X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=d9ed5166d9f88d04d0818007dc6114cd8f297b7f;hb=efff0826d9368314db6215e90a856059b86dbea8;hp=b18b8f4f71aa9a903ffe751f0a00972545322837;hpb=3a993bbe274824870c78bd7695c42fa93908cb30;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index b18b8f4..d9ed516 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,60 +1,65 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
 
-public class PIRFile
-    extends AlignFile
+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
   {
     super(source);
   }
-  public void parse()
-      throws IOException
+
+  @Override
+  public void parse() throws IOException
   {
     StringBuffer sequence;
     String line = null;
     ModellerDescription md;
 
-    while ( (line = nextLine()) != null)
+    while ((line = nextLine()) != null)
     {
       if (line.length() == 0)
       {
-        //System.out.println("blank line");
+        // System.out.println("blank line");
         continue;
       }
       if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
@@ -92,27 +97,22 @@ public class PIRFile
 
         seqs.addElement(newSeq);
 
-        md = new ModellerDescription(newSeq.
-                                     getDescription());
+        md = new ModellerDescription(newSeq.getDescription());
         md.updateSequenceI(newSeq);
       }
     }
   }
 
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
-
-  public String print(SequenceI[] s)
+  @Override
+  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;
 
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequenceAsString();
       seq = seq + "*";
@@ -130,16 +130,19 @@ public class PIRFile
         // 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(s[i].getName() + " "
+                  + (s[i].getEnd() - s[i].getStart() + 1));
+          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
@@ -147,26 +150,31 @@ public class PIRFile
 
         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], jvsuffix));
+          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");
+                    + (s[i].getEnd() - s[i].getStart() + 1) + " residues");
+            out.append(newline);
           }
         }
       }
-      int nochunks = (seq.length() / len) + 1;
+      int nochunks = (seq.length() / len)
+              + (seq.length() % len > 0 ? 1 : 0);
 
       for (int j = 0; j < nochunks; j++)
       {
@@ -175,11 +183,13 @@ public class PIRFile
 
         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);
         }
       }