JAL-629 implementation of --tempfac options

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 4016e71..c7ade20 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -33,6 +33,8 @@ import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentAnnotation.TFType;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
@@ -73,6 +75,8 @@ public class FileLoader implements Runnable
 
   private File selectedFile;
 
+  private AlignmentAnnotation.TFType temperatureFactorType = null;
+
   /**
    * default constructor always raised errors in GUI dialog boxes
    */
@@ -158,9 +162,26 @@ public class FileLoader implements Runnable
   public AlignFrame LoadFileWaitTillLoaded(String file,
           DataSourceType sourceType, FileFormatI format)
   {
+    return LoadFileWaitTillLoaded(file, sourceType, format, null);
+  }
+
+  /**
+   * Load alignment from (file, protocol) of type format with specified
+   * temperature factor type and wait till loaded
+   * 
+   * @param file
+   * @param sourceType
+   * @param format
+   * @param tempfacType
+   * @return alignFrame constructed from file contents
+   */
+  public AlignFrame LoadFileWaitTillLoaded(String file,
+          DataSourceType sourceType, FileFormatI format, AlignmentAnnotation.TFType tempfacType)
+  {
     this.file = file;
     this.protocol = sourceType;
     this.format = format;
+    this.temperatureFactorType = tempfacType;
     return _LoadFileWaitTillLoaded();
   }
 
@@ -272,6 +293,7 @@ public class FileLoader implements Runnable
             ? "Copied From Clipboard"
             : file;
     Runtime rt = Runtime.getRuntime();
+
     try
     {
       if (Desktop.instance != null)
@@ -378,12 +400,14 @@ public class FileLoader implements Runnable
             {
               if (selectedFile == null)
               {
-                al = fa.readFile(file, protocol, format);
+                al = fa.readFile(null, file, protocol, format,
+                        temperatureFactorType);
 
               }
               else
               {
-                al = fa.readFile(selectedFile, protocol, format);
+                al = fa.readFile(selectedFile, null, protocol, format,
+                        temperatureFactorType);
               }
               source = fa.getAlignFile(); // keep reference for later if