Highlight conserved genes

As stated in Sequence Filters, there is one extra option for the first reference track, as shown on the right. When it is selected: (1) If there are 2 tracks, this is equivalent to Hit Filter highlight Hit =2 genes, but the gene exons of the conserved genes are also highlighted. (2) If there are 3 tracks, the genes conserved across the 3 tracks will be highlighted, as shown below.

The above image has the settings Sequence Filter Conserved and the Hit Filter Hit =2 genes. Hence, the pink hit-wires and cyan exons indicate the conserved genes, and the green hit-wires have genes at both ends but are not conserved across the 3 tracks.

Caveats:

1. For a 3-chromosome view, say genes A-B-C are conserved. The hit for A-B may not overlap the hit for B-C. The algorithm only checks the A-B hit and B-C hit, but not the possible A-C hit.
2. There may be different numbers of highlighted genes on the different tracks or hit-wires between tracks. This is because multiple hits can align to a gene, and one gene can align to two different genes on the opposing genome.
3. When there are overlapping genes, a hit is assigned to just one of them, which causes some conserved genes to have incorrect pairing.
4. There are occasional tiny hits that just barely overlap genes; the current algorithm marks them as conserved genes.
5. Currently, the hits may align strictly in introns (especially for the long introns of mammalian genomes); the current algorithm marks these as conserved.

One other point, all other filters are pre-computed; this is computed on the fly. It does not recompute when zooming in, but it does recompute when using the history < and > buttons.