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

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 6ab49b2..f470dc6 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -547,7 +547,7 @@ 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 +698,7 @@ 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 +883,7 @@ 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 +908,7 @@ 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 +988,7 @@ 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 +1162,7 @@ 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());
         }
@@ -2770,7 +2770,7 @@ public class AlignmentUtils
                 fromRange[i + 1]);
         if (range == null)
         {
-          System.err.println("Error in mapping " + seqMap + " from "
+          jalview.bin.Console.errPrintln("Error in mapping " + seqMap + " from "
                   + fromSeq.getName());
           return false;
         }