Merge branch 'develop' into features/JAL-653_gffalignments

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

diff --git a/src/jalview/api/ComplexAlignFile.java b/src/jalview/api/ComplexAlignFile.java
new file mode 100644 (file)
index 0000000..133a739
--- /dev/null
+++ b/src/jalview/api/ComplexAlignFile.java
@@ -0,0 +1,43 @@
+package jalview.api;
+
+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();
+
+}