X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=a5a4e3665204717acb2a2d08004bd02c7f8788a7;hb=c424c88d659c131acbcc917fc34d89bff46f7b15;hp=c0328d5f0774d4edebe31a095c333d59adc31667;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index c0328d5..a5a4e36 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -20,13 +20,8 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
-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;
@@ -39,12 +34,23 @@ import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.zip.GZIPInputStream;
 
+import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 /**
  * implements a random access wrapper around a particular datasource, for
  * passing to identifyFile and AlignFile objects.
  */
 public class FileParse
 {
+  protected static final String SPACE = " ";
+
+  protected static final String TAB = "\t";
+
   /**
    * text specifying source of data. usually filename or url.
    */
@@ -52,6 +58,12 @@ 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.
@@ -61,7 +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
@@ -299,22 +311,44 @@ 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
   {
-    this.dataSourceType = sourceType;
+    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 IOException
+  {
+    bytes = Platform.getFileBytes(file);
+    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)
@@ -335,6 +369,15 @@ public class FileParse
         }
       }
     }
+    else if (sourceType == DataSourceType.RELATIVE_URL)
+    {
+      // BH 2018 hack for no support for access-origin
+      bytes = Platform.getFileAsBytes(fileStr);
+      dataIn = new BufferedReader(
+              new InputStreamReader(new ByteArrayInputStream(bytes)));
+      dataName = fileStr;
+
+    }
     else if (sourceType == DataSourceType.URL)
     {
       try
@@ -381,8 +424,7 @@ public class FileParse
     else if (sourceType == DataSourceType.CLASSLOADER)
     {
       errormessage = "RESOURCE CANNOT BE LOCATED";
-      java.io.InputStream is = getClass()
-              .getResourceAsStream("/" + fileStr);
+      InputStream is = getClass().getResourceAsStream("/" + fileStr);
       if (is == null)
       {
         String suffixLess = extractSuffix(fileStr);
@@ -393,7 +435,7 @@ public class FileParse
       }
       if (is != null)
       {
-        dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+        dataIn = new BufferedReader(new InputStreamReader(is));
         dataName = fileStr;
       }
       else
@@ -411,7 +453,8 @@ 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;
@@ -580,7 +623,7 @@ public class FileParse
   /**
    * @return the currently configured exportSettings for writing data.
    */
-  public AlignExportSettingI getExportSettings()
+  public AlignExportSettingsI getExportSettings()
   {
     return exportSettings;
   }
@@ -591,7 +634,7 @@ public class FileParse
    * @param exportSettings
    *          the exportSettings to set
    */
-  public void setExportSettings(AlignExportSettingI exportSettings)
+  public void setExportSettings(AlignExportSettingsI exportSettings)
   {
     this.exportSettings = exportSettings;
   }
@@ -626,4 +669,61 @@ public class FileParse
   {
     return dataSourceType;
   }
+
+  /**
+   * Returns a buffered reader for the input object. Returns null, or throws
+   * IOException, on failure.
+   * 
+   * @param file
+   *          a File, or a String which is a name of a file
+   * @param sourceType
+   * @return
+   * @throws IOException
+   */
+  public BufferedReader getBufferedReader(Object file,
+          DataSourceType sourceType) throws IOException
+  {
+    BufferedReader in = null;
+    byte[] bytes;
+
+    switch (sourceType)
+    {
+    case FILE:
+      if (file instanceof String)
+      {
+        return new BufferedReader(new FileReader((String) file));
+      }
+      bytes = Platform.getFileBytes((File) file);
+      if (bytes != null)
+      {
+        return new BufferedReader(
+                new InputStreamReader(new ByteArrayInputStream(bytes)));
+      }
+      return new BufferedReader(new FileReader((File) file));
+    case URL:
+      URL url = new URL(file.toString());
+      in = new BufferedReader(new InputStreamReader(url.openStream()));
+      break;
+    case RELATIVE_URL: // JalviewJS only
+      bytes = Platform.getFileAsBytes(file.toString());
+      if (bytes != null)
+      {
+        in = new BufferedReader(
+                new InputStreamReader(new ByteArrayInputStream(bytes)));
+      }
+      break;
+    case PASTE:
+      in = new BufferedReader(new StringReader(file.toString()));
+      break;
+    case CLASSLOADER:
+      InputStream is = getClass().getResourceAsStream("/" + file);
+      if (is != null)
+      {
+        in = new BufferedReader(new InputStreamReader(is));
+      }
+      break;
+    }
+
+    return in;
+  }
 }