X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=2340283ea2e31f0f538a1b4561f411ca3fb95e6f;hb=199068cbd16767a5d47ef4322793ef62d1e96a1f;hp=6d6ab5c4383e32211ffd067a70df046c5f92fc63;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 6d6ab5c..2340283 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -40,7 +40,8 @@ import java.util.Vector;
  * @author $author$
  * @version $Revision$
  */
-public abstract class AlignFile extends FileParse implements AlignmentFileI
+public abstract class AlignFile extends FileParse
+        implements AlignmentFileReaderI, AlignmentFileWriterI
 {
   int noSeqs = 0;
 
@@ -65,14 +66,12 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
   /**
    * Properties to be added to generated alignment object
    */
-  protected Hashtable properties;
+  private Hashtable properties;
 
   long start;
 
   long end;
 
-  boolean jvSuffix = true;
-
   private boolean parseCalled;
 
   /**
@@ -86,6 +85,12 @@ 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.
    * 
@@ -113,8 +118,7 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
    * @throws IOException
    */
   public AlignFile(boolean parseImmediately, String dataObject,
-          DataSourceType sourceType)
-          throws IOException
+          DataSourceType sourceType) throws IOException
   {
     super(dataObject, sourceType);
     initData();
@@ -170,11 +174,6 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
     }
     parseCalled = true;
     parse();
-    // sets the index of each sequence in the alignment
-    for (int i = 0, c = seqs.size(); i < c; i++)
-    {
-      seqs.get(i).setIndex(i);
-    }
   }
 
   /**
@@ -277,9 +276,8 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
   {
     if (key == null)
     {
-      throw new Error(
-              MessageManager
-                      .getString("error.implementation_error_cannot_have_null_alignment"));
+      throw new Error(MessageManager.getString(
+              "error.implementation_error_cannot_have_null_alignment"));
     }
     if (value == null)
     {
@@ -335,18 +333,6 @@ 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
@@ -378,14 +364,21 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
   }
 
   /**
-   * Creates the output id. Adds prefix Uniprot format source|id And suffix
-   * Jalview /start-end
+   * Creates the output id. Adds prefix Uniprot format source|id and optionally
+   * suffix Jalview /start-end
+   * 
+   * @param jvsuffix
    * 
    * @String id Id to be parsed
    */
+  String printId(SequenceI seq, boolean jvsuffix)
+  {
+    return seq.getDisplayId(jvsuffix);
+  }
+
   String printId(SequenceI seq)
   {
-    return seq.getDisplayId(jvSuffix);
+    return printId(seq, true);
   }
 
   /**
@@ -417,4 +410,8 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
     }
   }
 
+  protected void addSequence(SequenceI seq)
+  {
+    seqs.add(seq);
+  }
 }