X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=c7ade20da180eea51bb50cc66d5e38c92caf4e8f;hb=c0e43acd458a2e19a5ab3be56a53bc88932657c4;hp=f244d14a12500d827f88fe1dc11aefdf5c25382c;hpb=d14b06cdb877e90cd67b96cb3e7b580992dd8dab;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index f244d14..c7ade20 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -20,12 +20,21 @@
  */
 package jalview.io;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.SwingUtilities;
+
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureSettingsModelI;
 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;
@@ -41,19 +50,6 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.ws.utils.UrlDownloadClient;
 
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.SwingUtilities;
-
 public class FileLoader implements Runnable
 {
   String file;
@@ -79,6 +75,8 @@ public class FileLoader implements Runnable
 
   private File selectedFile;
 
+  private AlignmentAnnotation.TFType temperatureFactorType = null;
+
   /**
    * default constructor always raised errors in GUI dialog boxes
    */
@@ -102,7 +100,8 @@ public class FileLoader implements Runnable
           DataSourceType protocol, FileFormatI format)
   {
     this.viewport = viewport;
-    if (file instanceof File) {
+    if (file instanceof File)
+    {
       this.selectedFile = (File) file;
       file = selectedFile.getPath();
     }
@@ -163,9 +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();
   }
 
@@ -214,6 +230,7 @@ public class FileLoader implements Runnable
   protected AlignFrame _LoadFileWaitTillLoaded()
   {
     this.run();
+
     return alignFrame;
   }
 
@@ -276,6 +293,7 @@ public class FileLoader implements Runnable
             ? "Copied From Clipboard"
             : file;
     Runtime rt = Runtime.getRuntime();
+
     try
     {
       if (Desktop.instance != null)
@@ -290,7 +308,8 @@ public class FileLoader implements Runnable
           format = new IdentifyFile().identify(source, false);
           // identify stream and rewind rather than close
         }
-        else if (selectedFile != null) {
+        else if (selectedFile != null)
+        {
           format = new IdentifyFile().identify(selectedFile, protocol);
         }
         else
@@ -339,7 +358,8 @@ public class FileLoader implements Runnable
           // We read the data anyway - it might make sense.
         }
         // BH 2018 switch to File object here instead of filename
-        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
+        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(
+                selectedFile == null ? file : selectedFile);
       }
       else
       {
@@ -367,27 +387,31 @@ public class FileLoader implements Runnable
                       file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
-              
+
               // BH - switching to File object here so as to hold
               // ._bytes array directly
               File tempFile = new File(tempStructureFileStr);
               UrlDownloadClient.download(file, tempFile);
-              
-              al = fa.readFile(tempFile, DataSourceType.FILE,
-                      format);
+
+              al = fa.readFile(tempFile, DataSourceType.FILE, format);
               source = fa.getAlignFile();
             }
             else
             {
-              if (selectedFile == null) {
-                al = fa.readFile(file, protocol, format);
-                
-              } else {
-                al = fa.readFile(selectedFile, protocol, format);
-                             }
+              if (selectedFile == null)
+              {
+                al = fa.readFile(null, file, protocol, format,
+                        temperatureFactorType);
+
+              }
+              else
+              {
+                al = fa.readFile(selectedFile, null, protocol, format,
+                        temperatureFactorType);
+              }
               source = fa.getAlignFile(); // keep reference for later if
-              
-                                          // necessary.
+
+              // necessary.
             }
           }
         } catch (java.io.IOException ex)
@@ -421,12 +445,9 @@ public class FileLoader implements Runnable
                   .getFeatureColourScheme();
           if (viewport != null)
           {
-            if (proxyColourScheme != null)
-            {
-              viewport.applyFeaturesStyle(proxyColourScheme);
-            }
             // append to existing alignment
             viewport.addAlignment(al, title);
+            viewport.applyFeaturesStyle(proxyColourScheme);
           }
           else
           {
@@ -491,8 +512,8 @@ public class FileLoader implements Runnable
 
             try
             {
-              alignFrame.setMaximum(jalview.bin.Cache
-                      .getDefault("SHOW_FULLSCREEN", false));
+              alignFrame.setMaximum(
+                      Cache.getDefault("SHOW_FULLSCREEN", false));
             } catch (java.beans.PropertyVetoException ex)
             {
             }
@@ -640,21 +661,4 @@ public class FileLoader implements Runnable
     return tempStructFile.toString();
   }
 
-  /**
-   * 
-   * @param file a File, or a String which is a name of a file
-   * @return
-   * @throws FileNotFoundException 
-   */
-  @SuppressWarnings("unused")
-  public static BufferedReader getBuffereReader(Object file) throws FileNotFoundException {
-    if (file instanceof String)
-      return new BufferedReader(new FileReader((String) file));
-    
-    byte[] bytes = /** @j2sNative file._bytes || */ null;
-    if (bytes != null)
-      return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
-    return  new BufferedReader(new FileReader((File) file));
-  }
-
 }