vamsasDemo new branch

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

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 65890a9..d4b818b 100755 (executable)
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -48,9 +48,6 @@ public class PIRFile
   {\r
     try\r
     {\r
-      String id;\r
-      String start;\r
-      String end;\r
       StringBuffer sequence;\r
       String line = null;\r
 \r
@@ -62,31 +59,11 @@ public class PIRFile
           continue;\r
         }\r
 \r
-        id = "No id";\r
-        start = "1";\r
-        end = "-1";\r
-\r
-        try\r
-        {\r
-          int slashIndex = line.indexOf("/");\r
-          if(slashIndex!=-1)\r
-          {\r
-            id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));\r
-            line = line.substring(line.indexOf("/") + 1);\r
-            start = line.substring(0, line.indexOf("-"));\r
-            end = line.substring(line.indexOf("-") + 1);\r
-          }\r
-          else\r
-          {\r
-            id = line.substring(line.indexOf(";")+1);\r
-          }\r
-        }\r
-        catch (Exception ex)\r
-        {    }// Default id, start and end unchanged\r
+        Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));\r
 \r
         sequence = new StringBuffer();\r
 \r
-        line = nextLine(); // this is the title line\r
+        newSeq.setDescription(nextLine()); // this is the title line\r
 \r
         boolean starFound = false;\r
 \r
@@ -108,9 +85,7 @@ public class PIRFile
         {\r
           sequence.setLength(sequence.length() - 1);\r
 \r
-          Sequence newSeq = new Sequence(id, sequence.toString(),\r
-                                         Integer.parseInt(start),\r
-                                         Integer.parseInt(end));\r
+          newSeq.setSequence(sequence.toString());\r
           seqs.addElement(newSeq);\r
         }\r
       }\r
@@ -126,41 +101,27 @@ public class PIRFile
     return print(getSeqsAsArray());\r
   }\r
 \r
-  public static String print(SequenceI[] s)\r
-  {\r
-    return print(s, 72, true);\r
-  }\r
-\r
-  public static String print(SequenceI[] s, int len)\r
-  {\r
-    return print(s, len, true);\r
-  }\r
-\r
-  public static String print(SequenceI[] s, int len, boolean gaps)\r
+  public String print(SequenceI[] s)\r
   {\r
+    boolean is_NA = jalview.util.Comparison.isNucleotide(s);\r
+    int len = 72;\r
     StringBuffer out = new StringBuffer();\r
     int i = 0;\r
 \r
     while ( (i < s.length) && (s[i] != null))\r
     {\r
-      String seq = "";\r
+      String seq = s[i].getSequence();\r
+      seq = seq + "*";\r
 \r
-      if (gaps)\r
-      {\r
-        seq = s[i].getSequence() + "*";\r
-      }\r
+      out.append(">P1;" + printId(s[i]) + "\n");\r
+\r
+      if(s[i].getDescription()!=null)\r
+        out.append(s[i].getDescription()+"\n");\r
       else\r
       {\r
-        seq = AlignSeq.extractGaps(s[i].getSequence(), "-");\r
-        seq = AlignSeq.extractGaps(seq, ".");\r
-        seq = AlignSeq.extractGaps(seq, " ");\r
-        seq = seq + "*";\r
+        out.append(s[i].getName()+" "+ (s[i].getEnd() - s[i].getStart() + 1));\r
+        out.append( is_NA ? " bases\n" : " residues\n");\r
       }\r
-\r
-      out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
-                 s[i].getEnd() + "\n");\r
-      out.append(" Dummy title\n");\r
-\r
       int nochunks = (seq.length() / len) + 1;\r
 \r
       for (int j = 0; j < nochunks; j++)\r