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

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

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 65fd110..e1d5669 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -826,7 +826,7 @@ public class AlignSeq
       }
     }
 
-    System.out.println(max + " " + min);
+    jalview.bin.Console.outPrintln(max + " " + min);
 
     for (int i = 0; i < n; i++)
     {
@@ -835,12 +835,12 @@ public class AlignSeq
         int x = psize * i;
         int y = psize * j;
 
-        // System.out.println(mat[i][j]);
+        // jalview.bin.Console.outPrintln(mat[i][j]);
         float score = (float) (mat[i][j] - min) / (float) (max - min);
         g.setColor(new Color(score, 0, 0));
         g.fillRect(x, y, psize, psize);
 
-        // System.out.println(x + " " + y + " " + score);
+        // jalview.bin.Console.outPrintln(x + " " + y + " " + score);
       }
     }
   }
@@ -890,7 +890,8 @@ public class AlignSeq
         pdbpos++;
       }
 
-      if (allowmismatch || c1 == c2)
+      // ignore case differences
+      if (allowmismatch || (c1 == c2) || (Math.abs(c2-c1)==('a'-'A')))
       {
         // extend mapping interval
         if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
@@ -982,7 +983,7 @@ public class AlignSeq
             bestm = msq;
           }
         }
-        // System.out.println("Best Score for " + (matches.size() + 1) + " :"
+        // jalview.bin.Console.outPrintln("Best Score for " + (matches.size() + 1) + " :"
         // + bestscore);
         matches.add(bestm);
         aligns.add(bestaseq);