JAL-4026 if relative path in recently opened exists from PWD, use it.

[jalview.git] / src / jalview / io / AppletFormatAdapter.java

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 60eb9cc..9a4e982 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -36,7 +36,6 @@ import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
-import jalview.structure.StructureImportSettings.TFType;
 import jalview.util.Platform;
 
 /**
@@ -168,11 +167,7 @@ public class AppletFormatAdapter
   {
 
     this.selectedFile = selectedFile;
-    if (selectedFile != null)
-    {
-      this.inFile = selectedFile.getPath();
-    }
-    this.inFile = file;
+    this.inFile = selectedFile != null ? selectedFile.getPath() : file;
     try
     {
       if (fileFormat.isStructureFile())
@@ -184,12 +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,
-                  tempfacType);
+                  StructureImportSettings.getTemperatureFactorType());
         }
         else
         {