Merge branch 'develop' into improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews

[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index de98c64..7e6b904 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -126,7 +126,7 @@ public class AlignmentAnnotation
       invalidrnastruc = -1;
     } catch (WUSSParseException px)
     {
-      // DEBUG System.out.println(px);
+      // DEBUG jalview.bin.Console.outPrintln(px);
       invalidrnastruc = px.getProblemPos();
     }
     if (invalidrnastruc > -1)
@@ -142,7 +142,7 @@ public class AlignmentAnnotation
       scaleColLabel = true;
       _markRnaHelices();
     }
-    // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+    // jalview.bin.Console.outPrintln("featuregroup " + _rnasecstr[0].getFeatureGroup());
 
   }
 
@@ -156,10 +156,10 @@ public class AlignmentAnnotation
     {
 
       /*
-       * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+       * jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" +
        * this.annotation._rnasecstr[x].getBegin());
        */
-      // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+      // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup());
       int val = 0;
       try
       {
@@ -386,7 +386,7 @@ public class AlignmentAnnotation
     char firstChar = 0;
     for (int i = 0; i < annotations.length; i++)
     {
-      // DEBUG System.out.println(i + ": " + annotations[i]);
+      // DEBUG jalview.bin.Console.outPrintln(i + ": " + annotations[i]);
       if (annotations[i] == null)
       {
         continue;
@@ -394,14 +394,14 @@ public class AlignmentAnnotation
       if (annotations[i].secondaryStructure == 'H'
               || annotations[i].secondaryStructure == 'E')
       {
-        // DEBUG System.out.println( "/H|E/ '" +
+        // DEBUG jalview.bin.Console.outPrintln( "/H|E/ '" +
         // annotations[i].secondaryStructure + "'");
         hasIcons |= true;
       }
       else
       // Check for RNA secondary structure
       {
-        // DEBUG System.out.println( "/else/ '" +
+        // DEBUG jalview.bin.Console.outPrintln( "/else/ '" +
         // annotations[i].secondaryStructure + "'");
         // TODO: 2.8.2 should this ss symbol validation check be a function in
         // RNA/ResidueProperties ?
@@ -446,7 +446,7 @@ public class AlignmentAnnotation
         }
       }
 
-      // System.out.println("displaychar " + annotations[i].displayCharacter);
+      // jalview.bin.Console.outPrintln("displaychar " + annotations[i].displayCharacter);
 
       if (annotations[i].displayCharacter == null
               || annotations[i].displayCharacter.length() == 0)