hidden region recovery in JPred and new hidden region pruning function

[jalview.git] / src / jalview / ws / JPredClient.java

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 72bef07..55e65a5 100755 (executable)
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -547,7 +547,7 @@ public class JPredClient
         else
           if (job.sequence!=null)
           {
-            job.jobId = server.predict(job.sequence);
+            job.jobId = server.predict(job.sequence); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";//
           }
 
         if (job.jobId != null)
@@ -729,7 +729,7 @@ public class JPredClient
                  throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");
                } else {
                  // test this.
-                 ((ColumnSelection) alandcolsel[1]).compensateForEdits(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));
+                 ((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));//gapMap returns insert list, interpreted as delete list by pruneDeletions
                }
              }
              af = new AlignFrame(res, (ColumnSelection) alandcolsel[1]);