Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index becc434..3ad74c7 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -24,6 +24,7 @@ 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.AlignmentI;
 import jalview.datamodel.ColumnSelection;
@@ -48,11 +49,11 @@ public class FileLoader implements Runnable
 {
   String file;
 
-  String protocol;
+  DataSourceType protocol;
 
-  String format;
+  FileFormatI format;
 
-  FileParse source = null; // alternative specification of where data comes
+  AlignmentFileI source = null; // alternative specification of where data comes
 
   // from
 
@@ -86,13 +87,14 @@ public class FileLoader implements Runnable
   }
 
   public void LoadFile(AlignViewport viewport, String file,
-          String protocol, String format)
+          DataSourceType protocol, FileFormatI format)
   {
     this.viewport = viewport;
     LoadFile(file, protocol, format);
   }
 
-  public void LoadFile(String file, String protocol, String format)
+  public void LoadFile(String file, DataSourceType protocol,
+          FileFormatI format)
   {
     this.file = file;
     this.protocol = protocol;
@@ -116,7 +118,7 @@ public class FileLoader implements Runnable
    * @param file
    * @param protocol
    */
-  public void LoadFile(String file, String protocol)
+  public void LoadFile(String file, DataSourceType protocol)
   {
     LoadFile(file, protocol, null);
   }
@@ -125,27 +127,28 @@ public class FileLoader implements Runnable
    * Load alignment from (file, protocol) and wait till loaded
    * 
    * @param file
-   * @param protocol
+   * @param sourceType
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(String file, String protocol)
+  public AlignFrame LoadFileWaitTillLoaded(String file,
+          DataSourceType sourceType)
   {
-    return LoadFileWaitTillLoaded(file, protocol, null);
+    return LoadFileWaitTillLoaded(file, sourceType, null);
   }
 
   /**
    * Load alignment from (file, protocol) of type format and wait till loaded
    * 
    * @param file
-   * @param protocol
+   * @param sourceType
    * @param format
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
-          String format)
+  public AlignFrame LoadFileWaitTillLoaded(String file,
+          DataSourceType sourceType, FileFormatI format)
   {
     this.file = file;
-    this.protocol = protocol;
+    this.protocol = sourceType;
     this.format = format;
     return _LoadFileWaitTillLoaded();
   }
@@ -157,12 +160,13 @@ public class FileLoader implements Runnable
    * @param format
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
+  public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source,
+          FileFormatI format)
   {
     this.source = source;
 
     file = source.getInFile();
-    protocol = source.type;
+    protocol = source.getDataSourceType();
     this.format = format;
     return _LoadFileWaitTillLoaded();
   }
@@ -194,13 +198,13 @@ public class FileLoader implements Runnable
   public void updateRecentlyOpened()
   {
     Vector recent = new Vector();
-    if (protocol.equals(FormatAdapter.PASTE))
+    if (protocol == DataSourceType.PASTE)
     {
       // do nothing if the file was pasted in as text... there is no filename to
       // refer to it as.
       return;
     }
-    String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE"
+    String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
             : "RECENT_URL";
 
     String historyItems = jalview.bin.Cache.getProperty(type);
@@ -229,18 +233,18 @@ public class FileLoader implements Runnable
       newHistory.append(recent.elementAt(i));
     }
 
-    jalview.bin.Cache.setProperty(type, newHistory.toString());
+    Cache.setProperty(type, newHistory.toString());
 
-    if (protocol.equals(FormatAdapter.FILE))
+    if (protocol == DataSourceType.FILE)
     {
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+      Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString());
     }
   }
 
   @Override
   public void run()
   {
-    String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard"
+    String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard"
             : file;
     Runtime rt = Runtime.getRuntime();
     try
@@ -254,10 +258,8 @@ public class FileLoader implements Runnable
         // just in case the caller didn't identify the file for us
         if (source != null)
         {
-          format = new IdentifyFile().identify(source, false); // identify
-          // stream and
-          // rewind rather
-          // than close
+          format = new IdentifyFile().identify(source, false);
+          // identify stream and rewind rather than close
         }
         else
         {
@@ -266,7 +268,7 @@ public class FileLoader implements Runnable
 
       }
 
-      if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
+      if (format == null)
       {
         Desktop.instance.stopLoading();
         System.err.println("The input file \"" + file
@@ -296,7 +298,7 @@ public class FileLoader implements Runnable
       loadtime = -System.currentTimeMillis();
       AlignmentI al = null;
 
-      if (format.equalsIgnoreCase("Jalview"))
+      if (FileFormat.Jalview.equals(format))
       {
         if (source != null)
         {
@@ -310,14 +312,12 @@ public class FileLoader implements Runnable
       else
       {
         String error = AppletFormatAdapter.SUPPORTED_FORMATS;
-        if (FormatAdapter.isValidFormat(format))
-        {
           try
           {
             if (source != null)
             {
               // read from the provided source
-              al = new FormatAdapter().readFromFile(source, format);
+            al = new FormatAdapter().readFromFile(source, format);
             }
             else
             {
@@ -332,15 +332,6 @@ public class FileLoader implements Runnable
           {
             error = ex.getMessage();
           }
-        }
-        else
-        {
-          if (format != null && format.length() > 7)
-          {
-            // ad hoc message in format.
-            error = format + "\n" + error;
-          }
-        }
 
         if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
         {
@@ -410,7 +401,7 @@ public class FileLoader implements Runnable
               }
             }
             // add metadata and update ui
-            if (!protocol.equals(AppletFormatAdapter.PASTE))
+            if (!(protocol == DataSourceType.PASTE))
             {
               alignFrame.setFileName(file, format);
             }