X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=d6e67677b522f248344f9da41d6598004fd02014;hb=e57f77dc13f5a295cf49a403da05770a68a6e22b;hp=4d8794f5326f6654d651418bf081ba4937cd5e38;hpb=2305d687bac5ed8a76ecb93c54c7b090a928e362;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 4d8794f..d6e6767 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -20,7 +20,11 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
+import java.io.File;
+import java.io.IOException;
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -30,11 +34,10 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.TFType;
 import jalview.util.Comparison;
 
-import java.io.IOException;
-import java.util.Locale;
-
 /**
  * Additional formatting methods used by the application in a number of places.
  * 
@@ -56,21 +59,18 @@ 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 (Cache.getDefault("STRUCT_FROM_PDB", true))
     {
-      annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
-              true);
-      localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
-              true);
-      serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
-              true);
+      annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN", true);
+      localSecondaryStruct = Cache.getDefault("ADD_SS_ANN", true);
+      serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW", true);
     }
     else
     {
@@ -162,8 +162,8 @@ public class FormatAdapter extends AppletFormatAdapter
 
   public boolean getCacheSuffixDefault(FileFormatI format)
   {
-    return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
-            true);
+    return Cache.getDefault(
+            format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX", true);
   }
 
   public String formatSequences(FileFormatI format, AlignmentI alignment,
@@ -229,6 +229,16 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   @Override
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat,
+          StructureImportSettings.TFType tempfacType) throws IOException
+  {
+    AlignmentI al = super.readFile(selectedFile, file, sourceType,
+            fileFormat, tempfacType);
+    return al;
+  }
+
+  @Override
   public AlignmentI readFile(String file, DataSourceType sourceType,
           FileFormatI fileFormat) throws IOException
   {
@@ -236,6 +246,13 @@ 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