Merge branch 'develop' into bug/JAL-1775

[jalview.git] / src / jalview / api / ComplexAlignFile.java

diff --git a/src/jalview/api/ComplexAlignFile.java b/src/jalview/api/ComplexAlignFile.java
index 0d731cd..133a739 100644 (file)
--- a/src/jalview/api/ComplexAlignFile.java
+++ b/src/jalview/api/ComplexAlignFile.java
@@ -4,14 +4,40 @@ 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 Alignment data
+ * 
+ *
+ */
 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();
 
 }