X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FComplexAlignFile.java;fp=src%2Fjalview%2Fapi%2FComplexAlignFile.java;h=133a739b8b1fac58ab499c41f3fc791a97ba321f;hb=2a9991ef1eb02d97e9c8ed1644f292117ae6f600;hp=0000000000000000000000000000000000000000;hpb=2ce465aaa3047e1ef758a26af2fbfcf8626b4a69;p=jalview.git

diff --git a/src/jalview/api/ComplexAlignFile.java b/src/jalview/api/ComplexAlignFile.java
new file mode 100644
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--- /dev/null
+++ b/src/jalview/api/ComplexAlignFile.java
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+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();
+
+}