X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=3fa4ac2b01e6b889664462ad976fef63ea6b616f;hb=558597672640984d936ea22409a674293192a09c;hp=0691d82d47e10dd93bb8721fb3866f8ce860a917;hpb=c3c305755d392741176209a0274a47897ac4d8a8;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 0691d82..3fa4ac2 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -36,7 +36,7 @@ public abstract class AlignFile extends FileParse
     int noSeqs = 0;
     int maxLength = 0;
     Vector seqs;
-    Vector headers;
+    Vector annotations;
     long start;
     long end;
     boolean jvSuffix = true;
@@ -86,13 +86,24 @@ public abstract class AlignFile extends FileParse
         return s;
     }
 
+    public void addAnnotations(Alignment al)
+    {
+      for(int i=0; i<annotations.size(); i++)
+      {
+        al.addAnnotation(
+            (AlignmentAnnotation)annotations.elementAt(i)
+            );
+      }
+
+    }
+
     /**
      * Initialise objects to store sequence data in.
      */
     protected void initData()
     {
         seqs = new Vector();
-        headers = new Vector();
+        annotations = new Vector();
     }
 
     /**
@@ -110,20 +121,7 @@ public abstract class AlignFile extends FileParse
         }
     }
 
-    // Checks whether sequence is valid aa characters
-    protected boolean isValidProteinSequence(String sequence)
-    {
-        for (int i = 0; i < sequence.length(); i++)
-            if (jalview.schemes.ResidueProperties.aaIndex[sequence.charAt(i)]==-1)
-            {
-                invalidCharacter = sequence.charAt(i);
-                return false;
-            }
-
-        return true;
-    }
 
-    char invalidCharacter;
 
     /**
      * This method must be implemented to parse the contents of the file.