JAL-2256 Corrected AllCols/Rows iterator behaviour for single element

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index d36a588..7333075 100755 (executable)
--- 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;
 
@@ -65,7 +66,7 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
   /**
    * Properties to be added to generated alignment object
    */
-  protected Hashtable properties;
+  private Hashtable properties;
 
   long start;
 
@@ -370,8 +371,8 @@ 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
    * 
@@ -382,6 +383,11 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
     return seq.getDisplayId(jvsuffix);
   }
 
+  String printId(SequenceI seq)
+  {
+    return printId(seq, true);
+  }
+
   /**
    * vector of String[] treeName, newickString pairs
    */
@@ -411,4 +417,8 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
     }
   }
 
+  protected void addSequence(SequenceI seq)
+  {
+    seqs.add(seq);
+  }
 }