X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=b0414afae2e56a0373f549442dc55afd3c40ffef;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=7647a16aa8f53cf3ad24d77b98b443a7b9bff085;hpb=14b1b2a878190d5fffda298c4b9a901c72c74ad3;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 7647a16..b0414af 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -20,7 +20,7 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -30,8 +30,10 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Preferences;
 import jalview.util.Comparison;
 
+import java.io.File;
 import java.io.IOException;
 
 /**
@@ -55,20 +57,23 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   public FormatAdapter(AlignmentViewPanel alignPanel,
-          AlignExportSettingI settings)
+          AlignExportSettingsI settings)
   {
     super(alignPanel, settings);
   }
 
   private void init()
   {
-    if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+    if (jalview.bin.Cache.getDefault(Preferences.STRUCT_FROM_PDB, true))
     {
-      annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+      annotFromStructure = jalview.bin.Cache.getDefault(
+              Preferences.ADD_TEMPFACT_ANN,
               true);
-      localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+      localSecondaryStruct = jalview.bin.Cache.getDefault(
+              Preferences.ADD_SS_ANN,
               true);
-      serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+      serviceSecondaryStruct = jalview.bin.Cache
+              .getDefault(Preferences.USE_RNAVIEW,
               true);
     }
     else
@@ -212,12 +217,12 @@ public class FormatAdapter extends AppletFormatAdapter
           AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
           if (selgp != null)
           {
-            hidden.makeVisibleAnnotation(selgp.getStartRes(),
-                    selgp.getEndRes(), na);
+            na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(),
+                    hidden);
           }
           else
           {
-            hidden.makeVisibleAnnotation(na);
+            na.makeVisibleAnnotation(hidden);
           }
           alv.addAnnotation(na);
         }
@@ -235,6 +240,13 @@ public class FormatAdapter extends AppletFormatAdapter
     return al;
   }
 
+  public AlignmentI readFile(File file, DataSourceType sourceType,
+          FileFormatI fileFormat) throws IOException
+  {
+    AlignmentI al = super.readFile(file, null, sourceType, fileFormat);
+    return al;
+  }
+
   @Override
   public AlignmentI readFromFile(FileParse source, FileFormatI format)
           throws IOException