X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=d20b4681c298f9392a6ba18ddf045ad14e6d4b87;hb=1f491c8c9e66b3accb8bb9eae78c7d9caa63c1ac;hp=1e6757940b9dda43795a8de37e1292f4ae4077fa;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 1e67579..d20b468 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,25 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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.util.zip.GZIPInputStream;
 
 /**
  * implements a random access wrapper around a particular datasource, for
@@ -27,14 +30,35 @@ import java.net.*;
  */
 public class FileParse
 {
+  /**
+   * text specifying source of data. usually filename or url.
+   */
+  private String dataName = "unknown source";
+
   public File inFile = null;
 
   public int index = 1; // sequence counter for FileParse object created from
-                        // same data source
+
+  // same data source
 
   protected char suffixSeparator = '#';
 
   /**
+   * character used to write newlines
+   */
+  protected String newline = System.getProperty("line.separator");
+
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
+
+  public String getNewlineString()
+  {
+    return newline;
+  }
+
+  /**
    * '#' separated string tagged on to end of filename or url that was clipped
    * off to resolve to valid filename
    */
@@ -87,6 +111,7 @@ public class FileParse
     {
       mark();
     }
+    dataName = from.dataName;
   }
 
   /**
@@ -120,17 +145,75 @@ 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 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);
-    dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    //
+    // 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
+    {
+      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    } catch (IOException q)
+    {
+      if (e != null)
+      {
+        throw new IOException("Failed to resolve GZIP stream", e);
+      }
+      throw q;
+    }
+    // record URL as name of datasource.
+    dataName = fileStr;
     return false;
   }
 
@@ -158,10 +241,10 @@ 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 type -
-   *                protocol of source
+   * @param fileStr
+   *          - datasource locator/content
+   * @param type
+   *          - protocol of source
    * @throws MalformedURLException
    * @throws IOException
    */
@@ -230,6 +313,7 @@ public class FileParse
     {
       errormessage = "PASTE INACCESSIBLE!";
       dataIn = new BufferedReader(new StringReader(fileStr));
+      dataName = "Paste";
     }
     else if (type.equals(AppletFormatAdapter.CLASSLOADER))
     {
@@ -245,6 +329,7 @@ public class FileParse
       if (is != null)
       {
         dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+        dataName = fileStr;
       }
       else
       {
@@ -356,9 +441,34 @@ public class FileParse
     }
   }
 
-  public Reader getReader() throws IOException
+  /**
+   * @return the dataName
+   */
+  public String getDataName()
+  {
+    return dataName;
+  }
+
+  /**
+   * set the (human readable) name or URI for this datasource
+   * 
+   * @param dataname
+   */
+  protected void setDataName(String dataname)
+  {
+    dataName = dataname;
+  }
+
+  /**
+   * get the underlying bufferedReader for this data source.
+   * 
+   * @return null if no reader available
+   * @throws IOException
+   */
+  public Reader getReader()
   {
-    if (dataIn != null && dataIn.ready())
+    if (dataIn != null) // Probably don't need to test for readiness &&
+                        // dataIn.ready())
     {
       return dataIn;
     }