JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

[jalview.git] / src / jalview / renderer / AnnotationRenderer.java

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index ad1fa4a..65631e3 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -229,7 +229,7 @@ public class AnnotationRenderer
           int iconOffset, int startRes, int column, boolean validRes,
           boolean validEnd)
   {
-    // System.out.println(nonCanColor);
+    // jalview.bin.Console.outPrintln(nonCanColor);
 
     g.setColor(nonCanColor);
     int sCol = (lastSSX / charWidth)
@@ -245,7 +245,7 @@ public class AnnotationRenderer
     boolean diffdownstream = !validRes || !validEnd
             || row_annotations[column] == null
             || !dc.equals(row_annotations[column].displayCharacter);
-    // System.out.println("Column "+column+" diff up: "+diffupstream+"
+    // jalview.bin.Console.outPrintln("Column "+column+" diff up: "+diffupstream+"
     // down:"+diffdownstream);
     // If a closing base pair half of the stem, display a backward arrow
     if (column > 0 && Rna.isClosingParenthesis(dc))
@@ -784,7 +784,7 @@ public class AnnotationRenderer
               {
 
                 // int nb_annot = x - temp;
-                // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre
+                // jalview.bin.Console.outPrintln("\t type :"+lastSS+"\t x :"+x+"\t nbre
                 // annot :"+nb_annot);
                 switch (lastSS)
                 {
@@ -1006,7 +1006,7 @@ public class AnnotationRenderer
           case 'y':
           case 'Z':
           case 'z':
-            // System.out.println(lastSS);
+            // jalview.bin.Console.outPrintln(lastSS);
             Color nonCanColor = getNotCanonicalColor(lastSS);
             drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
                     x, y, iconOffset, startRes, column, validRes, validEnd);
@@ -1091,7 +1091,7 @@ public class AnnotationRenderer
               }
               else
               {
-                System.err.println(
+                jalview.bin.Console.errPrintln(
                         "rendered with " + renderer.getClass().toString());
               }
             }
@@ -1122,17 +1122,17 @@ public class AnnotationRenderer
       {
         if (clipst)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Start clip at : " + yfrom + " (index " + f_i + ")");
         }
         if (clipend)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "End clip at : " + yto + " (index " + f_to + ")");
         }
       }
       ;
-      System.err.println("Annotation Rendering time:"
+      jalview.bin.Console.errPrintln("Annotation Rendering time:"
               + (System.currentTimeMillis() - stime));
     }
     ;
@@ -1455,7 +1455,7 @@ public class AnnotationRenderer
           // lm is not necessary - we can just use fm - could be off by no more
           // than 0.5 px
           // LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
-          // System.out.println(asc + " " + dec + " " + (asc - lm.getAscent())
+          // jalview.bin.Console.outPrintln(asc + " " + dec + " " + (asc - lm.getAscent())
           // + " " + (dec - lm.getDescent()));
 
           double asc = fm.getAscent();
@@ -1749,7 +1749,7 @@ public class AnnotationRenderer
       return new Color(0, 80, 255);
 
     default:
-      System.out.println("This is not a interaction : " + lastss);
+      jalview.bin.Console.outPrintln("This is not a interaction : " + lastss);
       return null;
 
     }