Merge branch 'JAL-1445' into develop

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index c03bcba..5307e95 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,24 +1,24 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
 import java.io.*;
-import java.net.*;
 
 /**
  * DOCUMENT ME!
@@ -132,6 +132,13 @@ public class IdentifyFile
 
           break;
         }
+        
+        if ((data.indexOf("<") > -1))
+        {
+          reply = "RNAML";
+          
+          break;
+        }
 
         if ((data.length() < 1) || (data.indexOf("#") == 0))
         {
@@ -160,10 +167,12 @@ public class IdentifyFile
 
           break;
         }
+        
+        
         else if (data.indexOf(">") > -1)
         {
           // FASTA, PIR file or BLC file
-          boolean checkPIR = false;
+          boolean checkPIR = false, starterm = false;
           if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
           {
             // watch for PIR file attributes
@@ -180,8 +189,13 @@ public class IdentifyFile
           else
           {
             // Is this a single line BLC file?
-            source.nextLine();
+            String data1 = source.nextLine();
             String data2 = source.nextLine();
+            if (checkPIR)
+            {
+              starterm = (data1 != null && data1.indexOf("*") > -1)
+                      || (data2 != null && data2.indexOf("*") > -1);
+            }
             if (data2 != null && data.indexOf("*") > -1)
             {
               if (data.indexOf("*") == data2.indexOf("*"))
@@ -196,13 +210,49 @@ public class IdentifyFile
               // TODO : AMSA File is indicated if there is annotation in the
               // FASTA file - but FASTA will automatically generate this at the
               // mo.
-              break;
+              if (!checkPIR)
+              {
+                break;
+              }
             }
           }
-          // TODO final check for PIR content. require
+          // final check for PIR content. require
           // >P1;title\n<blah>\nterminated sequence to occur at least once.
-          // the PIR/fasta ambiguity may be the use case that is needed to have
+
+          // TODO the PIR/fasta ambiguity may be the use case that is needed to
+          // have
           // a 'Parse as type XXX' parameter for the applet/application.
+          if (checkPIR)
+          {
+            String dta = null;
+            if (!starterm)
+            {
+              do
+              {
+                try
+                {
+                  dta = source.nextLine();
+                } catch (IOException ex)
+                {
+                }
+                ;
+                if (dta != null && dta.indexOf("*") > -1)
+                {
+                  starterm = true;
+                }
+              } while (dta != null && !starterm);
+            }
+            if (starterm)
+            {
+              reply = "PIR";
+              break;
+            }
+            else
+            {
+              reply = "FASTA"; // probably a bad choice!
+            }
+          }
+          // read as a FASTA (probably)
           break;
         }
         else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)