X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=910d18929e48d60b65664bc33312104b556b1335;hb=ce886100c1eae01eac7d59c961e694f4493d4bcb;hp=a33e118625585a423e6f9f4a15d0ebb365906be4;hpb=558597672640984d936ea22409a674293192a09c;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index a33e118..910d189 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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -40,57 +40,60 @@ public class PIRFile
     super(inFile, type);
   }
 
-  public void parse() throws IOException
+  public void parse()
+      throws IOException
   {
-      StringBuffer sequence;
-      String line = null;
-      ModellerDescription md;
+    StringBuffer sequence;
+    String line = null;
+    ModellerDescription md;
 
-      while ( (line = nextLine()) != null)
+    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();
+        //System.out.println("blank line");
+        continue;
+      }
+      if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
+      {
+        continue;
+      }
+      Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
 
-        newSeq.setDescription(nextLine()); // this is the title line
+      sequence = new StringBuffer();
 
-        boolean starFound = false;
+      newSeq.setDescription(nextLine()); // this is the title line
 
-        while(!starFound)
-        {
-          line = nextLine();
-          sequence.append(line);
+      boolean starFound = false;
 
-          if (line == null)
-            break;
+      while (!starFound)
+      {
+        line = nextLine();
+        sequence.append(line);
 
-          if (line.indexOf("*") > -1)
-          {
-            starFound = true;
-          }
+        if (line == null)
+        {
+          break;
         }
 
-        if (sequence.length() > 0)
+        if (line.indexOf("*") > -1)
         {
-          sequence.setLength(sequence.length() - 1);
-          newSeq.setSequence(sequence.toString());
+          starFound = true;
+        }
+      }
 
-          seqs.addElement(newSeq);
+      if (sequence.length() > 0)
+      {
+        sequence.setLength(sequence.length() - 1);
+        newSeq.setSequence(sequence.toString());
 
-          md = new ModellerDescription(newSeq.
-                getDescription());
-          md.updateSequenceI(newSeq);
-        }
+        seqs.addElement(newSeq);
+
+        md = new ModellerDescription(newSeq.
+                                     getDescription());
+        md.updateSequenceI(newSeq);
       }
+    }
   }
 
   public String print()
@@ -111,19 +114,18 @@ public class PIRFile
       String seq = s[i].getSequenceAsString();
       seq = seq + "*";
 
-
       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
+        // 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)
@@ -134,28 +136,32 @@ public class PIRFile
         }
         else
         {
-          out.append(s[i].getDescription()+"\n");
+          out.append(s[i].getDescription() + "\n");
         }
       }
       else
       {
 
-       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");
-       }
+        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;