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

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

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
new file mode 100644 (file)
index 0000000..e575b91
--- /dev/null
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -0,0 +1,149 @@
+/*
+ * 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();
+  }
+
+}