X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=9a4e9823ce1999d4054e8447502679f7d3c4a81d;hb=d4271d32477e99e9fbbfa5db3e11f1b79324e60d;hp=5de14a43272af4839a79231ca98976b92b67128d;hpb=fbfbbe26bee37143d5279fe4d254a5a89c96b021;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 5de14a4..9a4e982 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,6 +20,10 @@
  */
 package jalview.io;
 
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
 import java.util.Locale;
 
 import jalview.api.AlignExportSettingsI;
@@ -28,18 +32,12 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SeqDistanceContactMatrix;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
 import jalview.util.Platform;
 
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
-
 /**
  * A low level class for alignment and feature IO with alignment formatting
  * methods used by both applet and application for generating flat alignment
@@ -160,13 +158,16 @@ public class AppletFormatAdapter
           DataSourceType sourceType, FileFormatI fileFormat)
           throws IOException
   {
+    return readFile(selectedFile, file, sourceType, fileFormat, null);
+  }
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat,
+          StructureImportSettings.TFType tempfacType) throws IOException
+  {
 
     this.selectedFile = selectedFile;
-    if (selectedFile != null)
-    {
-      this.inFile = selectedFile.getPath();
-    }
-    this.inFile = file;
+    this.inFile = selectedFile != null ? selectedFile.getPath() : file;
     try
     {
       if (fileFormat.isStructureFile())
@@ -178,11 +179,16 @@ public class AppletFormatAdapter
                         .toString());
         StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
+        if (tempfacType != null)
+        {
+          StructureImportSettings.setTemperatureFactorType(tempfacType);
+        }
         if (isParseWithJMOL)
         {
           // needs a File option
           alignFile = new JmolParser(
-                  selectedFile == null ? inFile : selectedFile, sourceType);
+                  selectedFile == null ? inFile : selectedFile, sourceType,
+                  StructureImportSettings.getTemperatureFactorType());
         }
         else
         {