clarified help documentation for annotation file format and tweaked reader code to...

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

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index ec52bac..7cb381d 100755 (executable)
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.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) 2006 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
@@ -32,11 +32,6 @@ public class PfamFile
   {\r
   }\r
 \r
-  public PfamFile(String inStr)\r
-  {\r
-    super(inStr);\r
-  }\r
-\r
   public PfamFile(String inFile, String type)\r
       throws IOException\r
   {\r
@@ -48,8 +43,7 @@ public class PfamFile
     super.initData();\r
   }\r
 \r
-  public void parse()\r
-      throws IOException\r
+  public void parse() throws IOException\r
   {\r
     int i = 0;\r
     String line;\r
@@ -118,8 +112,9 @@ public class PfamFile
 \r
         if (!isValidProteinSequence(newSeq.getSequence()))\r
         {\r
-          throw new IOException(\r
-              "Not a valid protein sequence - (PFAM input)");\r
+          throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
+                                +" : "+ newSeq.getName()\r
+                                +" : "+invalidCharacter);\r
         }\r
       }\r
       else\r
@@ -143,9 +138,9 @@ public class PfamFile
     {\r
       String tmp = printId(s[i]);\r
 \r
-      if (s[i].getSequence().length() > max)\r
+      if (s[i].getSequence().length > max)\r
       {\r
-        max = s[i].getSequence().length();\r
+        max = s[i].getSequence().length;\r
       }\r
 \r
       if (tmp.length() > maxid)\r
@@ -167,7 +162,7 @@ public class PfamFile
     {\r
       out.append(new Format("%-" + maxid + "s").form( printId(s[j])+" "));\r
 \r
-      out.append(s[j].getSequence() + "\n");\r
+      out.append(s[j].getSequenceAsString() + "\n");\r
       j++;\r
     }\r
 \r