*

* $Author: alokito $

* $RCSfile: KnnDendroView.java,v $

* $Revision: 1.2 $

* $Date: 2006-09-21 17:18:55 $

* $Name:  $

*

* This file is part of Java TreeView

* Copyright (C) 2001-2003 Alok Saldanha, All Rights Reserved. Modified by Alex Segal 2004/08/13. Modifications Copyright (C) Lawrence Berkeley Lab.

*

* This software is provided under the GNU GPL Version 2. In particular,

*

* 1) If you modify a source file, make a comment in it containing your name and the date.

* 2) If you distribute a modified version, you must do it under the GPL 2.

* 3) Developers are encouraged but not required to notify the Java TreeView maintainers at alok@genome.stanford.edu when they make a useful addition. It would be nice if significant contributions could be merged into the main distribution.

*

* A full copy of the license can be found in gpl.txt or online at

* http://www.gnu.org/licenses/gpl.txt

*

* END_HEADER

*/

*  This class encapsulates a dendrogram view, which is the classic Eisen

*  treeview. It uses a drag grid panel to lay out a bunch of linked

*  visualizations of the data, a la Eisen. In addition to laying out

*  components, it also manages the GlobalZoomMap. This is necessary since both

*  the GTRView (gene tree) and KnnGlobalView need to know where to lay out genes

*  using the same map.

*

* @author     Alok Saldanha <alok@genome.stanford.edu>

* @version $Revision: 1.2 $ $Date: 2006-09-21 17:18:55 $

*/

  /**

   *  Constructor for the KnnDendroView object

   *

   * @param  tVModel   model this KnnDendroView is to represent

   * @param  vFrame  parent ViewFrame of KnnDendroView

   */

  public KnnDendroView(KnnModel tVModel, ViewFrame vFrame) {

    super(tVModel, vFrame);

  }

  public KnnDendroView(DataModel tVModel, ConfigNode root, ViewFrame vFrame) {

    super(tVModel, root, vFrame, "KnnDendrogram");

  }

  /**

   *  This method should be called only during initial setup of the modelview

   *

   *  It sets up the views and binds them all to config nodes.

   *

   */

  protected void setupViews() {

    DataModel knnModel = getDataModel();

    hintpanel = new MessagePanel("Usage Hints");

    statuspanel = new MessagePanel("View Status");

    ColorPresets colorPresets = DendrogramFactory.getColorPresets();

    ColorExtractor colorExtractor = new ColorExtractor();

    colorExtractor.setDefaultColorSet(colorPresets.getDefaultColorSet());

    colorExtractor.setMissing(KnnModel.NODATA, KnnModel.EMPTY);

    KnnArrayDrawer kArrayDrawer = new KnnArrayDrawer();

    kArrayDrawer.setColorExtractor(colorExtractor);

    arrayDrawer = kArrayDrawer;

    //XXX shouldn't need to observer, should be immuable?

    ((Observable) getDataModel()).addObserver(arrayDrawer);

  globalview = new GlobalView();

  // scrollbars, mostly used by maps

  globalXscrollbar = new JScrollBar(JScrollBar.HORIZONTAL, 0,1,0,1);

  globalYscrollbar = new JScrollBar(JScrollBar.VERTICAL,0,1,0,1);

  zoomXscrollbar = new JScrollBar(JScrollBar.HORIZONTAL, 0,1,0,1);

  zoomYscrollbar = new JScrollBar(JScrollBar.VERTICAL,0,1,0,1);

     zoomXmap = new MapContainer();

     zoomXmap.setDefaultScale(12.0);

     zoomXmap.setScrollbar(zoomXscrollbar);

     zoomYmap = new MapContainer();

     zoomYmap.setDefaultScale(12.0);

     zoomYmap.setScrollbar(zoomYscrollbar);

     // globalmaps tell globalview, atrview, and gtrview

     // where to draw each data point.

  // the scrollbars "scroll" by communicating with the maps.

    globalXmap = new MapContainer();

    globalXmap.setDefaultScale(2.0);

    globalXmap.setScrollbar(globalXscrollbar);

    globalYmap = new MapContainer();

    globalYmap.setDefaultScale(2.0);

    globalYmap.setScrollbar(globalYscrollbar);

    globalview.setXMap(globalXmap);

    globalview.setYMap(globalYmap);

    globalview.setZoomYMap(getZoomYmap());

    globalview.setZoomXMap(getZoomXmap());

    arraynameview = new ArrayNameView(getDataModel().getArrayHeaderInfo());

    leftTreeDrawer = new LeftTreeDrawer();

    gtrview = new GTRView();

    gtrview.setMap(globalYmap);

    gtrview.setLeftTreeDrawer(leftTreeDrawer);

    invertedTreeDrawer = new InvertedTreeDrawer();

    atrview = new ATRView();

    atrview.setMap(globalXmap);

    atrview.setInvertedTreeDrawer(invertedTreeDrawer);

    atrzview = new ATRZoomView();

    atrzview.setZoomMap(getZoomXmap());

    atrzview.setInvertedTreeDrawer(invertedTreeDrawer);

    zoomview = new ZoomView();

    zoomview.setYMap(getZoomYmap());

    zoomview.setXMap(getZoomXmap());

    zoomview  .setArrayDrawer(arrayDrawer);

    globalview.setArrayDrawer(arrayDrawer);

    arraynameview.setMapping(getZoomXmap());

    arraynameview.setUrlExtractor(viewFrame.getArrayUrlExtractor());

    textview = new TextViewManager(getDataModel().getGeneHeaderInfo(), viewFrame.getUrlExtractor());

    textview.setMap(getZoomYmap());

    doDoubleLayout();

    // reset persistent popups

    settingsFrame = null;

    settingsPanel = null;

    // color extractor

    colorExtractor.bindConfig(getFirst("ColorExtractor"));

    // set data first to avoid adding auto-genereated contrast to documentConfig.

    kArrayDrawer.setDataMatrix(knnModel.getDataMatrix());

    kArrayDrawer.bindConfig(getFirst("ArrayDrawer"));

    // responsible for adding and removing components...

    bindTrees();

   

    globalXmap.bindConfig(getFirst("GlobalXMap"));

    globalYmap.bindConfig(getFirst("GlobalYMap"));

    getZoomXmap().bindConfig(getFirst("ZoomXMap"));

    getZoomYmap().bindConfig(getFirst("ZoomYMap"));

    textview.bindConfig(getFirst("TextViewParent"));

    arraynameview.bindConfig(getFirst("ArrayNameView"));

    // perhaps I could remember this stuff in the MapContainer...

    DataMatrix dataMatrix = getDataModel().getDataMatrix();

    globalXmap.setIndexRange(0, dataMatrix.getNumCol() - 1);

    globalYmap.setIndexRange(0, dataMatrix.getNumRow() - 1);

    getZoomXmap().setIndexRange(-1, -1);

    getZoomYmap().setIndexRange(-1, -1);

    globalXmap.notifyObservers();

    globalYmap.notifyObservers();

    getZoomXmap().notifyObservers();

    getZoomYmap().notifyObservers();

  }

 

}