X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=4b6f8e40a9b0da997593a5f088033967ebfaf60d;hb=fcb39fa3bc47777bf4e0eb209f765dd254dc3cb9;hp=bc91e09365ec62d51056ba79de7a5d592056148e;hpb=74b531f56bbaad5c5e06a4744980256fe8110923;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index bc91e09..4b6f8e4 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -30,8 +30,6 @@ import java.io.IOException;
  */
 public class IdentifyFile
 {
-  public static final String FeaturesFile = "GFF or Jalview features";
-
   /**
    * Identify a datasource's file content.
    *
@@ -74,7 +72,7 @@ public class IdentifyFile
     // preserves original behaviour prior to version 2.3
   }
 
-  public FileFormatI identify(AlignmentFileI file, boolean closeSource)
+  public FileFormatI identify(AlignmentFileReaderI file, boolean closeSource)
           throws IOException
   {
     FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType());
@@ -143,6 +141,11 @@ public class IdentifyFile
         }
         data = data.toUpperCase();
 
+        if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
+        {
+          reply = FileFormat.ScoreMatrix;
+          break;
+        }
         if (data.startsWith("##GFF-VERSION"))
         {
           // GFF - possibly embedded in a Jalview features file!
@@ -261,7 +264,7 @@ public class IdentifyFile
         }
         int lessThan = data.indexOf("<");
         if ((lessThan > -1)) // possible Markup Language data i.e HTML,
-                                      // RNAML, XML
+                             // RNAML, XML
         {
           String upper = data.toUpperCase();
           if (upper.substring(lessThan).startsWith("<HTML"))
@@ -372,8 +375,9 @@ public class IdentifyFile
   }
 
   /**
-   * Returns true if the data has at least 6 tab-delimited fields _and_ 
-   * fields 4 and 5 are integer (start/end) 
+   * Returns true if the data has at least 6 tab-delimited fields _and_ fields 4
+   * and 5 are integer (start/end)
+   * 
    * @param data
    * @return
    */
@@ -384,14 +388,17 @@ public class IdentifyFile
       return false;
     }
     String[] columns = data.split("\t");
-    if (columns.length < 6) {
+    if (columns.length < 6)
+    {
       return false;
     }
     for (int col = 3; col < 5; col++)
     {
-      try {
+      try
+      {
         Integer.parseInt(columns[col]);
-      } catch (NumberFormatException e) {
+      } catch (NumberFormatException e)
+      {
         return false;
       }
     }