X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=13c0f4311854153ddbb07fc1b743b22a0924ae60;hb=070cda5fcdc40af294bf8267f9c32104ce9bfd82;hp=7e1940fe0b1ca18b14e313bb1a2c00aae6d6be4c;hpb=5969ead0fd401f4435a3435ede9e4e87cf9c1d0b;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 7e1940f..13c0f43 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -20,13 +20,15 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsModelI;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileReader;
@@ -39,8 +41,6 @@ import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.zip.GZIPInputStream;
 
-import javajs.util.Rdr;
-
 /**
  * implements a random access wrapper around a particular datasource, for
  * passing to identifyFile and AlignFile objects.
@@ -58,8 +58,12 @@ public class FileParse
 
   public File inFile = null;
 
-  public byte[] bytes; // from JavaScript
+  private byte[] bytes; // from JavaScript
 
+  public byte[] getBytes()
+  {
+    return bytes;
+  }
   /**
    * a viewport associated with the current file operation. May be null. May
    * move to different object.
@@ -69,7 +73,7 @@ public class FileParse
   /**
    * specific settings for exporting data from the current context
    */
-  private AlignExportSettingI exportSettings;
+  private AlignExportSettingsI exportSettings;
 
   /**
    * sequence counter for FileParse object created from same data source
@@ -307,38 +311,31 @@ public class FileParse
    * Create a datasource for input to Jalview. See AppletFormatAdapter for the
    * types of sources that are handled.
    * 
-   * @param fileStr
-   *          - datasource locator/content
+   * @param file
+   *          - datasource locator/content as File or String
    * @param sourceType
    *          - protocol of source
    * @throws MalformedURLException
    * @throws IOException
    */
-  public FileParse(String fileStr, DataSourceType sourceType)
-          throws MalformedURLException, IOException
-  {
-
-    this(null, fileStr, sourceType, false);
-  }
-
-  public FileParse(File file, DataSourceType sourceType)
+  public FileParse(Object file, DataSourceType sourceType)
           throws MalformedURLException, IOException
   {
-
-    this(file, file.getPath(), sourceType, true);
+    if (file instanceof File)
+    {
+      parse((File) file, ((File) file).getPath(), sourceType, true);
+    }
+    else
+    {
+      parse(null, file.toString(), sourceType, false);
+    }
   }
 
-  private FileParse(File file, String fileStr, DataSourceType sourceType,
+  private void parse(File file, String fileStr, DataSourceType sourceType,
           boolean isFileObject) throws MalformedURLException, IOException
   {
-
-    /**
-     * @j2sNative
-     * 
-     *            this.bytes = file && file._bytes;
-     * 
-     */
-    this.dataSourceType = sourceType;
+    bytes = Platform.getFileBytes(file);
+    dataSourceType = sourceType;
     error = false;
 
     if (sourceType == DataSourceType.FILE)
@@ -348,7 +345,7 @@ public class FileParse
       {
         // this will be from JavaScript
         inFile = file;
-        dataIn = new BufferedReader(new StringReader(new String(bytes)));
+        dataIn = new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
         dataName = fileStr;
       }
       else if (checkFileSource(fileStr))
@@ -374,18 +371,9 @@ public class FileParse
     }
     else if (sourceType == DataSourceType.RELATIVE_URL)
     {
-      String data = null;
-      /**
-       * BH 2018 hack for no support for access-origin
-       * 
-       * @j2sNative
-       * 
-       *            data = $.ajax({url:fileStr, async:false}).responseText;
-       * 
-       */
-
-      System.out.println(data);
-      dataIn = Rdr.getBR(data);
+      // BH 2018 hack for no support for access-origin
+      bytes = Platform.getFileAsBytes(fileStr);
+      dataIn = new BufferedReader(new java.io.InputStreamReader(new ByteArrayInputStream(bytes)));      
       dataName = fileStr;
 
     }
@@ -635,7 +623,7 @@ public class FileParse
   /**
    * @return the currently configured exportSettings for writing data.
    */
-  public AlignExportSettingI getExportSettings()
+  public AlignExportSettingsI getExportSettings()
   {
     return exportSettings;
   }
@@ -646,7 +634,7 @@ public class FileParse
    * @param exportSettings
    *          the exportSettings to set
    */
-  public void setExportSettings(AlignExportSettingI exportSettings)
+  public void setExportSettings(AlignExportSettingsI exportSettings)
   {
     this.exportSettings = exportSettings;
   }