From bd37e6102cbb5e5a2e12d8375ece436cbfbb1bc2 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Mon, 15 Jun 2015 11:29:46 +0100
Subject: [PATCH] JAL-1641 docs for ComplexAlignFile interface

---
 src/jalview/api/ComplexAlignFile.java    |   27 +++++++++++++++++++++++++++
 src/jalview/gui/CutAndPasteTransfer.java |   14 --------------
 2 files changed, 27 insertions(+), 14 deletions(-)

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();
 
 }
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 3d52ee1..f3c4d87 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -237,21 +237,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
           af.changeColour(cs);
-          // ((HtmlFile) source).applySettingsToAlignmentView(af);
         }
-        // else if (source instanceof JSONFile)
-        // {
-        // ColumnSelection colSel = ((JSONFile) source).getColumnSelection();
-        // SequenceI[] hiddenSeqs = ((JSONFile) source).getHiddenSequences();
-        // boolean showSeqFeatures = ((HtmlFile) source).isShowSeqFeatures();
-        // ColourSchemeI cs = ((HtmlFile) source).getColourScheme();
-        // af = new AlignFrame(al, hiddenSeqs, colSel,
-        // AlignFrame.DEFAULT_WIDTH,
-        // AlignFrame.DEFAULT_HEIGHT);
-        // af.getViewport().setShowSequenceFeatures(showSeqFeatures);
-        // af.changeColour(cs);
-        // // ((JSONFile) source).applySettingsToAlignmentView(af);
-        // }
         else
         {
           af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
-- 
1.7.10.2