X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=be5133fe64b05d4630ae79131b3b5751bc98d3aa;hb=98a277d5e5bd7a034b2acbc4d28544210ada392e;hp=1158c53bb37dec432977f5bf1182587fe9d9ae3b;hpb=80b889f0cca49103e1b20ed806755a0719789906;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 1158c53..be5133f 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -547,7 +547,8 @@ public class AlignmentUtils
       if (translated == null || !(aaRes == translated.charAt(0)))
       {
         // debug
-        // System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
+        // jalview.bin.Console.outPrintln(("Mismatch at " + i + "/" + aaResidue
+        // + ": "
         // + codon + "(" + translated + ") != " + aaRes));
         return false;
       }
@@ -698,7 +699,8 @@ public class AlignmentUtils
          * unmapped position; treat like a gap
          */
         sourceGapMappedLength += ratio;
-        // System.err.println("Can't align: no codon mapping to residue "
+        // jalview.bin.Console.errPrintln("Can't align: no codon mapping to
+        // residue "
         // + sourceDsPos + "(" + sourceChar + ")");
         // return;
         continue;
@@ -883,7 +885,8 @@ public class AlignmentUtils
   {
     if (protein.isNucleotide() || !dna.isNucleotide())
     {
-      System.err.println("Wrong alignment type in alignProteinAsDna");
+      jalview.bin.Console
+              .errPrintln("Wrong alignment type in alignProteinAsDna");
       return 0;
     }
     List<SequenceI> unmappedProtein = new ArrayList<>();
@@ -908,7 +911,8 @@ public class AlignmentUtils
   {
     if (protein.isNucleotide() || !dna.isNucleotide())
     {
-      System.err.println("Wrong alignment type in alignProteinAsDna");
+      jalview.bin.Console
+              .errPrintln("Wrong alignment type in alignProteinAsDna");
       return 0;
     }
     // todo: implement this
@@ -988,7 +992,7 @@ public class AlignmentUtils
                           .getLength() == mappedFromLength - 1);
           if (cdsLength != mappedToLength && !addStopCodon)
           {
-            System.err.println(String.format(
+            jalview.bin.Console.errPrintln(String.format(
                     "Can't align cds as protein (length mismatch %d/%d): %s",
                     cdsLength, mappedToLength, cdsSeq.getName()));
           }
@@ -1162,7 +1166,7 @@ public class AlignmentUtils
         AlignedCodon codon = sequenceCodon.getValue();
         if (codon.peptideCol > 1)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Problem mapping protein with >1 unmapped start positions: "
                           + seq.getName());
         }
@@ -1512,7 +1516,9 @@ public class AlignmentUtils
    * @param alignment
    *          the alignment to add them to
    * @param selectionGroup
-   *          current selection group (or null if none)
+   *          current selection group - may be null, if provided then any added
+   *          annotation will be trimmed to just those columns in the selection
+   *          group
    */
   public static void addReferenceAnnotations(
           Map<SequenceI, List<AlignmentAnnotation>> annotations,
@@ -1536,7 +1542,9 @@ public class AlignmentUtils
    * @param seq
    * @param ann
    * @param selectionGroup
-   *          - may be null
+   *          current selection group - may be null, if provided then any added
+   *          annotation will be trimmed to just those columns in the selection
+   *          group
    * @return annotation added to {@code seq and {@code alignment}
    */
   public static AlignmentAnnotation addReferenceAnnotationTo(
@@ -2770,8 +2778,8 @@ public class AlignmentUtils
                 fromRange[i + 1]);
         if (range == null)
         {
-          System.err.println("Error in mapping " + seqMap + " from "
-                  + fromSeq.getName());
+          jalview.bin.Console.errPrintln("Error in mapping " + seqMap
+                  + " from " + fromSeq.getName());
           return false;
         }
         int fromCol = fromSeq.findIndex(fromRange[i]);