X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFileParse.java;h=809bc8f2d13a3ebb9b48877c8cfc9b41a377b314;hb=dd8112aefe2c3a08c51f1684d5cda16be938c74f;hp=7117d0fcf537a5ae211577c0e290a59d8404af84;hpb=acf9118bba86938c8406e7041b4e5a507f4f37a3;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 7117d0f..809bc8f 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -20,13 +20,14 @@
  */
 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 java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileReader;
@@ -56,6 +57,12 @@ public class FileParse
 
   public File inFile = null;
 
+  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.
@@ -65,7 +72,7 @@ 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
@@ -303,22 +310,49 @@ 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)
+  public FileParse(Object file, DataSourceType sourceType)
           throws MalformedURLException, IOException
   {
+    if (file instanceof File)
+    {
+      parse((File) file, ((File) file).getPath(), sourceType, true);
+    }
+    else
+    {
+      parse(null, file.toString(), sourceType, false);
+    }
+  }
+
+  private void parse(File file, String fileStr, DataSourceType sourceType,
+          boolean isFileObject) throws MalformedURLException, IOException
+  {
+    /**
+     * @j2sNative
+     * 
+     *            this.bytes = file && file._bytes;
+     * 
+     */
     this.dataSourceType = sourceType;
     error = false;
 
     if (sourceType == DataSourceType.FILE)
     {
-      if (checkFileSource(fileStr))
+
+      if (bytes != null)
+      {
+        // this will be from JavaScript
+        inFile = file;
+        dataIn = new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
+        dataName = fileStr;
+      }
+      else if (checkFileSource(fileStr))
       {
         String suffixLess = extractSuffix(fileStr);
         if (suffixLess != null)
@@ -339,6 +373,21 @@ public class FileParse
         }
       }
     }
+    else if (sourceType == DataSourceType.RELATIVE_URL)
+    {
+      /**
+       * BH 2018 hack for no support for access-origin
+       * 
+       * @j2sNative
+       * 
+       * this.bytes = swingjs.JSUtil.getFileAsBytes$O(fileStr);
+       * 
+       */
+
+      dataIn = new BufferedReader(new java.io.InputStreamReader(new ByteArrayInputStream(bytes)));      
+      dataName = fileStr;
+
+    }
     else if (sourceType == DataSourceType.URL)
     {
       try
@@ -415,7 +464,8 @@ public class FileParse
     {
       // pass up the reason why we have no source to read from
       throw new IOException(MessageManager.formatMessage(
-              "exception.failed_to_read_data_from_source", new String[]
+              "exception.failed_to_read_data_from_source",
+              new String[]
               { errormessage }));
     }
     error = false;
@@ -584,7 +634,7 @@ public class FileParse
   /**
    * @return the currently configured exportSettings for writing data.
    */
-  public AlignExportSettingI getExportSettings()
+  public AlignExportSettingsI getExportSettings()
   {
     return exportSettings;
   }
@@ -595,7 +645,7 @@ public class FileParse
    * @param exportSettings
    *          the exportSettings to set
    */
-  public void setExportSettings(AlignExportSettingI exportSettings)
+  public void setExportSettings(AlignExportSettingsI exportSettings)
   {
     this.exportSettings = exportSettings;
   }