JAL-4366 avoid corrupting map when no complete mapping available for chain to sequence

[jalview.git] / src / jalview / io / gff / GffHelperBase.java

diff --git a/src/jalview/io/gff/GffHelperBase.java b/src/jalview/io/gff/GffHelperBase.java
index 3db1755..0097343 100644 (file)
--- a/src/jalview/io/gff/GffHelperBase.java
+++ b/src/jalview/io/gff/GffHelperBase.java
@@ -114,8 +114,9 @@ public abstract class GffHelperBase implements GffHelperI
      */
     if (!trimMapping(from, to, fromRatio, toRatio))
     {
-      System.err.println("Ignoring mapping from " + Arrays.toString(from)
-              + " to " + Arrays.toString(to) + " as counts don't match!");
+      jalview.bin.Console.errPrintln(
+              "Ignoring mapping from " + Arrays.toString(from) + " to "
+                      + Arrays.toString(to) + " as counts don't match!");
       return null;
     }
 
@@ -166,7 +167,7 @@ public abstract class GffHelperBase implements GffHelperI
       {
         from[1] += fromOverlap / toRatio;
       }
-      System.err.println(Arrays.toString(from));
+      jalview.bin.Console.errPrintln(Arrays.toString(from));
       return true;
     }
     else if (fromOverlap < 0 && fromOverlap % fromRatio == 0)
@@ -185,7 +186,7 @@ public abstract class GffHelperBase implements GffHelperI
       {
         to[1] += fromOverlap / fromRatio;
       }
-      System.err.println(Arrays.toString(to));
+      jalview.bin.Console.errPrintln(Arrays.toString(to));
       return true;
     }
 
@@ -381,7 +382,8 @@ public abstract class GffHelperBase implements GffHelperI
    * @return
    */
   protected SequenceFeature buildSequenceFeature(String[] gff,
-          int typeColumn, String group, Map<String, List<String>> attributes)
+          int typeColumn, String group,
+          Map<String, List<String>> attributes)
   {
     try
     {
@@ -443,7 +445,8 @@ public abstract class GffHelperBase implements GffHelperI
       return sf;
     } catch (NumberFormatException nfe)
     {
-      System.err.println("Invalid number in gff: " + nfe.getMessage());
+      jalview.bin.Console
+              .errPrintln("Invalid number in gff: " + nfe.getMessage());
       return null;
     }
   }
@@ -503,7 +506,7 @@ public abstract class GffHelperBase implements GffHelperI
 
     if (!valid)
     {
-      System.err.println(INVALID_GFF_ATTRIBUTE_FORMAT + s);
+      jalview.bin.Console.errPrintln(INVALID_GFF_ATTRIBUTE_FORMAT + s);
       return map;
     }
 
@@ -525,7 +528,7 @@ public abstract class GffHelperBase implements GffHelperI
       theKey = theKey.trim();
       if (theKey.isEmpty())
       {
-        System.err.println(INVALID_GFF_ATTRIBUTE_FORMAT + s);
+        jalview.bin.Console.errPrintln(INVALID_GFF_ATTRIBUTE_FORMAT + s);
         map.clear();
         return map;
       }