General viewer notes:

There are five frames.  Upper-left shows list of contigs.  Lower-left
shows list of interesting events.  Upper-right shows how trusted paths
run along the selected contig.  Lowest-right has two frames: the 
left one shows how trusted paths
captured by the selected contig run along the reference ("local legend); the right one
shows for each genome part how trusted paths from all contigs run
along it, on both strands ("global legend").

Hyperlinks:

Clicking on a trusted path name in the local legend or global legend
frame shows the beginning of that trusted path; you may need to zoom
in to see it.

Troubleshooting the viewer:

Increase the memory available to Java applets (configure your OS
and/or browser).

If you click on contig number on the left and the contig graph isn't
displayed, wait a bit -- sometimes it takes a while.

If that doesn't help, you can use the standalone ZGRViewer instead of
the applet version (go to /wga/dev/ilya/zgrviewer and run run.sh)
to view the contigN.dot file in your showTrusted/ directory.
The corresponding legend file (normally shown in the lower frame of
the viewer) is contigN.dot.legend.html .

Sometimes the contig graph initially won't appear -- you have to
move the mouse into the graph window, and possibly click there,
to make it appear.

Finding features/events in the assembly:

Hidden labels are added to the graph at the location of various
features.  Use the search box on the right to find the next/previous
feature.  Note that the number of matches through which you're
stepping is shown at the bottom-left of the graph viewer.

    Search for... to find...

        src - sources
        snk - sinks
        zp - edges through which no trusted paths pass (sorted
	   from longest to shortest)
	mp - edges through which multiple trusted paths pass
	   ( sorted from longest to shortest )
	[A - beginning of trusted path A
	A] - end of trusted path A


Also, there is a global list of events (mulpaths and nopaths) in the
lower-left frame.  You see the length of the edge with the event,
the link to the contig page, and the hidden text label for which
to search to find that edge.


Tooltips:

   Hover over...    to see...

       end of edge (the arrow) - edge length
       trusted path name on an edge - the alignment of that trusted
           path segment to the reference,
	   and the length of the overall trusted path.  If the
	   trusted path passes over the edge multiple
	   times, the range shown is the smallest range on the
	   reference that contains the alignments to the reference
	   of all segments of this trusted path that pass over
	   this contig edge.


General useful viewer commands:

 Moving around:

    left-click somewhere in the graph, and drag a line in any
    direction -- the view moves in that direction.
    the longer the line, the faster it moves.

    also, the arrow keys and the controls in the viewer upper-right
    corner work for moving.
    

 Zoom/unzoom:

    press shift & drag a bounding box to zoom in on a region
    
    press shift, press left mouse button and drag up to zoom in,
    down to zoom out.  the further you drag from where you pressed the
    button, the faster it zooms in/out.

    also PgDn zooms, PgUp unzooms, and there are zoom/unzoom controls
    (magnifying glass with + and -) in the upper-right of the viewer.

Showing alignment of pairs to the assembly ("bridges" between edges):
 
( see also paths/WritePairAligns.cc, paths/PrintPairAligns.cc and
  paths/PrintPairAlignsAsDot.cc for alternate displays of the same
  information ).

Above each edge to which some reads were aligned, there is a star
("*") symbol that is a "handle" for this edge.  Toggle whether the
edge is selected by clicking on the handle (it's green when selected).
A line will be drawn between two handles if there are at least some
pairs bridging the two handles' edges, and
either both handles are selected, or one handle is selected and the
"show bridges only if both ends selected" checkbox on the right
is unchecked.  Also, if you type a minimal bridge thickness 
(number of aligned pairs in a link between two edges) in the
text field at the bottom-right, only bridges at least this thick
will be shown.

In the middle of each bridge there's an orange octagon -- its tooltip
gives information about the bridge.

The tooltip for the "*" symbol shows the edge id.  The bridges
and their thicknesses for contig N are in the file
contigN.svg.xml in the showTrusted/ subdir.

The pairs are currently taken from hyper.pair_aligns in the dir above
showTrusted/ .