consider situations where there are custom colors in genetic overlay

Closes #1686 (closed)

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/LegendGenerator.java

@@ -80,22 +80,33 @@ public class LegendGenerator {
     Color oldColor = graphics.getColor();
     Font oldFont = graphics.getFont();
 
-    Map<Integer, Color> colors = new HashMap<>();
+    Map<Integer, Set<Color>> colorByCount = new HashMap<>();
     for (DataOverlayEntry entry : overlay.getEntries()) {
-      colors.put(((GeneVariantDataOverlayEntry) entry).getGeneVariants().size(), colorExtractor.getNormalizedColor(entry));
+      int count = ((GeneVariantDataOverlayEntry) entry).getGeneVariants().size();
+      Set<Color> colors = colorByCount.get(count);
+      if (colors == null) {
+        colors = new HashSet<>();
+        colorByCount.put(count, colors);
+      }
+      colors.add(colorExtractor.getNormalizedColor(entry));
     }
     int width = WIDTH - 2 * MARGIN;
 
-    double elementWidth = ((double) width) / (double) (colors.size());
+    double elementWidth = ((double) width) / (double) (colorByCount.size());
 
-    List<Integer> counters = new ArrayList<>(colors.keySet());
+    List<Integer> counters = new ArrayList<>(colorByCount.keySet());
     Collections.sort(counters);
 
     for (int i = 0; i < counters.size(); i++) {
       int count = counters.get(i);
-      Rectangle2D rectangle = new Rectangle2D.Double(MARGIN + i * elementWidth, MARGIN, elementWidth, COLOR_HEIGHT);
-      graphics.setColor(colors.get(count));
-      graphics.fill(rectangle);
+      List<Color> colors = new ArrayList<>(colorByCount.get(count));
+      for (int j = 0; j < colors.size(); j++) {
+        Color color = colors.get(j);
+        double x = MARGIN + i * elementWidth + elementWidth / colors.size() * j;
+        Rectangle2D rectangle = new Rectangle2D.Double(x, MARGIN, elementWidth / colors.size(), COLOR_HEIGHT);
+        graphics.setColor(color);
+        graphics.fill(rectangle);
+      }
     }
 
     graphics.setFont(new Font(Font.SANS_SERIF, 0, 18));
@@ -196,7 +207,7 @@ public class LegendGenerator {
     for (int i = 0; i < width; i++) {
       Rectangle2D rectangle = new Rectangle2D.Double(MARGIN + i, MARGIN, 1, COLOR_HEIGHT);
       GenericDataOverlayEntry entry = new GenericDataOverlayEntry();
-      entry.setValue(((double) (i - width / 2)) / (double) (width / 2.0));
+      entry.setValue((i - width / 2) / (width / 2.0));
       graphics.setColor(colorExtractor.getNormalizedColor(entry));
       graphics.fill(rectangle);
     }