JAL-4315 identify feature settings file from its xml schema header

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index ea87058..11d96a3 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -35,6 +35,8 @@ import jalview.bin.Console;
 public class IdentifyFile
 {
 
+  private static final String XMLHEADER = "<?XML VERSION=\"1.0\" ENCODING=\"UTF-8\" STANDALONE=\"YES\"?>";
+
   public FileFormatI identify(Object file, DataSourceType protocol)
           throws FileFormatException
   {
@@ -134,6 +136,7 @@ public class IdentifyFile
     String data;
     int bytesRead = 0;
     int trimmedLength = 0;
+    boolean isXml = false; // set true if first line is XMLHEADER
     boolean lineswereskipped = false;
     boolean isBinary = false; // true if length is non-zero and non-printable
     // characters are encountered
@@ -188,6 +191,10 @@ public class IdentifyFile
           reply = FileFormat.ScoreMatrix;
           break;
         }
+        if (data.startsWith(XMLHEADER) && !lineswereskipped)
+        {
+          isXml = true;
+        }
         if (data.startsWith("LOCUS"))
         {
           reply = FileFormat.GenBank;
@@ -346,6 +353,11 @@ public class IdentifyFile
             reply = FileFormat.Rnaml;
             break;
           }
+          if (isXml && data.contains("<NS2:JALVIEWUSERCOLOURS SCHEMENAME=\"SEQUENCE FEATURES\" XMLNS:NS2=\"WWW.JALVIEW.ORG/COLOURS\">"))
+          {
+            reply = FileFormat.FeatureSettings;
+            break;
+          }
         }
 
         if ((data.length() < 1) || (data.indexOf("#") == 0))