Cut tomatoes in 1/4 inch slices and discard seeds. If using cherry tomatoes, cut in half. Sprinkle tomato slices with sea salt on both sides and let drain in a colander to remove excess moisture. Let set while making focaccia dough.
Dissolve yeast in the warm water in a large bowl. Let stand for 5 minutes until the yeast softens and begins to foam. Stir in 1 teaspoon of sea salt, 2 teaspoons olive oil, whole wheat flour, and all-purpose flour until the dough comes together. Knead on a well floured surface until smooth and elastic, about 5 minutes. Lightly oil a large bowl, place the dough in the bowl and turn to coat with oil. Cover with a damp cloth and let rise in a warm place until doubled in volume, about 20 minutes.
Preheat oven to 425 degrees F.
Punch down dough and place on an oiled baking sheet, forming into an oval or circle. Use the tips of your fingers to make indentations all over the dough spaced about 1 inch apart. Drizzle the focaccia with 2 tablespoons olive oil. Space the tomatoes evenly across the surface of the focaccia, then sprinkle the basil leaves, pine nuts, and parmigiano-reggiano cheese over the top. Let rise for 10 minutes
Bake about 20 minutes or until golden brown. Serve warm or at room temperature.
