Set consensus as hashtble[]

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

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 72bef07..2713078 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)
@@ -720,7 +720,10 @@ public class JPredClient
           {
             AlignFrame af;
            if (input==null) {
-             af = new AlignFrame(res);
+             af = new AlignFrame(res,
+                                 AlignFrame.DEFAULT_WIDTH,
+                                 AlignFrame.DEFAULT_HEIGHT);
+
            } else {
              java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());
 
@@ -729,14 +732,16 @@ 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]);
+             af = new AlignFrame(res, (ColumnSelection) alandcolsel[1],
+                                           AlignFrame.DEFAULT_WIDTH,
+                                           AlignFrame.DEFAULT_HEIGHT);
            }
             Desktop.addInternalFrame(af, altitle,
-                                     AlignFrame.NEW_WINDOW_WIDTH,
-                                     AlignFrame.NEW_WINDOW_HEIGHT);
+                                     AlignFrame.DEFAULT_WIDTH,
+                                     AlignFrame.DEFAULT_HEIGHT);
           }
           else
           {