Use Classification object in DendrogramPanel instead of individual ob…

…jects cluster, mapping and colors
mastodon-sc · Nov 2, 2023 · 7c38107 · 7c38107
1 parent 95f1d77
commit 7c38107
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Showing 3 changed files with 17 additions and 25 deletions.
diff --git a/src/main/java/org/mastodon/mamut/clustering/ui/DendrogramPanel.java b/src/main/java/org/mastodon/mamut/clustering/ui/DendrogramPanel.java
@@ -3,6 +3,7 @@
 import com.apporiented.algorithm.clustering.Cluster;
 import com.apporiented.algorithm.clustering.visualization.ClusterComponent;
 import com.apporiented.algorithm.clustering.visualization.VCoord;
+import org.mastodon.mamut.clustering.util.Classification;
 
 import javax.annotation.Nullable;
 import javax.swing.JPanel;
@@ -26,18 +27,12 @@ public class DendrogramPanel< T > extends JPanel
 
 	private static final long serialVersionUID = 1L;
 
-	private final Cluster cluster;
+	private final Classification< T > classification;
 
 	private final CustomizedClusterComponent component;
 
-	private final Map< Cluster, Integer > clusterColors;
-
-	private final Map< String, T > leafMapping;
-
 	private final ModelMetrics modelMetrics;
 
-	private final double cutoff;
-
 	private double scaleValueInterval = 0;
 
 	private int scaleValueDecimalDigits = 0;
@@ -67,30 +62,25 @@ public class DendrogramPanel< T > extends JPanel
 	public DendrogramPanel()
 	{
 		super();
-		this.cluster = null;
-		this.clusterColors = null;
-		this.cutoff = 0d;
-		this.leafMapping = null;
+		this.classification = null;
 		this.component = null;
 		this.modelMetrics = null;
 	}
 
-	public DendrogramPanel(
-			final Cluster cluster, final Map< Cluster, Integer > clusterColors, final double cutoff, final Map< String, T > leafMapping
-	)
+	public DendrogramPanel( final Classification< T > classification )
 	{
 		super();
-		this.cluster = cluster;
-		this.clusterColors = clusterColors;
-		this.cutoff = cutoff;
-		this.leafMapping = leafMapping;
-		this.component = createComponent( cluster );
+		this.classification = classification;
+		this.component = createComponent( classification.getAlgorithmResult() );
 		this.modelMetrics = createModelMetrics( this.component );
 		adaptScaleBar();
 	}
 
 	private void adaptScaleBar()
 	{
+		if ( classification == null )
+			return;
+		Cluster cluster = classification.getAlgorithmResult();
 		if ( cluster == null )
 			return;
 		if ( cluster.getDistanceValue() > 1d )
@@ -152,7 +142,7 @@ public void paint( Graphics g )
 	private void paintCutoffLine( final Graphics g, final DisplayMetrics displayMetrics )
 	{
 		Stroke stroke = new BasicStroke( 1.75f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL, 0, new float[] { 5, 5 }, 0 );
-		paintVerticalLine( g, stroke, cutoff, displayMetrics );
+		paintVerticalLine( g, stroke, classification.getCutoff(), displayMetrics );
 	}
 
 	private void paintVerticalLine( final Graphics g, final Stroke stroke, final double xValue, final DisplayMetrics displayMetrics )
@@ -234,8 +224,10 @@ private CustomizedClusterComponent createComponent(
 		if ( cluster == null )
 			return null;
 
+		Map< Cluster, Integer > clusterColors = classification.getClusterColors();
 		if ( clusterColors != null && ( clusterColors.containsKey( cluster ) ) )
 			color = new Color( clusterColors.get( cluster ) );
+		Map< String, T > leafMapping = classification.getLeafMapping();
 		if ( leafMapping != null && cluster.isLeaf() && leafMapping.containsKey( cluster.getName() ) )
 			cluster.setName( leafMapping.get( cluster.getName() ).toString() );
 		CustomizedClusterComponent clusterComponent = new CustomizedClusterComponent( cluster, cluster.isLeaf(), initialCoordinate, color );

diff --git a/src/main/java/org/mastodon/mamut/clustering/ui/DendrogramView.java b/src/main/java/org/mastodon/mamut/clustering/ui/DendrogramView.java
@@ -43,9 +43,7 @@ public JPanel getPanel()
 			dendrogramPanel = new DendrogramPanel<>(); // NB: empty dendrogram
 		else
 		{
-			dendrogramPanel = new DendrogramPanel<>( classification.getAlgorithmResult(), classification.getClusterColors(),
-					classification.getCutoff(), classification.getLeafMapping()
-			);
+			dendrogramPanel = new DendrogramPanel<>( classification );
 			dendrogramPanel.setBackground( Color.WHITE );
 		}
 

diff --git a/src/test/java/org/mastodon/mamut/clustering/ui/DendrogramPanelDemo.java b/src/test/java/org/mastodon/mamut/clustering/ui/DendrogramPanelDemo.java
@@ -4,13 +4,14 @@
 import com.apporiented.algorithm.clustering.Cluster;
 import com.apporiented.algorithm.clustering.ClusteringAlgorithm;
 import com.apporiented.algorithm.clustering.DefaultClusteringAlgorithm;
-import com.apporiented.algorithm.clustering.Distance;
+import org.mastodon.mamut.clustering.util.Classification;
 
 import javax.swing.JFrame;
 import javax.swing.JPanel;
 import javax.swing.WindowConstants;
 import java.awt.BorderLayout;
 import java.awt.Color;
+import java.util.Collections;
 
 public class DendrogramPanelDemo
 {
@@ -23,7 +24,8 @@ public static void main( String[] args )
 
 		JPanel content = new JPanel();
 		Cluster cluster = createSampleCluster();
-		DendrogramPanel< String > dp = new DendrogramPanel<>( cluster, null, 6d, null );
+		Classification< String > classification = new Classification<>( Collections.emptyList(), cluster, null, 6d );
+		DendrogramPanel< String > dp = new DendrogramPanel<>( classification );
 
 		frame.setContentPane( content );
 		content.setBackground( Color.red );