X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=a5a4e3665204717acb2a2d08004bd02c7f8788a7;hb=c424c88d659c131acbcc917fc34d89bff46f7b15;hp=f9440fab4d2c134539e1f6f117fd90037331e826;hpb=f6b241598c33de657b7587117b295d2777f2e1b0;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index f9440fa..a5a4e36 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,32 +1,56 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import java.io.*;
-import java.net.*;
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+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.
    */
@@ -34,10 +58,32 @@ public class FileParse
 
   public File inFile = null;
 
-  public int index = 1; // sequence counter for FileParse object created from
+  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.
+   */
+  private AlignViewportI viewport;
+
+  /**
+   * specific settings for exporting data from the current context
+   */
+  private AlignExportSettingsI exportSettings;
 
-  // same data source
+  /**
+   * sequence counter for FileParse object created from same data source
+   */
+  public int index = 1;
 
+  /**
+   * separator for extracting specific 'frame' of a datasource for formats that
+   * support multiple records (e.g. BLC, Stockholm, etc)
+   */
   protected char suffixSeparator = '#';
 
   /**
@@ -61,11 +107,11 @@ public class FileParse
    */
   protected String suffix = null;
 
-  protected String type = null;
+  protected DataSourceType dataSourceType = null;
 
   protected BufferedReader dataIn = null;
 
-  protected String errormessage = "UNITIALISED SOURCE";
+  protected String errormessage = "UNINITIALISED SOURCE";
 
   protected boolean error = true;
 
@@ -91,18 +137,20 @@ public class FileParse
   {
     if (from == null)
     {
-      throw new Error(
-              "Implementation error. Null FileParse in copy constructor");
+      throw new Error(MessageManager
+              .getString("error.implementation_error_null_fileparse"));
     }
     if (from == this)
+    {
       return;
+    }
     index = ++from.index;
     inFile = from.inFile;
     suffixSeparator = from.suffixSeparator;
     suffix = from.suffix;
     errormessage = from.errormessage; // inherit potential error messages
     error = false; // reset any error condition.
-    type = from.type;
+    dataSourceType = from.dataSourceType;
     dataIn = from.dataIn;
     if (dataIn != null)
     {
@@ -142,41 +190,71 @@ public class FileParse
     }
     if (!error)
     {
+      if (fileStr.toLowerCase().endsWith(".gz"))
+      {
+        try
+        {
+          dataIn = tryAsGzipSource(new FileInputStream(fileStr));
+          dataName = fileStr;
+          return error;
+        } catch (Exception x)
+        {
+          warningMessage = "Failed  to resolve as a GZ stream ("
+                  + x.getMessage() + ")";
+          // x.printStackTrace();
+        }
+        ;
+      }
+
       dataIn = new BufferedReader(new FileReader(fileStr));
       dataName = fileStr;
     }
     return error;
   }
 
-  private boolean checkURLSource(String fileStr) throws IOException,
-          MalformedURLException
+  private BufferedReader tryAsGzipSource(InputStream inputStream)
+          throws Exception
+  {
+    BufferedReader inData = new BufferedReader(
+            new InputStreamReader(new GZIPInputStream(inputStream)));
+    inData.mark(2048);
+    inData.read();
+    inData.reset();
+    return inData;
+  }
+
+  private boolean checkURLSource(String fileStr)
+          throws IOException, MalformedURLException
   {
     errormessage = "URL NOT FOUND";
     URL url = new URL(fileStr);
     //
-    // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via Kenny Sabir
-    Exception e=null;
-    if (fileStr.endsWith(".gz")) {
-      try {
-          InputStream inputStream = url.openStream();
-          dataIn = new BufferedReader(new InputStreamReader(new GZIPInputStream(inputStream)));
-          dataIn.mark(2048);
-          dataIn.read();
-          dataIn.reset();
-          
-          dataName = fileStr;
-          return false;
-      } catch (Exception ex) {
-        e=ex;
+    // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via
+    // Kenny Sabir
+    Exception e = null;
+    if (fileStr.toLowerCase().endsWith(".gz"))
+    {
+      try
+      {
+        InputStream inputStream = url.openStream();
+        dataIn = tryAsGzipSource(inputStream);
+        dataName = fileStr;
+        return false;
+      } catch (Exception ex)
+      {
+        e = ex;
       }
     }
 
-    try {
+    try
+    {
       dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    } catch (IOException q) {
-      if (e!=null)
+    } catch (IOException q)
+    {
+      if (e != null)
       {
-        throw new IOException("Failed to resolve GZIP stream", e);
+        throw new IOException(MessageManager
+                .getString("exception.failed_to_resolve_gzip_stream"), e);
       }
       throw q;
     }
@@ -206,43 +284,101 @@ public class FileParse
   }
 
