fileFormat enum wip changes

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 6d6ab5c..d36a588 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -71,8 +71,6 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
 
   long end;
 
-  boolean jvSuffix = true;
-
   private boolean parseCalled;
 
   /**
@@ -86,6 +84,12 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
     initData();
   }
 
+  public AlignFile(SequenceI[] seqs)
+  {
+    this();
+    setSeqs(seqs);
+  }
+
   /**
    * Constructor which parses the data from a file of some specified type.
    * 
@@ -335,18 +339,6 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
   public abstract void parse() throws IOException;
 
   /**
-   * Print out in alignment file format the Sequences in the seqs Vector.
-   */
-  @Override
-  public abstract String print();
-
-  @Override
-  public void addJVSuffix(boolean b)
-  {
-    jvSuffix = b;
-  }
-
-  /**
    * A general parser for ids.
    * 
    * @String id Id to be parsed
@@ -381,11 +373,13 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
    * Creates the output id. Adds prefix Uniprot format source|id And suffix
    * Jalview /start-end
    * 
+   * @param jvsuffix
+   * 
    * @String id Id to be parsed
    */
-  String printId(SequenceI seq)
+  String printId(SequenceI seq, boolean jvsuffix)
   {
-    return seq.getDisplayId(jvSuffix);
+    return seq.getDisplayId(jvsuffix);
   }
 
   /**