(JAL-963) refactor RNA helix helper class to schemes

[jalview.git] / src / jalview / gui / RNAHelicesColourChooser.java

diff --git a/src/jalview/gui/RNAHelicesColourChooser.java b/src/jalview/gui/RNAHelicesColourChooser.java
deleted file mode 100644 (file)
index e575b91..0000000
--- a/src/jalview/gui/RNAHelicesColourChooser.java
+++ /dev/null
@@ -1,149 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
- * 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/>.
- */
-package jalview.gui;
-
-import java.util.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-/**
- * Helps generate the colors for RNA secondary structure. Future: add option to
- * change colors based on covariation.
- * 
- * @author Lauren Michelle Lui
- * 
- */
-public class RNAHelicesColourChooser
-{
-
-  AlignViewport av;
-
-  AlignmentPanel ap;
-
-  ColourSchemeI oldcs;
-
-  Hashtable oldgroupColours;
-
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
-
-  boolean adjusting = false;
-
-  public RNAHelicesColourChooser(AlignViewport av, final AlignmentPanel ap)
-  {
-    oldcs = av.getGlobalColourScheme();
-    if (av.getAlignment().getGroups() != null)
-    {
-      oldgroupColours = new Hashtable();
-      Vector allGroups = ap.av.getAlignment().getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-        if (sg.cs != null)
-        {
-          oldgroupColours.put(sg, sg.cs);
-        }
-      }
-    }
-    this.av = av;
-    this.ap = ap;
-
-    if (oldcs instanceof RNAHelicesColour)
-    {
-      RNAHelicesColour rhc = (RNAHelicesColour) oldcs;
-
-    }
-
-    adjusting = true;
-    Vector list = new Vector();
-    int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
-    {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-        list.addElement(label);
-      else
-        list.addElement(label + "_" + (index++));
-    }
-
-    adjusting = false;
-
-    changeColour();
-
-  }
-
-  void changeColour()
-  {
-    // Check if combobox is still adjusting
-    if (adjusting)
-    {
-      return;
-    }
-
-    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-
-    RNAHelicesColour rhc = null;
-
-    rhc = new RNAHelicesColour(currentAnnotation);
-
-    av.setGlobalColourScheme(rhc);
-
-    if (av.getAlignment().getGroups() != null)
-    {
-      Vector allGroups = ap.av.getAlignment().getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-
-        if (sg.cs == null)
-        {
-          continue;
-        }
-
-        sg.cs = new RNAHelicesColour(currentAnnotation);
-
-      }
-    }
-
-    ap.paintAlignment(false);
-  }
-
-  void reset()
-  {
-    av.setGlobalColourScheme(oldcs);
-    if (av.getAlignment().getGroups() != null)
-    {
-      Vector allGroups = ap.av.getAlignment().getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-        sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
-      }
-    }
-  }
-
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
-}