X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FComplexAlignFile.java;h=92243fbdf42a989a4eecd17db5a38fcd79ef84f5;hb=bd37e6102cbb5e5a2e12d8375ece436cbfbb1bc2;hp=0d731cdfc7265545f800da8c65400711471e099d;hpb=b7940b625391851ce4c07839e0db161b66c9091f;p=jalview.git

diff --git a/src/jalview/api/ComplexAlignFile.java b/src/jalview/api/ComplexAlignFile.java
index 0d731cd..92243fb 100644
--- a/src/jalview/api/ComplexAlignFile.java
+++ b/src/jalview/api/ComplexAlignFile.java
@@ -4,14 +4,41 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
+/**
+ * This interface should be implemented by complex file parser with the ability
+ * to store linked data and complex view states in addition to alingment data
+ * 
+ * @author tcnofoegbu
+ *
+ */
 public interface ComplexAlignFile
 {
+  /**
+   * Determines if Sequence features should be shown
+   * 
+   * @return
+   */
   public boolean isShowSeqFeatures();
 
+  /**
+   * Obtains the colour scheme from a complex file parser
+   * 
+   * @return
+   */
   public ColourSchemeI getColourScheme();
 
+  /**
+   * Retrieves the Column selection/hidden column from a complex file parser
+   * 
+   * @return
+   */
   public ColumnSelection getColumnSelection();
 
+  /**
+   * Retrieves hidden sequences from a complex file parser
+   * 
+   * @return
+   */
   public SequenceI[] getHiddenSequences();
 
 }