P1 changed to N1

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

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 724fea8..6d6e525 100755 (executable)
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -21,7 +21,6 @@ package jalview.io;
 import java.io.*;\r
 import java.util.*;\r
 \r
-import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
 \r
 public class PIRFile\r
@@ -44,10 +43,8 @@ public class PIRFile
     super(inFile, type);\r
   }\r
 \r
-  public void parse()\r
+  public void parse() throws IOException\r
   {\r
-    try\r
-    {\r
       StringBuffer sequence;\r
       String line = null;\r
 \r
@@ -88,17 +85,19 @@ public class PIRFile
         {\r
           sequence.setLength(sequence.length() - 1);\r
           newSeq.setSequence(sequence.toString());\r
+          if (!isValidProteinSequence(newSeq.getSequence()))\r
+          {\r
+            throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
+                                  +" : "+ newSeq.getName()\r
+                                  +" : "+invalidCharacter);\r
+          }\r
+\r
           seqs.addElement(newSeq);\r
           ModellerDescription md = new ModellerDescription(newSeq.\r
               getDescription());\r
           md.updateSequenceI(newSeq);\r
         }\r
       }\r
-    }\r
-    catch (Exception ex)\r
-    {\r
-      ex.printStackTrace();\r
-    }\r
   }\r
 \r
   public String print()\r
@@ -122,7 +121,7 @@ public class PIRFile
       {\r
         // modeller doesn't really do nucleotides, so we don't do anything fancy\r
         // Nucleotide sequence tags should have a >DL; prefix\r
-        out.append(">P1;" + s[i].getName() + "\n"); // JBPNote Should change >P to >N\r
+        out.append(">N1;" + s[i].getName() + "\n"); // JBPNote Should change >P to >N\r
         if (s[i].getDescription() == null)\r
         {\r
           out.append(s[i].getName() + " " +\r