Set wrapped mode even if false

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 300cbd5..95912fe 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -804,6 +804,7 @@ public class Jalview2XML
 \r
     String loadPDBFile(String file, String pdbId)\r
     {\r
+      System.out.println("load file "+file);\r
       try\r
       {\r
         JarInputStream jin = null;\r
@@ -911,14 +912,17 @@ public class Jalview2XML
               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
               entry.setId(ids[p].getId());\r
               entry.setType(ids[p].getType());\r
-              if(!pdbloaded.containsKey(ids[p].getId()))\r
+              if (ids[p].getFile() != null)\r
               {\r
-                String tmppdb = loadPDBFile(file, ids[p].getId());\r
-                entry.setFile(tmppdb);\r
-                pdbloaded.put(ids[p].getId(), tmppdb);\r
+                if (!pdbloaded.containsKey(ids[p].getFile()))\r
+                {\r
+                  String tmppdb = loadPDBFile(file, ids[p].getId());\r
+                  entry.setFile(tmppdb);\r
+                  pdbloaded.put(ids[p].getId(), tmppdb);\r
+                }\r
+                else\r
+                  entry.setFile(pdbloaded.get(ids[p].getId()).toString());\r
               }\r
-              else\r
-                entry.setFile(pdbloaded.get(ids[p].getId()).toString());\r
 \r
               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
             }\r
@@ -1160,16 +1164,11 @@ public class Jalview2XML
         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 \r
-        if (view.getWrapAlignment())\r
-        {\r
-            af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
-        }\r
-        else\r
-        {\r
-            af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
-            af.viewport.setShowAnnotation(view.getShowAnnotation());\r
-            af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
-        }\r
+        af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
+\r
+        af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
+        af.viewport.setShowAnnotation(view.getShowAnnotation());\r
+        af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 \r
         af.viewport.setShowBoxes(view.getShowBoxes());\r
         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r