X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=910d18929e48d60b65664bc33312104b556b1335;hb=ce886100c1eae01eac7d59c961e694f4493d4bcb;hp=65890a9543561baefead60ff4135acbe18e55794;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 65890a9..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) 2005 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
@@ -21,23 +21,19 @@ 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()
   {
   }
 
-  public PIRFile(String inStr)
-  {
-    super(inStr);
-  }
-
   public PIRFile(String inFile, String type)
       throws IOException
   {
@@ -45,79 +41,58 @@ public class PIRFile
   }
 
   public void parse()
+      throws IOException
   {
-    try
-    {
-      String id;
-      String start;
-      String end;
-      StringBuffer sequence;
-      String line = null;
+    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;
-        }
-
-        id = "No id";
-        start = "1";
-        end = "-1";
+        //System.out.println("blank line");
+        continue;
+      }
+      if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
+      {
+        continue;
+      }
+      Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
 
-        try
-        {
-          int slashIndex = line.indexOf("/");
-          if(slashIndex!=-1)
-          {
-            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);
-          }
-          else
-          {
-            id = line.substring(line.indexOf(";")+1);
-          }
-        }
-        catch (Exception ex)
-        {    }// Default id, start and end unchanged
+      sequence = new StringBuffer();
 
-        sequence = new StringBuffer();
+      newSeq.setDescription(nextLine()); // this is the title line
 
-        line = nextLine(); // this is the title line
+      boolean starFound = false;
 
-        boolean starFound = false;
+      while (!starFound)
+      {
+        line = nextLine();
+        sequence.append(line);
 
-        while(!starFound)
+        if (line == null)
         {
-          line = nextLine();
-          sequence.append(line);
-
-          if (line == null)
-            break;
-
-          if (line.indexOf("*") > -1)
-          {
-            starFound = true;
-          }
+          break;
         }
 
-        if(sequence.length()>0)
+        if (line.indexOf("*") > -1)
         {
-          sequence.setLength(sequence.length() - 1);
-
-          Sequence newSeq = new Sequence(id, sequence.toString(),
-                                         Integer.parseInt(start),
-                                         Integer.parseInt(end));
-          seqs.addElement(newSeq);
+          starFound = true;
         }
       }
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
+
+      if (sequence.length() > 0)
+      {
+        sequence.setLength(sequence.length() - 1);
+        newSeq.setSequence(sequence.toString());
+
+        seqs.addElement(newSeq);
+
+        md = new ModellerDescription(newSeq.
+                                     getDescription());
+        md.updateSequenceI(newSeq);
+      }
     }
   }
 
@@ -126,41 +101,68 @@ 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;
+    ModellerDescription md;
 
     while ( (i < s.length) && (s[i] != null))
     {
-      String seq = "";
+      String seq = s[i].getSequenceAsString();
+      seq = seq + "*";
 
-      if (gaps)
+      if (is_NA)
       {
-        seq = s[i].getSequence() + "*";
+        // 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
       {
-        seq = AlignSeq.extractGaps(s[i].getSequence(), "-");
-        seq = AlignSeq.extractGaps(seq, ".");
-        seq = AlignSeq.extractGaps(seq, " ");
-        seq = seq + "*";
-      }
-
-      out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +
-                 s[i].getEnd() + "\n");
-      out.append(" Dummy title\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;
 
       for (int j = 0; j < nochunks; j++)