X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=b958456265cb655472c75d783329a3ab2a07887f;hb=38299bef6dfd4b713f615781e631dcb66e1155f2;hp=d4b818b4d64c554c8433b687e811fc1168985c00;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index d4b818b..b958456 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -21,12 +21,13 @@ package jalview.io;
 import java.io.*;
 import java.util.*;
 
-import jalview.analysis.*;
 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()
@@ -44,21 +45,23 @@ public class PIRFile
     super(inFile, type);
   }
 
-  public void parse()
+  public void parse() throws IOException
   {
-    try
-    {
       StringBuffer sequence;
       String line = null;
+      ModellerDescription md;
 
       while ( (line = nextLine()) != null)
       {
-        if(line.length()==0)
+        if (line.length() == 0)
         {
           //System.out.println("blank line");
           continue;
         }
-
+        if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
+        {
+          continue;
+        }
         Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
 
         sequence = new StringBuffer();
@@ -81,19 +84,24 @@ public class PIRFile
           }
         }
 
-        if(sequence.length()>0)
+        if (sequence.length() > 0)
         {
           sequence.setLength(sequence.length() - 1);
-
           newSeq.setSequence(sequence.toString());
+          if (!isValidProteinSequence(newSeq.getSequence()))
+          {
+            throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
+                                  +" : "+ newSeq.getName()
+                                  +" : "+invalidCharacter);
+          }
+
           seqs.addElement(newSeq);
+
+          md = new ModellerDescription(newSeq.
+                getDescription());
+          md.updateSequenceI(newSeq);
         }
       }
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
   }
 
   public String print()
@@ -107,20 +115,58 @@ 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 + "*";
 
-      out.append(">P1;" + printId(s[i]) + "\n");
 
-      if(s[i].getDescription()!=null)
-        out.append(s[i].getDescription()+"\n");
+      if (is_NA)
+      {
+          // 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() + " " +
+                     (s[i].getEnd() - s[i].getStart() + 1));
+          out.append(is_NA ? " bases\n" : " residues\n");
+        }
+        else
+        {
+          out.append(s[i].getDescription()+"\n");
+        }
+      }
       else
       {
-        out.append(s[i].getName()+" "+ (s[i].getEnd() - s[i].getStart() + 1));
-        out.append( is_NA ? " bases\n" : " residues\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;