<li>normal thread shutdown needs to be written up and debugged <i>as not previously implemented</i>. View connection data needs to be cleared up.
<li>pipeServer not to be asked for featuresets or styles to avoid log message
<li>zmapView.c/processDataRequests() needs to merge the source_2_featureset not just assign it
<li>delayed server needs to free view_con->context etc etc (memory leak)
<li>implement X-Remote progress message (source finished has been done, need more detail ie % complete.
<li>pipe server GFF gives 'cant find style log messages seqRequest() line 1072 <b>(this is a real error in the data)</b>
<li>sequence server is assumed to be ACEDB or some other server that is not delayed and there can be only one
<li>Styles have 3 fields that appear to be misplaced as they refer to column data: loaded, deferred, and cur_bump_mode. Most importantly <b>deferred styles</b> need to be looked at esp as commented around <b>zmapViewRemoteReceive.c #1242</b>
<li><ahref="Design_notes/modules/zmapView.shtml#DNA_memory">Scope and memory allocation issues</a> with DNA sequence data
<li><b>zMapFeatureString2QuarkList()</b> could be moved to zmapConfig and renamed: see <b>zMapConfigIniGetColumns</b>
<li>zMapFeaturesetCreateID() and zmapStyleCreateId() and ZMapGFFSet and ZMapGFFSource could benefit from a review. The problem is that sometimes we want names normalised and sometimes we want them capitalised as given. Perhaps the best way woule be to have all key values as normalised and duplicate quarks used for display names. There are 86 calls to these functions, and this in not all the code that would have to be checked.
width=30.0 # make enough space for left and right pointing hooks
frame-mode=only-1 # is frame specific so will use the colours
show-reverse-strand=true # (see below)
glyph-strand=flip-x # on other side of origin
frame-mode=only-1 # is frame specific so will use the colours, display in 1 column
strand-specific=true
show-reverse-strand=false # NB there are no rev strand features
show_when_empty=false
glyph-score-mode=width
score-mode=width
min-score= -2.0 # as in previous ACEDB style
max-score = 4.0
glyph-5 = dn-hook
...
...
@@ -78,8 +78,10 @@ glyph-3 = up-hook
colours = normal fill grey # for central vertical line if we draw it
frame0-colours = normal fill red; normal border red
frame1-colours = normal fill red; normal border green
frame2-colours = normal fill red; normal border blue
frame1-colours = normal fill green; normal border green
frame2-colours = normal fill blue; normal border blue
bump-mode=unbump
</pre>
<h4> Handling 3F-splice markers</h4>
<p>These are a little non standard. The data is for the forwards strand only and the min and max scores can be set in the GeneFinder application and typically are -2.0 to +4.0. These scores are the log probability of there being a splice site, so -ve values (hooks on the left) are less likely than random.
