X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=fa9a28bf6b99eb04ffaefa5982493f9f9450569f;hb=a282e50f4076e9ec6da6a0500df2c80652a2353d;hp=6d6e52578aa4f66dcd1d184e1aeb2c964794300b;hpb=2535623533691d27fb7a23aef13d0f4f13be0a68;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 6d6e525..fa9a28b 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -26,17 +26,14 @@ import jalview.datamodel.*;
 public class PIRFile
     extends AlignFile
 {
+  public static boolean useModellerOutput = false;
+
   Vector words = new Vector(); //Stores the words in a line after splitting
 
   public PIRFile()
   {
   }
 
-  public PIRFile(String inStr)
-  {
-    super(inStr);
-  }
-
   public PIRFile(String inFile, String type)
       throws IOException
   {
@@ -47,6 +44,7 @@ public class PIRFile
   {
       StringBuffer sequence;
       String line = null;
+      ModellerDescription md;
 
       while ( (line = nextLine()) != null)
       {
@@ -93,8 +91,9 @@ public class PIRFile
           }
 
           seqs.addElement(newSeq);
-          ModellerDescription md = new ModellerDescription(newSeq.
-              getDescription());
+
+          md = new ModellerDescription(newSeq.
+                getDescription());
           md.updateSequenceI(newSeq);
         }
       }
@@ -111,17 +110,28 @@ public class PIRFile
     int len = 72;
     StringBuffer out = new StringBuffer();
     int i = 0;
+    ModellerDescription md;
 
     while ( (i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequence();
       seq = seq + "*";
 
+
       if (is_NA)
       {
-        // modeller doesn't really do nucleotides, so we don't do anything fancy
-        // Nucleotide sequence tags should have a >DL; prefix
-        out.append(">N1;" + s[i].getName() + "\n"); // JBPNote Should change >P to >N
+          // modeller doesn't really do nucleotides, so we don't do anything fancy
+          // Official tags area as follows, for now we'll use P1 and DL
+          // Protein (complete) P1
+          // Protein (fragment) F1
+          // DNA (linear) Dl
+          // DNA (circular) DC
+          // RNA (linear) RL
+          // RNA (circular) RC
+          // tRNA N3
+          // other functional RNA N1
+
+        out.append(">N1;" + s[i].getName() + "\n");
         if (s[i].getDescription() == null)
         {
           out.append(s[i].getName() + " " +
@@ -135,9 +145,23 @@ public class PIRFile
       }
       else
       {
-        out.append(">P1;" + s[i].getName() + "\n");
-        ModellerDescription md = new ModellerDescription(s[i]);
-        out.append(md.getDescriptionLine() + "\n");
+
+       if(useModellerOutput)
+       {
+         out.append(">P1;" + s[i].getName() + "\n");
+         md = new ModellerDescription(s[i]);
+         out.append(md.getDescriptionLine() + "\n");
+       }
+       else
+       {
+         out.append(">P1;" + printId(s[i]) + "\n");
+         if (s[i].getDescription() != null)
+           out.append(s[i].getDescription() + "\n");
+         else
+           out.append(s[i].getName() + " "
+                      + (s[i].getEnd() - s[i].getStart() + 1)
+                      + " residues\n");
+       }
       }
       int nochunks = (seq.length() / len) + 1;