JAL-3675 release notes for JAL-3750 JAL-3751

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

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index e575b91..9809fa9 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -1,92 +1,97 @@
 /*
- * 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
+ * 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.
- * 
+ * 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/>.
+ * 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.gui;
+package jalview.schemes;
 
-import java.util.*;
-import java.awt.event.*;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
 
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Vector;
 
 /**
  * Helps generate the colors for RNA secondary structure. Future: add option to
  * change colors based on covariation.
  * 
  * @author Lauren Michelle Lui
- * 
+ * @deprecated this seems to be unfinished - just use RNAHelicesColour
  */
+@Deprecated
 public class RNAHelicesColourChooser
 {
 
-  AlignViewport av;
+  AlignViewportI av;
 
-  AlignmentPanel ap;
+  AlignmentViewPanel ap;
 
   ColourSchemeI oldcs;
 
-  Hashtable oldgroupColours;
+  Map<SequenceGroup, ColourSchemeI> oldgroupColours;
 
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  AlignmentAnnotation currentAnnotation;
 
   boolean adjusting = false;
 
-  public RNAHelicesColourChooser(AlignViewport av, final AlignmentPanel ap)
+  public RNAHelicesColourChooser(AlignViewportI av,
+          final AlignmentViewPanel 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++)
+      oldgroupColours = new Hashtable<>();
+      for (SequenceGroup sg : ap.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
-        if (sg.cs != null)
+        if (sg.getColourScheme() != null)
         {
-          oldgroupColours.put(sg, sg.cs);
+          oldgroupColours.put(sg, sg.getColourScheme());
         }
       }
     }
     this.av = av;
     this.ap = ap;
 
-    if (oldcs instanceof RNAHelicesColour)
-    {
-      RNAHelicesColour rhc = (RNAHelicesColour) oldcs;
-
-    }
-
     adjusting = true;
-    Vector list = new Vector();
+    Vector<String> list = new Vector<>();
     int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns != null)
     {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-        list.addElement(label);
-      else
-        list.addElement(label + "_" + (index++));
+      for (int i = 0; i < anns.length; i++)
+      {
+        String label = anns[i].label;
+        if (!list.contains(label))
+        {
+          list.addElement(label);
+        }
+        else
+        {
+          list.addElement(label + "_" + (index++));
+        }
+      }
     }
 
     adjusting = false;
-
     changeColour();
-
   }
 
   void changeColour()
@@ -96,54 +101,10 @@ public class RNAHelicesColourChooser
     {
       return;
     }
-
-    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-
-    RNAHelicesColour rhc = null;
-
-    rhc = new RNAHelicesColour(currentAnnotation);
+    RNAHelicesColour rhc = new RNAHelicesColour(av.getAlignment());
 
     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);
-      }
-    }
+    ap.paintAlignment(true, true);
   }
-
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
 }