Properly integrated endGaps option for AlignSeq.traceAlignment()

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

diff --git a/src/jalview/analysis/ccAnalysis.java b/src/jalview/analysis/ccAnalysis.java
index 948aa8f..5e149b8 100755 (executable)
--- a/src/jalview/analysis/ccAnalysis.java
+++ b/src/jalview/analysis/ccAnalysis.java
@@ -792,6 +792,7 @@ public class ccAnalysis
 
   /**
   * check the termination condition for nonlinear least squares
+  * TODO can be removed and added just as one line in trf (: terminationStatus = (ftolSatisfied condition || xtolSatisfied condition) ? 1 : 0;)  doesnt matter as long as distinguished between 0 and rest
   *
   * @param actualReduction
   * @param cost