Add support RNAML format

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

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index e6181fd..5bc7bd5 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 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,14 @@ package jalview.io;
 import java.io.*;
 import java.util.*;
 
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+
 import jalview.datamodel.*;
 
 public class PIRFile extends AlignFile
@@ -32,12 +40,12 @@ public class PIRFile extends AlignFile
   {
   }
 
-  public PIRFile(String inFile, String type) throws IOException
+  public PIRFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
   {
     super(inFile, type);
   }
 
-  public PIRFile(FileParse source) throws IOException
+  public PIRFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
   {
     super(source);
   }
@@ -127,16 +135,19 @@ public class PIRFile extends AlignFile
         // tRNA N3
         // other functional RNA N1
 
-        out.append(">N1;" + s[i].getName() + "\n");
+        out.append(">N1;" + s[i].getName());
+        out.append(newline);
         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");
+          out.append(is_NA ? " bases" : " residues");
+          out.append(newline);
         }
         else
         {
-          out.append(s[i].getDescription() + "\n");
+          out.append(s[i].getDescription());
+          out.append(newline);
         }
       }
       else
@@ -144,23 +155,26 @@ public class PIRFile extends AlignFile
 
         if (useModellerOutput)
         {
-          out.append(">P1;" + s[i].getName() + "\n");
+          out.append(">P1;" + s[i].getName());
+          out.append(newline);
           md = new ModellerDescription(s[i]);
-          out.append(md.getDescriptionLine() + "\n");
+          out.append(md.getDescriptionLine());
+          out.append(newline);
         }
         else
         {
-          out.append(">P1;" + printId(s[i]) + "\n");
+          out.append(">P1;" + printId(s[i]));
+          out.append(newline);
           if (s[i].getDescription() != null)
           {
-            out.append(s[i].getDescription() + "\n");
+            out.append(s[i].getDescription());
+            out.append(newline);
           }
           else
           {
-            out
-                    .append(s[i].getName() + " "
-                            + (s[i].getEnd() - s[i].getStart() + 1)
-                            + " residues\n");
+            out.append(s[i].getName() + " "
+                    + (s[i].getEnd() - s[i].getStart() + 1) + " residues");
+            out.append(newline);
           }
         }
       }
@@ -173,11 +187,13 @@ public class PIRFile extends AlignFile
 
         if (end < seq.length())
         {
-          out.append(seq.substring(start, end) + "\n");
+          out.append(seq.substring(start, end));
+          out.append(newline);
         }
         else if (start < seq.length())
         {
-          out.append(seq.substring(start) + "\n");
+          out.append(seq.substring(start));
+          out.append(newline);
         }
       }