   /**
+   * not for general use, creates a fileParse object for an existing reader with
+   * configurable values for the origin and the type of the source
+   */
+  public FileParse(BufferedReader source, String originString,
+          DataSourceType sourceType)
+  {
+    dataSourceType = sourceType;
+    error = false;
+    inFile = null;
+    dataName = originString;
+    dataIn = source;
+    try
+    {
+      if (dataIn.markSupported())
+      {
+        dataIn.mark(READAHEAD_LIMIT);
+      }
+    } catch (IOException q)
+    {
+
+    }
+  }
+
+  /**
    * Create a datasource for input to Jalview. See AppletFormatAdapter for the
    * types of sources that are handled.
    * 
-   * @param fileStr
-   *          - datasource locator/content
-   * @param type
+   * @param file
+   *          - datasource locator/content as File or String
+   * @param sourceType
    *          - protocol of source
    * @throws MalformedURLException
    * @throws IOException
    */
-  public FileParse(String fileStr, String type)
+  public FileParse(Object file, DataSourceType sourceType)
           throws MalformedURLException, IOException
   {
-    this.type = type;
+    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 (type.equals(AppletFormatAdapter.FILE))
+    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)
         {
           if (checkFileSource(suffixLess))
           {
-            throw new IOException("Problem opening " + inFile
-                    + " (also tried " + suffixLess + ") : " + errormessage);
+            throw new IOException(MessageManager.formatMessage(
+                    "exception.problem_opening_file_also_tried",
+                    new String[]
+                    { inFile.getName(), suffixLess, errormessage }));
           }
         }
         else
         {
-          throw new IOException("Problem opening " + inFile + " : "
-                  + errormessage);
+          throw new IOException(MessageManager.formatMessage(
+                  "exception.problem_opening_file", new String[]
+                  { inFile.getName(), errormessage }));
         }
       }
     }
-    else if (type.equals(AppletFormatAdapter.URL))
+    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
       {
@@ -250,7 +386,9 @@ public class FileParse
         {
           checkURLSource(fileStr);
           if (suffixSeparator == '#')
+          {
             extractSuffix(fileStr); // URL lref is stored for later reference.
+          }
         } catch (IOException e)
         {
           String suffixLess = extractSuffix(fileStr);
@@ -277,26 +415,27 @@ public class FileParse
         error = true;
       }
     }
-    else if (type.equals(AppletFormatAdapter.PASTE))
+    else if (sourceType == DataSourceType.PASTE)
     {
       errormessage = "PASTE INACCESSIBLE!";
       dataIn = new BufferedReader(new StringReader(fileStr));
       dataName = "Paste";
     }
-    else if (type.equals(AppletFormatAdapter.CLASSLOADER))
+    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);
         if (suffixLess != null)
+        {
           is = getClass().getResourceAsStream("/" + suffixLess);
+        }
       }
       if (is != null)
       {
-        dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+        dataIn = new BufferedReader(new InputStreamReader(is));
         dataName = fileStr;
       }
       else
@@ -307,14 +446,16 @@ public class FileParse
     else
     {
       errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '"
-              + (type != null ? type : "null") + "'";
+              + (sourceType != null ? sourceType : "null") + "'";
       error = true;
     }
     if (dataIn == null || error)
     {
       // pass up the reason why we have no source to read from
-      throw new IOException("Failed to read data from source:\n"
-              + errormessage);
+      throw new IOException(MessageManager.formatMessage(
+              "exception.failed_to_read_data_from_source",
+              new String[]
+              { errormessage }));
     }
     error = false;
     dataIn.mark(READAHEAD_LIMIT);
@@ -334,17 +475,35 @@ public class FileParse
     }
     else
     {
-      throw new IOException("Unitialised Source Stream");
+      throw new IOException(
+              MessageManager.getString("exception.no_init_source_stream"));
     }
   }
 
   public String nextLine() throws IOException
   {
     if (!error)
+    {
       return dataIn.readLine();
-    throw new IOException("Invalid Source Stream:" + errormessage);
+    }
+    throw new IOException(MessageManager
+            .formatMessage("exception.invalid_source_stream", new String[]
+            { errormessage }));
   }
 
+  /**
+   * 
+   * @return true if this FileParse is configured for Export only
+   */
+  public boolean isExporting()
+  {
+    return !error && dataIn == null;
+  }
+
+  /**
+   * 
+   * @return true if the data source is valid
+   */
   public boolean isValid()
   {
     return !error;
@@ -363,19 +522,27 @@ public class FileParse
   }
 
   /**
-   * rewinds the datasource the beginning.
+   * Rewinds the datasource to the marked point if possible
+   * 
+   * @param bytesRead
    * 
    */
-  public void reset() throws IOException
+  public void reset(int bytesRead) throws IOException
   {
+    if (bytesRead >= READAHEAD_LIMIT)
+    {
+      System.err.println(String.format(
+              "File reset error: read %d bytes but reset limit is %d",
+              bytesRead, READAHEAD_LIMIT));
+    }
     if (dataIn != null && !error)
     {
       dataIn.reset();
     }
     else
     {
-      throw new IOException(
-              "Implementation Error: Reset called for invalid source.");
+      throw new IOException(MessageManager.getString(
+              "error.implementation_error_reset_called_for_invalid_source"));
     }
   }
 
@@ -442,4 +609,121 @@ public class FileParse
     }
     return null;
   }
+
+  public AlignViewportI getViewport()
+  {
+    return viewport;
+  }
+
+  public void setViewport(AlignViewportI viewport)
+  {
+    this.viewport = viewport;
+  }
+
+  /**
+   * @return the currently configured exportSettings for writing data.
+   */
+  public AlignExportSettingsI getExportSettings()
+  {
+    return exportSettings;
+  }
+
+  /**
+   * Set configuration for export of data.
+   * 
+   * @param exportSettings
+   *          the exportSettings to set
+   */
+  public void setExportSettings(AlignExportSettingsI exportSettings)
+  {
+    this.exportSettings = exportSettings;
+  }
+
+  /**
+   * method overridden by complex file exporter/importers which support
+   * exporting visualisation and layout settings for a view
+   * 
+   * @param avpanel
+   */
+  public void configureForView(AlignmentViewPanel avpanel)
+  {
+    if (avpanel != null)
+    {
+      setViewport(avpanel.getAlignViewport());
+    }
+    // could also set export/import settings
+  }
+
+  /**
+   * Returns the preferred feature colour configuration if there is one, else
+   * null
+   * 
+   * @return
+   */
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return null;
+  }
+
+  public DataSourceType getDataSourceType()
+  {
+    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;
+  }
 }