X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FPIRFile.java;h=d4b818b4d64c554c8433b687e811fc1168985c00;hb=555416956c6668d4f49d0cbf5a1e784e20636afa;hp=a15a4cbf0b29cbeae9f2ff9edb3665048ddcddf0;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index a15a4cb..d4b818b 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -48,52 +48,46 @@ public class PIRFile
   {
     try
     {
-      String id;
-      String start;
-      String end;
       StringBuffer sequence;
       String line = null;
 
       while ( (line = nextLine()) != null)
       {
-        try
+        if(line.length()==0)
         {
-          id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));
-          line = line.substring(line.indexOf("/") + 1);
-          start = line.substring(0, line.indexOf("-"));
-          end = line.substring(line.indexOf("-") + 1);
-        }
-        catch (Exception ex)
-        {
-          id = "No id";
-          start = "0";
-          end = "0";
+          //System.out.println("blank line");
+          continue;
         }
 
+        Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
+
         sequence = new StringBuffer();
 
-        line = nextLine(); // this is the title line
+        newSeq.setDescription(nextLine()); // this is the title line
 
         boolean starFound = false;
 
-        do
+        while(!starFound)
         {
           line = nextLine();
           sequence.append(line);
 
+          if (line == null)
+            break;
+
           if (line.indexOf("*") > -1)
           {
             starFound = true;
           }
         }
-        while (!starFound);
 
-        sequence.setLength(sequence.length() - 1);
+        if(sequence.length()>0)
+        {
+          sequence.setLength(sequence.length() - 1);
 
-        Sequence newSeq = new Sequence(id, sequence.toString(),
-                                       Integer.parseInt(start),
-                                       Integer.parseInt(end));
-        seqs.addElement(newSeq);
+          newSeq.setSequence(sequence.toString());
+          seqs.addElement(newSeq);
+        }
       }
     }
     catch (Exception ex)
@@ -107,41 +101,27 @@ public class PIRFile
     return print(getSeqsAsArray());
   }
 
-  public static String print(SequenceI[] s)
-  {
-    return print(s, 72, true);
-  }
-
-  public static String print(SequenceI[] s, int len)
-  {
-    return print(s, len, true);
-  }
-
-  public static String print(SequenceI[] s, int len, boolean gaps)
+  public String print(SequenceI[] s)
   {
+    boolean is_NA = jalview.util.Comparison.isNucleotide(s);
+    int len = 72;
     StringBuffer out = new StringBuffer();
     int i = 0;
 
     while ( (i < s.length) && (s[i] != null))
     {
-      String seq = "";
+      String seq = s[i].getSequence();
+      seq = seq + "*";
 
-      if (gaps)
-      {
-        seq = s[i].getSequence() + "*";
-      }
+      out.append(">P1;" + printId(s[i]) + "\n");
+
+      if(s[i].getDescription()!=null)
+        out.append(s[i].getDescription()+"\n");
       else
       {
-        seq = AlignSeq.extractGaps(s[i].getSequence(), "-");
-        seq = AlignSeq.extractGaps(seq, ".");
-        seq = AlignSeq.extractGaps(seq, " ");
-        seq = seq + "*";
+        out.append(s[i].getName()+" "+ (s[i].getEnd() - s[i].getStart() + 1));
+        out.append( is_NA ? " bases\n" : " residues\n");
       }
-
-      out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +
-                 s[i].getEnd() + "\n");
-      out.append(" Dummy title\n");
-
       int nochunks = (seq.length() / len) + 1;
 
       for (int j = 0; j < nochunks; j++)
@@ -165,9 +145,4 @@ public class PIRFile
     return out.toString();
   }
 
-  public static void main(String[] args)
-  {
-    String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";
-    PIRFile fa = new PIRFile(inStr);
-  }
 }