JAL-2089 Merge branch releases/Release_2_10_Branch to master

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 40e9390..4ec5329 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  *
  * This file is part of Jalview.
  *
@@ -150,6 +150,13 @@ public class IdentifyFile
           reply = "STH";
           break;
         }
+        if (data.indexOf("_ENTRY.ID") > -1
+                || data.indexOf("_AUDIT_AUTHOR.NAME") > -1
+                || data.indexOf("_ATOM_SITE.") > -1)
+        {
+          reply = "mmCIF";
+          break;
+        }
         // if (data.indexOf(">") > -1)
         if (data.startsWith(">"))
         {
@@ -223,7 +230,6 @@ public class IdentifyFile
                 } catch (IOException ex)
                 {
                 }
-                ;
                 if (dta != null && dta.indexOf("*") > -1)
                 {
                   starterm = true;
@@ -243,34 +249,19 @@ public class IdentifyFile
           // read as a FASTA (probably)
           break;
         }
-        if ((data.indexOf("<") > -1)) // possible Markup Language data i.e HTML,
-                                      // RNAML, XML
+        int lessThan = data.indexOf("<");
+        if ((lessThan > -1)) // possible Markup Language data i.e HTML,
+                             // RNAML, XML
         {
-          // FIXME this is nuts - it consumes the rest of the file if no match
-          boolean identified = false;
-          do
-          {
-            if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
-            {
-              reply = HtmlFile.FILE_DESC;
-              identified = true;
-              break;
-            }
-
-            if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
-            {
-              reply = "RNAML";
-              identified = true;
-              break;
-            }
-          } while ((data = source.nextLine()) != null);
-
-          if (identified)
+          String upper = data.toUpperCase();
+          if (upper.substring(lessThan).startsWith("<HTML"))
           {
+            reply = HtmlFile.FILE_DESC;
             break;
           }
-          if (data == null)
+          if (upper.substring(lessThan).startsWith("<RNAML"))
           {
+            reply = "RNAML";
             break;
           }
         }
@@ -370,8 +361,9 @@ 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
    */
@@ -382,14 +374,17 @@ 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;
       }
     }