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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 74381fd..deeb2e9 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -62,7 +62,7 @@ public class Conservation {
        }\r
      } else {\r
        // JBPNote INFO level debug\r
-       System.out.println("calcSeqNum called with out of range sequence index for Alignment\n");\r
+       System.err.println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n");\r
      }\r
    }\r
    Vector total = new Vector();\r
@@ -351,7 +351,8 @@ public void findQuality(int start, int end) {
            x[ii]  += (double)cons2[j][i2] * BLOSUM62[ii][i2]+4;\r
          }\r
        } catch (Exception e) {\r
-         System.out.println("Exception : "  + e);\r
+         System.err.println("Exception during quality calculation.");\r
+          e.printStackTrace();\r
        }\r
        //System.out.println("X " + ii + " " + x[ii]);\r
        x[ii] /= (size);\r
@@ -373,6 +374,7 @@ public void findQuality(int start, int end) {
             sr = (double)BLOSUM62[i][seqNum]+4;\r
           } catch (Exception e) {\r
             System.out.println("Exception in sr: " + e);\r
+            e.printStackTrace();\r
           }\r
           //Calculate X with another loop over residues\r
 \r