JAL-674 futzing with bugs

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 6553e26..009b9e8 100644 (file)
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -157,7 +157,7 @@ public class PDBFileWithJmol extends AlignFile implements
                 {
                   char newseq[] = new char[len];
                   System.arraycopy(seq, 0, newseq, 0, len);
-                  Annotation asecstr[] = new Annotation[len];
+                  Annotation asecstr[] = new Annotation[len+firstrnum-1];
                   for (int p = 0; p < len; p++)
                   {
                     if (secstr[p] >= 'A' && secstr[p] <= 'z')
@@ -181,8 +181,13 @@ public class PDBFileWithJmol extends AlignFile implements
                     AlignmentAnnotation ann = new AlignmentAnnotation(
                             "Secondary Structure",
                             "Secondary Structure from PDB File", asecstr);
+                    ann.belowAlignment=true;
+                    ann.visible=true;
+                    ann.autoCalculated=false;
                     ann.setCalcId(getClass().getName());
                     sq.addAlignmentAnnotation(ann);
+                    ann.adjustForAlignment();
+                    ann.validateRangeAndDisplay();
                     annotations.add(ann);
                   }
                 }