X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=baee5314c0f4193245b0aecce67610eb108b0b1c;hb=85299bc2db43c8b108169661ebc1c4d9b2d3d2e5;hp=e2786aee0e0ff594719bd0d9d9c50f04b1b24c99;hpb=5969ead0fd401f4435a3435ede9e4e87cf9c1d0b;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index e2786ae..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!
@@ -31,9 +34,22 @@ import java.io.IOException;
  */
 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
+  {
+    // BH 2018
+    return (file instanceof File ? identify((File) file, protocol)
+            : identify((String) file, protocol));
+
+  }
+
   public FileFormatI identify(File file, DataSourceType sourceType)
           throws FileFormatException
   {
+    // BH 2018
     String emessage = "UNIDENTIFIED FILE PARSING ERROR";
     FileParse parser = null;
     try
@@ -45,8 +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)
@@ -81,8 +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)
@@ -122,6 +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
@@ -156,26 +171,43 @@ public class IdentifyFile
           if (source.inFile != null)
           {
             String fileStr = source.inFile.getName();
-            // possibly a Jalview archive.
-            if (fileStr.lastIndexOf(".jar") > -1
-                    || fileStr.lastIndexOf(".zip") > -1)
+            if (fileStr.contains(".jar") || fileStr.contains(".zip")
+                    || fileStr.contains(".jvp"))
             {
+              // possibly a Jalview archive (but check further)
               reply = FileFormat.Jalview;
             }
           }
           if (!lineswereskipped && data.startsWith("PK"))
           {
-            reply = FileFormat.Jalview; // archive.
+            reply = FileFormat.Jalview; // archive
             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;
+          break;
+        }
+        if (data.startsWith("ID "))
+        {
+          if (data.substring(2).trim().split(";").length == 7)
+          {
+            reply = FileFormat.Embl;
+            break;
+          }
+        }
         if (data.startsWith("H ") && !aaIndexHeaderRead)
         {
           aaIndexHeaderRead = true;
@@ -310,7 +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;
@@ -321,6 +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))
@@ -382,16 +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;
   }
 
@@ -443,6 +480,11 @@ public class IdentifyFile
     return true;
   }
 
+  /**
+   * 
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     for (int i = 0; args != null && i < args.length; i++)
@@ -454,15 +496,15 @@ 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> ...]");
     }
   }