JAL-2844 partitioning code made slightly clearer

[jalview.git] / forester / java / src / org / forester / archaeopteryx / TreePanel.java

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 42274e9..3b69ded 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -263,6 +263,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     HashMap<Long, Short>                  _nodeid_dist_to_leaf                               = new HashMap<Long, Short>();
     final private Arc2D                   _arc                                               = new Arc2D.Double();
     private AffineTransform               _at;
+    private int                             _clicked_x;
     private int                           _circ_max_depth;
     final private Set<Long>               _collapsed_external_nodeid_set                     = new HashSet<Long>();
     private JColorChooser                 _color_chooser                                     = null;
@@ -283,6 +284,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     private final FontRenderContext       _frc                                               = new FontRenderContext( null,
                                                                                                                       false,
                                                                                                                       false );
+    private float                           _furthest_node_x;
     private PHYLOGENY_GRAPHICS_TYPE       _graphics_type                                     = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
     private PhylogenyNode                 _highlight_node                                    = null;
     private boolean                       _in_ov                                             = false;
@@ -312,6 +314,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     private float                         _ov_y_distance                                     = 0;
     private int                           _ov_y_position                                     = 0;
     private int                           _ov_y_start                                        = 0;
+    private boolean                     _partition_tree                                     = false;
+    private float                            _partition_threshold                           = 0;
     private final boolean                 _phy_has_branch_lengths;
     private Phylogeny                     _phylogeny                                         = null;
     private final Path2D.Float            _polygon                                           = new Path2D.Float();
@@ -323,6 +327,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                                                                                                    RenderingHints.VALUE_RENDER_DEFAULT );
     private JTextArea                     _rollover_popup;
     private PhylogenyNode                 _root;
+    private float                           _root_x;
     private final StringBuilder           _sb                                                = new StringBuilder();
     private double                        _scale_distance                                    = 0.0;
     private String                        _scale_label                                       = null;
@@ -345,9 +350,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     private Map<String, AttributedString> _attributed_string_map                             = null;
     private int                           _depth_collapse_level                              = -1;
     private int                           _rank_collapse_level                               = -1;
-   // private boolean                     _partition_tree                                     = false;
-    //private float                           _root_x;
-    //private float                           _furthest_node_x;
+
+
+
     static {
         final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
         dfs.setDecimalSeparator( '.' );
@@ -1356,6 +1361,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     final private TreeFontSet getTreeFontSet() {
         return getMainPanel().getTreeFontSet();
     }
+    
+    final public float getThreshold() {
+        return _partition_threshold;
+    }
 
     final private float getUrtFactor() {
         return _urt_factor;
@@ -5286,7 +5295,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 && ( !node.isRoot() || ( _subtree_index > 0 ) ) );
     }
 
-    final boolean isCurrentTreeIsSubtree() {
+    public final boolean isCurrentTreeIsSubtree() {
         return ( _subtree_index > 0 );
     }
 
@@ -5387,22 +5396,26 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             else {
                 // no node was clicked so partition tree instead
-                int clicked_x = e.getX();
-//                _partition_tree = true;
                 _highlight_node = null;
-//                PhylogenyNode furthestNode = PhylogenyMethods.calculateNodeWithMaxDistanceToRoot( _phylogeny );
-//                _furthest_node_x = furthestNode.getXcoord();
-//                _root_x = _phylogeny.getRoot().getXcoord();
-//                
-//                if (_furthest_node_x != _root_x && !(clicked_x < _root_x || clicked_x > _furthest_node_x)) // don't
-//                                                                                                                // of tree
-//                {
-//                    float threshold = (clicked_x - _root_x) / (_furthest_node_x - _root_x);
-//                    //draw vertical line at clicked_x
-//                }
-//
-//                _partition_tree = false;}
-        }}
+                
+                _clicked_x = e.getX();
+                if (!getPhylogeny().isEmpty()) {
+
+                PhylogenyNode furthestNode = PhylogenyMethods.calculateNodeWithMaxDistanceToRoot( _phylogeny );
+                _furthest_node_x = furthestNode.getXcoord();
+                _root_x = _phylogeny.getRoot().getXcoord();
+                
+                // don't bother if 0 distance tree or clicked x lies outside of tree
+                if (_furthest_node_x != _root_x && !(_clicked_x < _root_x || _clicked_x > _furthest_node_x)) 
+                {
+                    _partition_tree = true;
+
+                }
+
+
+        }
+                }
+            }
         repaint();
     }
 
@@ -5668,6 +5681,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
     }
 
+    public final void paintFile( final Graphics2D g,
+                                 final boolean to_pdf,
+                                 final int graphics_file_width,
+                                 final int graphics_file_height,
+                                 final int graphics_file_x,
+                                 final int graphics_file_y ) {
+        paintPhylogeny(g,to_pdf,true,graphics_file_width,graphics_file_height,graphics_file_x,graphics_file_y);
+    }
     final void paintPhylogeny( final Graphics2D g,
                                final boolean to_pdf,
                                final boolean to_graphics_file,
@@ -5675,10 +5696,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                final int graphics_file_height,
                                final int graphics_file_x,
                                final int graphics_file_y ) {
-    //    if (_partition_tree) {
-     //       
-       // }
-        
+
         if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
             return;
         }
@@ -5879,8 +5897,17 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 g.setTransform( _at );
                 paintOvRectangle( g );
             }
-        }
+
+              
+        }            
+        if (_partition_tree) {
+            g.setColor( Color.BLACK );
+            _partition_threshold = (_clicked_x - _root_x) / (_furthest_node_x - _root_x);
+           drawLine( _clicked_x, 0, _clicked_x, getHeight(),g);
+             _partition_tree = false;
+         }
     }
+    
 
     final void recalculateMaxDistanceToRoot() {
         _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );