Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / datamodel / features / FeatureMatcher.java

diff --git a/src/jalview/datamodel/features/FeatureMatcher.java b/src/jalview/datamodel/features/FeatureMatcher.java
index e9fb9b2..124909c 100644 (file)
--- a/src/jalview/datamodel/features/FeatureMatcher.java
+++ b/src/jalview/datamodel/features/FeatureMatcher.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel.features;
 
+import java.util.Locale;
+
 import jalview.datamodel.SequenceFeature;
 import jalview.util.MessageManager;
 import jalview.util.matcher.Condition;
@@ -145,7 +147,7 @@ public class FeatureMatcher implements FeatureMatcherI
       int nextQuotePos = descriptor.indexOf(QUOTE, 1);
       if (nextQuotePos == -1)
       {
-        System.err.println(invalidFormat);
+        jalview.bin.Console.errPrintln(invalidFormat);
         return null;
       }
       firstField = descriptor.substring(1, nextQuotePos);
@@ -157,18 +159,18 @@ public class FeatureMatcher implements FeatureMatcherI
       int nextSpacePos = descriptor.indexOf(SPACE);
       if (nextSpacePos == -1)
       {
-        System.err.println(invalidFormat);
+        jalview.bin.Console.errPrintln(invalidFormat);
         return null;
       }
       firstField = descriptor.substring(0, nextSpacePos);
       leftToParse = descriptor.substring(nextSpacePos + 1).trim();
     }
-    String lower = firstField.toLowerCase();
-    if (lower.startsWith(LABEL.toLowerCase()))
+    String lower = firstField.toLowerCase(Locale.ROOT);
+    if (lower.startsWith(LABEL.toLowerCase(Locale.ROOT)))
     {
       byLabel = true;
     }
-    else if (lower.startsWith(SCORE.toLowerCase()))
+    else if (lower.startsWith(SCORE.toLowerCase(Locale.ROOT)))
     {
       byScore = true;
     }
@@ -191,7 +193,7 @@ public class FeatureMatcher implements FeatureMatcherI
       cond = Condition.fromString(leftToParse);
       if (cond == null || cond.needsAPattern())
       {
-        System.err.println(invalidFormat);
+        jalview.bin.Console.errPrintln(invalidFormat);
         return null;
       }
     }
@@ -212,7 +214,7 @@ public class FeatureMatcher implements FeatureMatcherI
         else
         {
           // unbalanced quote
-          System.err.println(invalidFormat);
+          jalview.bin.Console.errPrintln(invalidFormat);
           return null;
         }
       }
@@ -308,6 +310,7 @@ public class FeatureMatcher implements FeatureMatcherI
     byLabel = forLabel;
     byScore = forScore;
   }
+
   @Override
   public boolean matches(SequenceFeature feature)
   {
@@ -330,8 +333,8 @@ public class FeatureMatcher implements FeatureMatcherI
   }
 
   /**
-   * Answers a string description of this matcher, suitable for display, debugging
-   * or logging. The format may change in future.
+   * Answers a string description of this matcher, suitable for display,
+   * debugging or logging. The format may change in future.
    */
   @Override
   public String toString()
@@ -351,7 +354,7 @@ public class FeatureMatcher implements FeatureMatcherI
     }
 
     Condition condition = matcher.getCondition();
-    sb.append(SPACE).append(condition.toString().toLowerCase());
+    sb.append(SPACE).append(condition.toString().toLowerCase(Locale.ROOT));
     if (condition.isNumeric())
     {
       sb.append(SPACE).append(matcher.getPattern());
@@ -413,7 +416,7 @@ public class FeatureMatcher implements FeatureMatcherI
         sb.append(displayName);
       }
     }
-  
+
     Condition condition = matcher.getCondition();
     sb.append(SPACE).append(condition.getStableName());
     String pattern = matcher.getPattern();
@@ -431,7 +434,7 @@ public class FeatureMatcher implements FeatureMatcherI
         sb.append(SPACE).append(pattern);
       }
     }
-  
+
     return sb.toString();
   }
 }