JAL-1953 2.11.2 with Archeopteryx!

[jalview.git] / src / jalview / ext / treeviewer / TreeViewerUtils.java

diff --git a/src/jalview/ext/treeviewer/TreeViewerUtils.java b/src/jalview/ext/treeviewer/TreeViewerUtils.java
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+++ b/src/jalview/ext/treeviewer/TreeViewerUtils.java
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+package jalview.ext.treeviewer;
+
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Dimension;
+import java.io.File;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Static class containing generic methods for communicating between the tree
+ * viewer frame and Jalview, currently includes adding the frame to the Jalview
+ * Desktop and triggering an association between an {@link AlignmentViewport}
+ * and {@link TreeFrameI}.
+ * 
+ * @author kjvanderheide
+ *
+ */
+public final class TreeViewerUtils
+{
+  /**
+   * All tree viewers should be added to this map so that Jalview saves them to
+   * its project.
+   */
+  private static Map<TreeFrameI, TreeViewerBindingI> activeViews = new HashMap<>();
+
+  /**
+   * Adds the given tree frame to the Jalview {@link Desktop}.
+   * 
+   * @param treeFrame
+   * @return the same tree frame but now as part of Jalview.
+   */
+  public static TreeFrameI addTreeViewFrameToJalview(
+          final TreeFrameI treeFrame, int width, int height)
+  {
+    treeFrame.setMinimumSize(new Dimension(width, height));
+    // aptxApp.setFont(Desktop.instance.getFont());
+    // aptxApp.getMainPanel().setFont(Desktop.instance.getFont());
+    String frameTitle = MessageManager.getString("label.aptx_title");
+    File treeFile = treeFrame.getTreePanel().getTreeFile();
+    if (treeFile != null)
+    {
+      frameTitle += MessageManager.formatMessage("label.of_x",
+              new String[]
+              { treeFile.getAbsolutePath() });
+    }
+    // Usually redundant as this is done when associating nodes as well but that
+    // step could be bypassed
+    activeViews.put(treeFrame, treeFrame.getViewBinding());
+
+    treeFrame.addFrameToJalview(frameTitle, true, width, height, true,
+            false);
+    treeFrame.getTreeControls().displayEntireTree();
+    return treeFrame;
+  
+  }
+
+  /**
+   * Convience method for building the association between Jalview's alignment
+   * and the tree frame.
+   * 
+   * @param treeFrame
+   * @param jalviewAlignViewport
+   * @param alignMappedToNodes
+   * @param nodesMappedToAlign
+   * @return
+   */
+  public static TreeViewerBindingI associateNodesWithJalviewSequences(
+          final TreeFrameI treeFrame,
+          final AlignmentViewport jalviewAlignViewport,
+          final Map<SequenceI, TreeNodeI> alignMappedToNodes,
+          final Map<TreeNodeI, SequenceI> nodesMappedToAlign)
+  {
+    TreeViewerBindingI treeBinding = new JalviewBinding(treeFrame,
+            jalviewAlignViewport,
+            alignMappedToNodes, nodesMappedToAlign);
+    jalviewAlignViewport.setCurrentExtTree(treeFrame.getTree());
+    activeViews.put(treeFrame, treeFrame.getViewBinding());
+
+    return treeBinding;
+  }
+
+  public static Map<TreeFrameI, TreeViewerBindingI> getActiveTreeViews()
+  {
+    return activeViews;
+  }
+
+}