JAL-2738 copy to spikes/mungo

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 4b6f8e4..ff959b0 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -72,10 +72,11 @@ public class IdentifyFile
     // preserves original behaviour prior to version 2.3
   }
 
-  public FileFormatI identify(AlignmentFileReaderI file, boolean closeSource)
-          throws IOException
+  public FileFormatI identify(AlignmentFileReaderI file,
+          boolean closeSource) throws IOException
   {
-    FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType());
+    FileParse fp = new FileParse(file.getInFile(),
+            file.getDataSourceType());
     return identify(fp, closeSource);
   }
 
@@ -98,12 +99,15 @@ public class IdentifyFile
     boolean lineswereskipped = false;
     boolean isBinary = false; // true if length is non-zero and non-printable
     // characters are encountered
+
     try
     {
       if (!closeSource)
       {
         source.mark();
       }
+      boolean aaIndexHeaderRead = false;
+
       while ((data = source.nextLine()) != null)
       {
         bytesRead += data.length();
@@ -146,6 +150,15 @@ public class IdentifyFile
           reply = FileFormat.ScoreMatrix;
           break;
         }
+        if (data.startsWith("H ") && !aaIndexHeaderRead)
+        {
+          aaIndexHeaderRead = true;
+        }
+        if (data.startsWith("D ") && aaIndexHeaderRead)
+        {
+          reply = FileFormat.ScoreMatrix;
+          break;
+        }
         if (data.startsWith("##GFF-VERSION"))
         {
           // GFF - possibly embedded in a Jalview features file!
@@ -262,6 +275,11 @@ public class IdentifyFile
           // read as a FASTA (probably)
           break;
         }
+        if (data.indexOf("{\"") > -1)
+        {
+          reply = FileFormat.Json;
+          break;
+        }
         int lessThan = data.indexOf("<");
         if ((lessThan > -1)) // possible Markup Language data i.e HTML,
                              // RNAML, XML
@@ -279,11 +297,6 @@ public class IdentifyFile
           }
         }
 
-        if (data.indexOf("{\"") > -1)
-        {
-          reply = FileFormat.Json;
-          break;
-        }
         if ((data.length() < 1) || (data.indexOf("#") == 0))
         {
           lineswereskipped = true;
@@ -297,9 +310,8 @@ public class IdentifyFile
           break;
         }
 
-        if ((data.indexOf("//") == 0)
-                || ((data.indexOf("!!") > -1) && (data.indexOf("!!") < data
-                        .indexOf("_MULTIPLE_ALIGNMENT "))))
+        if ((data.indexOf("//") == 0) || ((data.indexOf("!!") > -1) && (data
+                .indexOf("!!") < data.indexOf("_MULTIPLE_ALIGNMENT "))))
         {
           reply = FileFormat.MSF;
 
@@ -349,8 +361,8 @@ public class IdentifyFile
     }
     if (trimmedLength == 0)
     {
-      System.err
-              .println("File Identification failed! - Empty file was read.");
+      System.err.println(
+              "File Identification failed! - Empty file was read.");
       throw new FileFormatException("EMPTY DATA FILE");
     }
     System.out.println("File format identified as " + reply.toString());
@@ -416,9 +428,9 @@ public class IdentifyFile
         type = ider.identify(args[i], DataSourceType.FILE);
       } catch (FileFormatException e)
       {
-        System.err.println(String.format(
-                "Error '%s' identifying file type for %s", args[i],
-                e.getMessage()));
+        System.err.println(
+                String.format("Error '%s' identifying file type for %s",
+                        args[i], e.getMessage()));
       }
       System.out.println("Type of " + args[i] + " is " + type);
     }