JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615 from feature/JAL-3615gzipXfam

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index f1d79fe..3013c0b 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -24,6 +24,7 @@ import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
 import jalview.util.MessageManager;
 
 import java.io.BufferedInputStream;
@@ -201,18 +202,41 @@ public class FileParse
     }
     return error;
   }
-  
+
   /**
-   * Recognise the 2-byte magic header for gzip streams
+   * Recognise the 2-byte magic header indicating a gzipped stream
    * 
+   * see
    * https://recalll.co/ask/v/topic/java-How-to-check-if-InputStream-is-Gzipped/555aadd62bd27354438b90f6
    * 
-   * @param bytes - at least two bytes 
-   * @return 
+   * @param input
+   *          - input stream that supports mark and contains at least two bytes
+   * 
+   * @return false if mark not supported or no magic header found
+   *
+   * @throws IOException
    */
-  private static boolean isGzipStream(byte[] bytes) {
-    int head = ((int) bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
-    return (GZIPInputStream.GZIP_MAGIC == head);
+  public static boolean isGzipStream(InputStream input) throws IOException
+  {
+    if (!input.markSupported())
+    {
+      Cache.log.error(
+              "FileParse.izGzipStream: input stream must support mark/reset");
+      return false;
+    }
+    input.mark(4);
+
+    // get first 2 bytes or return false
+    byte[] bytes = new byte[2];
+    int read = input.read(bytes);
+    input.reset();
+    if (read != bytes.length)
+    {
+      return false;
+    }
+
+    int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
+    return (GZIPInputStream.GZIP_MAGIC == header);
   }
 
   /**
@@ -226,16 +250,11 @@ public class FileParse
 
     // NB: stackoverflow https://stackoverflow.com/questions/4818468/how-to-check-if-inputstream-is-gzipped
     // could use a PushBackInputStream rather than a BufferedInputStream
-    
-    BufferedInputStream bufinput;
+        
     if (!input.markSupported()) {
-       bufinput= new BufferedInputStream(input,16);
-       input = bufinput;
+       input = new BufferedInputStream(input,16);
     }
-    input.mark(4);
-    byte[] bytes=input.readNBytes(2);
-    input.reset();
-    if (bytes.length==2 && isGzipStream(bytes)) {
+    if (isGzipStream(input)) {
       return getGzipReader(input);
     }
     // return a buffered reader for the stream.