Jalview-JS/JAL-3253-applet also comments relating to JAL-3268

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index aafe934..621cfac 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -20,6 +20,7 @@
  */
 package jalview.io;
 
+import java.io.File;
 import java.io.IOException;
 
 /**
@@ -30,6 +31,40 @@ import java.io.IOException;
  */
 public class IdentifyFile
 {
+  
+  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
+    {
+      parser = new FileParse(file, sourceType);
+      if (parser.isValid())
+      {
+        return identify(parser);
+      }
+    } catch (Exception e)
+    {
+      System.err.println("Error whilst identifying " + file);
+      e.printStackTrace(System.err);
+      emessage = e.getMessage();
+    }
+    if (parser != null)
+    {
+      throw new FileFormatException(parser.errormessage);
+    }
+    throw new FileFormatException(emessage);
+  }
+
   /**
    * Identify a datasource's file content.
    *
@@ -116,7 +151,7 @@ public class IdentifyFile
         {
           for (int i = 0; !isBinary && i < data.length(); i++)
           {
-            char c = data.charAt(i);
+            int c = data.charAt(i);
             isBinary = (c < 32 && c != '\t' && c != '\n' && c != '\r'
                     && c != 5 && c != 27); // nominal binary character filter
             // excluding CR, LF, tab,DEL and ^E
@@ -130,16 +165,17 @@ 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;
+              break;
             }
           }
           if (!lineswereskipped && data.startsWith("PK"))
           {
-            reply = FileFormat.Jalview; // archive.
+            reply = FileFormat.Jalview; // archive
             break;
           }
         }
@@ -417,6 +453,11 @@ public class IdentifyFile
     return true;
   }
 
+  /**
+   * 
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     for (int i = 0; args != null && i < args.length; i++)
@@ -439,4 +480,6 @@ public class IdentifyFile
       System.err.println("Usage: <Filename> [<Filename> ...]");
     }
   }
+
+ 
 }