Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index d986dc5..1f51d8c 100755 (executable)
--- 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;
 
@@ -225,24 +225,23 @@ public class FileParse
   {
     if (!input.markSupported())
     {
-      Cache.log.error(
+      Console.error(
               "FileParse.izGzipStream: input stream must support mark/reset");
       return false;
     }
     input.mark(4);
-    byte[] bytes = new byte[2]; // input.readNBytes(2);
+
+    // 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;
     }
-    if (bytes.length == 2)
-    {
-      int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
-      return (GZIPInputStream.GZIP_MAGIC == header);
-    }
-    return false;
+
+    int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
+    return (GZIPInputStream.GZIP_MAGIC == header);
   }
 
   /**
@@ -345,7 +344,7 @@ public class FileParse
     String encoding = _conn.getContentEncoding();
     String contentType = _conn.getContentType();
     boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType)
-            || "gzip".equals(encoding);
+            || contentType.endsWith("gzip") || "gzip".equals(encoding);
     Exception e = null;
     InputStream inputStream = _conn.getInputStream();
     if (isgzipped)
@@ -381,7 +380,7 @@ public class FileParse
     if (sfpos > -1 && sfpos < fileStr.length() - 1)
     {
       suffix = fileStr.substring(sfpos + 1);
-      // System.err.println("DEBUG: Found Suffix:"+suffix);
+      // jalview.bin.Console.errPrintln("DEBUG: Found Suffix:"+suffix);
       return fileStr.substring(0, sfpos);
     }
     return null;
@@ -635,7 +634,7 @@ public class FileParse
   {
     if (bytesRead >= READAHEAD_LIMIT)
     {
-      System.err.println(String.format(
+      jalview.bin.Console.errPrintln(String.format(
               "File reset error: read %d bytes but reset limit is %d",
               bytesRead, READAHEAD_LIMIT));
     }