Formatting

[jalview.git] / src / jalview / io / PIRFile.java

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 724fea8..910d189 100755 (executable)
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -21,23 +21,19 @@ package jalview.io;
 import java.io.*;\r
 import java.util.*;\r
 \r
-import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
 \r
 public class PIRFile\r
     extends AlignFile\r
 {\r
+  public static boolean useModellerOutput = false;\r
+\r
   Vector words = new Vector(); //Stores the words in a line after splitting\r
 \r
   public PIRFile()\r
   {\r
   }\r
 \r
-  public PIRFile(String inStr)\r
-  {\r
-    super(inStr);\r
-  }\r
-\r
   public PIRFile(String inFile, String type)\r
       throws IOException\r
   {\r
@@ -45,59 +41,58 @@ public class PIRFile
   }\r
 \r
   public void parse()\r
+      throws IOException\r
   {\r
-    try\r
-    {\r
-      StringBuffer sequence;\r
-      String line = null;\r
+    StringBuffer sequence;\r
+    String line = null;\r
+    ModellerDescription md;\r
 \r
-      while ( (line = nextLine()) != null)\r
+    while ( (line = nextLine()) != null)\r
+    {\r
+      if (line.length() == 0)\r
       {\r
-        if (line.length() == 0)\r
-        {\r
-          //System.out.println("blank line");\r
-          continue;\r
-        }\r
-        if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)\r
-        {\r
-          continue;\r
-        }\r
-        Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));\r
+        //System.out.println("blank line");\r
+        continue;\r
+      }\r
+      if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)\r
+      {\r
+        continue;\r
+      }\r
+      Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));\r
 \r
-        sequence = new StringBuffer();\r
+      sequence = new StringBuffer();\r
 \r
-        newSeq.setDescription(nextLine()); // this is the title line\r
+      newSeq.setDescription(nextLine()); // this is the title line\r
 \r
-        boolean starFound = false;\r
+      boolean starFound = false;\r
 \r
-        while(!starFound)\r
-        {\r
-          line = nextLine();\r
-          sequence.append(line);\r
-\r
-          if (line == null)\r
-            break;\r
+      while (!starFound)\r
+      {\r
+        line = nextLine();\r
+        sequence.append(line);\r
 \r
-          if (line.indexOf("*") > -1)\r
-          {\r
-            starFound = true;\r
-          }\r
+        if (line == null)\r
+        {\r
+          break;\r
         }\r
 \r
-        if (sequence.length() > 0)\r
+        if (line.indexOf("*") > -1)\r
         {\r
-          sequence.setLength(sequence.length() - 1);\r
-          newSeq.setSequence(sequence.toString());\r
-          seqs.addElement(newSeq);\r
-          ModellerDescription md = new ModellerDescription(newSeq.\r
-              getDescription());\r
-          md.updateSequenceI(newSeq);\r
+          starFound = true;\r
         }\r
       }\r
-    }\r
-    catch (Exception ex)\r
-    {\r
-      ex.printStackTrace();\r
+\r
+      if (sequence.length() > 0)\r
+      {\r
+        sequence.setLength(sequence.length() - 1);\r
+        newSeq.setSequence(sequence.toString());\r
+\r
+        seqs.addElement(newSeq);\r
+\r
+        md = new ModellerDescription(newSeq.\r
+                                     getDescription());\r
+        md.updateSequenceI(newSeq);\r
+      }\r
     }\r
   }\r
 \r
@@ -112,17 +107,27 @@ public class PIRFile
     int len = 72;\r
     StringBuffer out = new StringBuffer();\r
     int i = 0;\r
+    ModellerDescription md;\r
 \r
     while ( (i < s.length) && (s[i] != null))\r
     {\r
-      String seq = s[i].getSequence();\r
+      String seq = s[i].getSequenceAsString();\r
       seq = seq + "*";\r
 \r
       if (is_NA)\r
       {\r
         // modeller doesn't really do nucleotides, so we don't do anything fancy\r
-        // Nucleotide sequence tags should have a >DL; prefix\r
-        out.append(">P1;" + s[i].getName() + "\n"); // JBPNote Should change >P to >N\r
+        // Official tags area as follows, for now we'll use P1 and DL\r
+        // Protein (complete) P1\r
+        // Protein (fragment) F1\r
+        // DNA (linear) Dl\r
+        // DNA (circular) DC\r
+        // RNA (linear) RL\r
+        // RNA (circular) RC\r
+        // tRNA N3\r
+        // other functional RNA N1\r
+\r
+        out.append(">N1;" + s[i].getName() + "\n");\r
         if (s[i].getDescription() == null)\r
         {\r
           out.append(s[i].getName() + " " +\r
@@ -131,14 +136,32 @@ public class PIRFile
         }\r
         else\r
         {\r
-          out.append(s[i].getDescription()+"\n");\r
+          out.append(s[i].getDescription() + "\n");\r
         }\r
       }\r
       else\r
       {\r
-        out.append(">P1;" + s[i].getName() + "\n");\r
-        ModellerDescription md = new ModellerDescription(s[i]);\r
-        out.append(md.getDescriptionLine() + "\n");\r
+\r
+        if (useModellerOutput)\r
+        {\r
+          out.append(">P1;" + s[i].getName() + "\n");\r
+          md = new ModellerDescription(s[i]);\r
+          out.append(md.getDescriptionLine() + "\n");\r
+        }\r
+        else\r
+        {\r
+          out.append(">P1;" + printId(s[i]) + "\n");\r
+          if (s[i].getDescription() != null)\r
+          {\r
+            out.append(s[i].getDescription() + "\n");\r
+          }\r
+          else\r
+          {\r
+            out.append(s[i].getName() + " "\r
+                       + (s[i].getEnd() - s[i].getStart() + 1)\r
+                       + " residues\n");\r
+          }\r
+        }\r
       }\r
       int nochunks = (seq.length() / len) + 1;\r
 \r