X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FComplexAlignFile.java;h=1b579adc519f810b90dcfb33bf3b94b5cbf14edf;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=0d731cdfc7265545f800da8c65400711471e099d;hpb=70f9c4700f20a8fa57ed7eb974277d8bad0723c2;p=jalview.git

diff --git a/src/jalview/api/ComplexAlignFile.java b/src/jalview/api/ComplexAlignFile.java
index 0d731cd..1b579ad 100644
--- a/src/jalview/api/ComplexAlignFile.java
+++ b/src/jalview/api/ComplexAlignFile.java
@@ -1,17 +1,68 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.api;
 
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 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();
 
-  public ColourSchemeI getColourScheme();
+  /**
+   * Obtains the colour scheme from a complex file parser
+   * 
+   * @return
+   */
+  public String getGlobalColourScheme();
 
-  public ColumnSelection getColumnSelection();
+  /**
+   * Retrieves the Column selection/hidden column from a complex file parser
+   * 
+   * @return
+   */
+  public HiddenColumns getHiddenColumns();
 
+  /**
+   * Retrieves hidden sequences from a complex file parser
+   * 
+   * @return
+   */
   public SequenceI[] getHiddenSequences();
 
+  /**
+   * Retrieves displayed features from a complex file parser
+   * 
+   * @return
+   */
+  public FeaturesDisplayedI getDisplayedFeatures();
 }