype.toLowerCase().startsWith(ABOVE))
+        else if (ttype.toLowerCase(Locale.ROOT).startsWith(ABOVE))
         {
           featureColour.setAboveThreshold(true);
         }
         else
         {
-          if (!ttype.toLowerCase().startsWith("no"))
+          if (!ttype.toLowerCase(Locale.ROOT).startsWith("no"))
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "Ignoring unrecognised threshold type : " + ttype);
           }
         }
@@ -406,19 +409,20 @@ public class FeatureColour implements FeatureColourI
           featureColour.setThreshold(Float.valueOf(tval).floatValue());
         } catch (Exception e)
         {
-          System.err.println("Couldn't parse threshold value as a float: ("
-                  + tval + ")");
+          jalview.bin.Console
+                  .errPrintln("Couldn't parse threshold value as a float: ("
+                          + tval + ")");
         }
       }
       if (gcol.hasMoreTokens())
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Ignoring additional tokens in parameters in graduated colour specification\n");
         while (gcol.hasMoreTokens())
         {
-          System.err.println(BAR + gcol.nextToken());
+          jalview.bin.Console.errPrintln(BAR + gcol.nextToken());
         }
-        System.err.println("\n");
+        jalview.bin.Console.errPrintln("\n");
       }
       return featureColour;
     } catch (Exception e)
@@ -696,8 +700,8 @@ public class FeatureColour implements FeatureColourI
     {
       String label = attributeName == null ? feature.getDescription()
               : feature.getValueAsString(attributeName);
-      return label == null ? noColour : ColorUtils
-              .createColourFromName(label);
+      return label == null ? noColour
+              : ColorUtils.createColourFromName(label);
     }
 
     if (!isGraduatedColour())
@@ -823,7 +827,7 @@ public class FeatureColour implements FeatureColourI
         sb.append(BAR).append(Format.getHexString(getMinColour()))
                 .append(BAR);
         sb.append(Format.getHexString(getMaxColour())).append(BAR);
-        
+
         /*
          * 'no value' colour should be null, min or max colour;
          * if none of these, coerce to minColour