JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index a26bc46..3f0fea0 100755 (executable)
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,25 +20,25 @@
  */
 package jalview.io;
 
+import jalview.bin.Cache;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.io.IOException;
-import java.util.Vector;
 
 public class PIRFile extends AlignFile
 {
-  public static boolean useModellerOutput = false;
-
-  Vector words = new Vector(); // Stores the words in a line after splitting
+  // Vector words = new Vector(); // Stores the words in a line after splitting
 
   public PIRFile()
   {
   }
 
-  public PIRFile(String inFile, String type) throws IOException
+  public PIRFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public PIRFile(FileParse source) throws IOException
@@ -102,19 +102,14 @@ public class PIRFile extends AlignFile
   }
 
   @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
-
-  public String print(SequenceI[] s)
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
-    boolean is_NA = jalview.util.Comparison.isNucleotide(s);
+    boolean is_NA = Comparison.isNucleotide(s);
     int len = 72;
     StringBuffer out = new StringBuffer();
     int i = 0;
     ModellerDescription md;
-
+    boolean useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
     while ((i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequenceAsString();
@@ -150,7 +145,6 @@ public class PIRFile extends AlignFile
       }
       else
       {
-
         if (useModellerOutput)
         {
           out.append(">P1;" + s[i].getName());
@@ -161,7 +155,7 @@ public class PIRFile extends AlignFile
         }
         else
         {
-          out.append(">P1;" + printId(s[i]));
+          out.append(">P1;" + printId(s[i], jvsuffix));
           out.append(newline);
           if (s[i].getDescription() != null)
           {