JAL-1569 interactive editing of secondary structure char for RNA secondary structure

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a19e1db..b608b95 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1419,7 +1419,16 @@ public class Jalview2XML
         calcIdSet.add(aa[i].getCalcId());
         an.setCalcId(aa[i].getCalcId());
       }
-
+      if (aa[i].hasProperties())
+      {
+        for (String pr : aa[i].getProperties())
+        {
+          Property prop = new Property();
+          prop.setName(pr);
+          prop.setValue(aa[i].getProperty(pr));
+          an.addProperty(prop);
+        }
+      }
       AnnotationElement ae;
       if (aa[i].annotations != null)
       {
@@ -2367,7 +2376,9 @@ public class Jalview2XML
                 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
               }
             }
-
+            StructureSelectionManager.getStructureSelectionManager(
+                    Desktop.instance)
+                    .registerPDBEntry(entry);
             al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
           }
         }
@@ -2629,6 +2640,14 @@ public class Jalview2XML
           jaa.belowAlignment = an[i].isBelowAlignment();
         }
         jaa.setCalcId(an[i].getCalcId());
+        if (an[i].getPropertyCount() > 0)
+        {
+          for (jalview.schemabinding.version2.Property prop : an[i]
+                  .getProperty())
+          {
+            jaa.setProperty(prop.getName(), prop.getValue());
+          }
+        }
         if (jaa.autoCalculated)
         {
           autoAlan.add(new JvAnnotRow(i, jaa));