JAL-1432 updated copyright notices

[jalview.git] / src / jalview / io / FileParse.java

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index db4af46..69e801c 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,24 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
- * 
+ *  
  * 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/>.
+ * 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
@@ -40,6 +42,21 @@ public class FileParse
   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
    */
@@ -126,18 +143,63 @@ 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;
@@ -375,9 +437,26 @@ public class FileParse
     return dataName;
   }
 
-  public Reader getReader() throws IOException
+  /**
+   * 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;
     }