JAL-2798 added methods for getting/adding external tree viewer

[jalview.git] / src / jalview / schemabinding / version2 / JalviewModelSequence.java

diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
index c3f8182..5ff56dd 100644 (file)
--- a/src/jalview/schemabinding/version2/JalviewModelSequence.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -1,23 +1,3 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $(date) 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.
- *******************************************************************************/
 /*
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
@@ -76,6 +56,11 @@ public class JalviewModelSequence implements java.io.Serializable
    */
   private jalview.schemabinding.version2.FeatureSettings _featureSettings;
 
+  /**
+   * List of external trees
+   */
+  private java.util.Vector<jalview.ext.treeviewer.TreeFrameI> _extTreeList;
+
   // ----------------/
   // - Constructors -/
   // ----------------/
@@ -88,6 +73,7 @@ public class JalviewModelSequence implements java.io.Serializable
     this._viewportList = new java.util.Vector();
     this._userColoursList = new java.util.Vector();
     this._treeList = new java.util.Vector();
+    this._extTreeList = new java.util.Vector<>();
   }
 
   // -----------/
@@ -178,6 +164,16 @@ public class JalviewModelSequence implements java.io.Serializable
     this._treeList.add(index, vTree);
   }
 
+  public void addExtTreeViewer(jalview.ext.treeviewer.TreeFrameI treeViewer)
+  {
+    this._extTreeList.add(treeViewer);
+  }
+
+  public void addExtTreeViewer(final int index,
+          jalview.ext.treeviewer.TreeFrameI treeViewer)
+  {
+    this._extTreeList.add(index, treeViewer);
+  }
   /**
    * 
    * 
@@ -446,6 +442,31 @@ public class JalviewModelSequence implements java.io.Serializable
     return this._treeList.size();
   }
 
+  public jalview.ext.treeviewer.TreeFrameI getExtTreeViewer(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._extTreeList.size())
+    {
+      throw new IndexOutOfBoundsException("getExtTreeViewer: Index value '"
+              + index + "' not in range [0.."
+              + (this._extTreeList.size() - 1) + "]");
+    }
+
+    return _extTreeList.get(index);
+  }
+
+  public jalview.ext.treeviewer.TreeFrameI[] getExtTreeViewer()
+  {
+    jalview.ext.treeviewer.TreeFrameI[] array = new jalview.ext.treeviewer.TreeFrameI[0];
+    return this._extTreeList.toArray(array);
+  }
+
+  public int getExtTreeViewerCount()
+  {
+    return this._extTreeList.size();
+  }
+
   /**
    * Method getUserColours.
    *