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

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d41a5be..7e0b6b4 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -935,7 +935,7 @@ public abstract class AlignmentViewport
     }
     if (calculator.workingInvolvedWith(alignmentAnnotation))
     {
-      // System.err.println("grey out ("+alignmentAnnotation.label+")");
+      // jalview.bin.Console.errPrintln("grey out ("+alignmentAnnotation.label+")");
       return true;
     }
     return false;
@@ -1208,7 +1208,7 @@ public abstract class AlignmentViewport
   {
     if (sequenceSetID != null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Warning - overwriting a sequenceSetId for a viewport!");
     }
     sequenceSetID = new String(newid);
@@ -2101,7 +2101,7 @@ public abstract class AlignmentViewport
       {
         if (aa == null)
         {
-          System.err.println("Null annotation row: ignoring.");
+          jalview.bin.Console.errPrintln("Null annotation row: ignoring.");
           continue;
         }
         if (!aa.visible)
@@ -2133,7 +2133,7 @@ public abstract class AlignmentViewport
 
         if (aa.graph > 0)
         {
-          aa.height += aa.graphHeight;
+          aa.height += aa.graphHeight+20;
         }
 
         if (aa.height == 0)
@@ -2294,7 +2294,7 @@ public abstract class AlignmentViewport
   {
     if (this == av)
     {
-      System.err.println("Ignoring recursive setCodingComplement request");
+      jalview.bin.Console.errPrintln("Ignoring recursive setCodingComplement request");
     }
     else
     {
@@ -2957,7 +2957,6 @@ public abstract class AlignmentViewport
     return alignment.getContactMatrixFor(alignmentAnnotation);
   }
 
-
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
    * row.