X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=baee5314c0f4193245b0aecce67610eb108b0b1c;hb=a9177efb4097815d9a8031aa22700c61a7d6260a;hp=e7ee711989df0c4de8228147e5f57f0f37b4c493;hpb=f42cec3b999bbed0ce85045760b55701c527da32;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index e7ee711..baee531 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -22,6 +22,9 @@ package jalview.io;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.Locale;
+
+import jalview.bin.Console;
 
 /**
  * DOCUMENT ME!
@@ -31,12 +34,16 @@ import java.io.IOException;
  */
 public class IdentifyFile
 {
-  
-  public FileFormatI identify(Object file, DataSourceType protocol) throws FileFormatException
+
+  private static final String XMLHEADER = "<?XML VERSION=\"1.0\" ENCODING=\"UTF-8\" STANDALONE=\"YES\"?>";
+
+  public FileFormatI identify(Object file, DataSourceType protocol)
+          throws FileFormatException
   {
     // BH 2018
-    return (file instanceof File ? identify((File) file, protocol) : identify((String) file, protocol));
-    
+    return (file instanceof File ? identify((File) file, protocol)
+            : identify((String) file, protocol));
+
   }
 
   public FileFormatI identify(File file, DataSourceType sourceType)
@@ -54,8 +61,7 @@ public class IdentifyFile
       }
     } catch (Exception e)
     {
-      System.err.println("Error whilst identifying " + file);
-      e.printStackTrace(System.err);
+      Console.error("Error whilst identifying " + file, e);
       emessage = e.getMessage();
     }
     if (parser != null)
@@ -90,8 +96,7 @@ public class IdentifyFile
       }
     } catch (Exception e)
     {
-      System.err.println("Error whilst identifying " + file);
-      e.printStackTrace(System.err);
+      Console.error("Error whilst identifying " + file, e);
       emessage = e.getMessage();
     }
     if (parser != null)
@@ -131,6 +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
@@ -165,8 +171,8 @@ public class IdentifyFile
           if (source.inFile != null)
           {
             String fileStr = source.inFile.getName();
-            if (fileStr.contains(".jar")
-                    || fileStr.contains(".zip") || fileStr.contains(".jvp"))
+            if (fileStr.contains(".jar") || fileStr.contains(".zip")
+                    || fileStr.contains(".jvp"))
             {
               // possibly a Jalview archive (but check further)
               reply = FileFormat.Jalview;
@@ -178,13 +184,17 @@ public class IdentifyFile
             break;
           }
         }
-        data = data.toUpperCase();
+        data = data.toUpperCase(Locale.ROOT);
 
         if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
         {
           reply = FileFormat.ScoreMatrix;
           break;
         }
+        if (data.startsWith(XMLHEADER) && !lineswereskipped)
+        {
+          isXml = true;
+        }
         if (data.startsWith("LOCUS"))
         {
           reply = FileFormat.GenBank;
@@ -332,7 +342,7 @@ public class IdentifyFile
         if ((lessThan > -1)) // possible Markup Language data i.e HTML,
                              // RNAML, XML
         {
-          String upper = data.toUpperCase();
+          String upper = data.toUpperCase(Locale.ROOT);
           if (upper.substring(lessThan).startsWith("<HTML"))
           {
             reply = FileFormat.Html;
@@ -343,6 +353,12 @@ 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))
@@ -404,16 +420,15 @@ public class IdentifyFile
       }
     } catch (Exception ex)
     {
-      System.err.println("File Identification failed!\n" + ex);
+      Console.error("File Identification failed!\n" + ex);
       throw new FileFormatException(source.errormessage);
     }
     if (trimmedLength == 0)
     {
-      System.err.println(
-              "File Identification failed! - Empty file was read.");
+      Console.error("File Identification failed! - Empty file was read.");
       throw new FileFormatException("EMPTY DATA FILE");
     }
-    System.out.println("File format identified as " + reply.toString());
+    Console.debug("File format identified as " + reply.toString());
     return reply;
   }
 
@@ -481,17 +496,16 @@ public class IdentifyFile
         type = ider.identify(args[i], DataSourceType.FILE);
       } catch (FileFormatException e)
       {
-        System.err.println(
+        Console.error(
                 String.format("Error '%s' identifying file type for %s",
                         args[i], e.getMessage()));
       }
-      System.out.println("Type of " + args[i] + " is " + type);
+      Console.debug("Type of " + args[i] + " is " + type);
     }
     if (args == null || args.length == 0)
     {
-      System.err.println("Usage: <Filename> [<Filename> ...]");
+      Console.error("Usage: <Filename> [<Filename> ...]");
     }
   }
 
- 
 }