X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=d3a6ba936b86c3f65feaa7bc165995e4e31575ae;hb=7fe4dbd0f30dd29c51daaf291d3710af7b1c88b9;hp=3726c6bd5b17699b8d5438572f46077eb1c7530a;hpb=f60987555392a60449a37fe08a0f53003c26937b;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 3726c6b..d3a6ba9 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -41,7 +41,7 @@ import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
@@ -219,24 +219,29 @@ public class FileParse
    * @param bytes
    *          - at least two bytes
    * @return
-   * @throws IOException 
+   * @throws IOException
    */
   public static boolean isGzipStream(InputStream input) throws IOException
   {
     if (!input.markSupported())
     {
-      Cache.log.error("FileParse.izGzipStream: input stream must support mark/reset");
+      Console.error(
+              "FileParse.izGzipStream: input stream must support mark/reset");
       return false;
     }
     input.mark(4);
-    byte[] bytes = { (byte) input.read(), (byte) input.read() }; // input.readNBytes(2);
+
+    // get first 2 bytes or return false
+    byte[] bytes = new byte[2];
+    int read = input.read(bytes);
     input.reset();
-    if (bytes.length == 2)
+    if (read != bytes.length)
     {
-      int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
-      return (GZIPInputStream.GZIP_MAGIC == header);
+      return false;
     }
-    return false;
+
+    int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
+    return (GZIPInputStream.GZIP_MAGIC == header);
   }
 
   /**
@@ -338,7 +343,7 @@ public class FileParse
     }
     String encoding = _conn.getContentEncoding();
     String contentType = _conn.getContentType();
-    boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType)
+    boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType) || contentType.endsWith("gzip")
             || "gzip".equals(encoding);
     Exception e = null;
     InputStream inputStream = _conn.getInputStream();