JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index d0b61e4..2dec559 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -20,11 +20,6 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingsI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureSettingsModelI;
-import jalview.util.MessageManager;
-
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
@@ -42,6 +37,12 @@ import java.net.URL;
 import java.net.URLConnection;
 import java.util.zip.GZIPInputStream;
 
+import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Console;
+import jalview.util.MessageManager;
 import jalview.util.Platform;
 
 /**
@@ -209,18 +210,38 @@ public class FileParse
     }
     return error;
   }
-  
+
   /**
    * Recognise the 2-byte magic header for gzip streams
    * 
    * https://recalll.co/ask/v/topic/java-How-to-check-if-InputStream-is-Gzipped/555aadd62bd27354438b90f6
    * 
-   * @param bytes - at least two bytes 
-   * @return 
+   * @param bytes
+   *          - at least two bytes
+   * @return
+   * @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())
+    {
+      Console.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);
   }
 
   /**
@@ -230,27 +251,26 @@ public class FileParse
    * @param input
    * @return
    */
-  private BufferedReader checkForGzipStream(InputStream input) throws Exception {
-
-    // NB: stackoverflow https://stackoverflow.com/questions/4818468/how-to-check-if-inputstream-is-gzipped
+  private BufferedReader checkForGzipStream(InputStream input)
+          throws Exception
+  {
+    // 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;
+    if (!input.markSupported())
+    {
+      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.
-    InputStreamReader isReader= new InputStreamReader(input);
-    BufferedReader toReadFrom=new BufferedReader(isReader);
+    InputStreamReader isReader = new InputStreamReader(input);
+    BufferedReader toReadFrom = new BufferedReader(isReader);
     return toReadFrom;
   }
+
   /**
    * Returns a {@code BufferedReader} which wraps the input stream with a
    * GZIPInputStream. Throws a {@code ZipException} if a GZIP format error
@@ -303,16 +323,21 @@ public class FileParse
         throw new IOException(
                 "Response status from " + urlStr + " was " + rc);
       }
-    } else {
-      try {
-      dataIn = checkForGzipStream(_conn.getInputStream());
-      dataName=urlStr;
+    }
+    else
+    {
+      try
+      {
+        dataIn = checkForGzipStream(_conn.getInputStream());
+        dataName = urlStr;
       } catch (IOException ex)
       {
-        throw new IOException("Failed to handle non-HTTP URI stream",ex);
+        throw new IOException("Failed to handle non-HTTP URI stream", ex);
       } catch (Exception ex)
       {
-        throw new IOException("Failed to determine type of input stream for given URI",ex);
+        throw new IOException(
+                "Failed to determine type of input stream for given URI",
+                ex);
       }
       return;
     }