diff --git a/doc/project/2006_01_06.meeting b/doc/project/2006_01_06.meeting new file mode 100755 index 0000000000000000000000000000000000000000..63a5b841e4852ccc77898c45570acd9d34cb73ac --- /dev/null +++ b/doc/project/2006_01_06.meeting @@ -0,0 +1,165 @@ +ZMap Meeting + + +Date: 06.01.2006 + + +Present: Ed, Roy + + + +lace system: + +status - needs testing for robustness and speed... **EG to install on his account and try it. + +problems - + +Currently + +Actions - **Roy to arrange a meeting with James et al. to dicuss following issues: + +1) Does the lace system read any data from the acedb database at the end of the +session or is the database effectively READONLY ? + +2) Unique ids...can James supply these in the data from the database so we can read +them directly. We already have a slot in our feature data struct for them. This unique +id may be good to use in a separte hash of unique_ids -> canvas features which could +unambiguously go from one to the other. + +3) Genefinder - can this be run from the perl code and then the results sent across +to us as a Style + the data ? It makes for this to be done in the lace layer because +gene finder is principally about interactive annotation. + +4) we have a performance problem with the g_dataset, to circumvent this can we reduce +the number of homols being displayed ? + +5) Can we migrate quickly from the dual xace/zmap system to a zmap only system. **RS to check. + +6) discuss adding whole columns with James, e.g. genefinder data. + + + +XML-xremote mechanism: + +Currently we do not have the basic functions to add/modify/remove features to support +this. We need this, and we may also need a function to get the server to parse in +data. Can be tested via the feature editor. **EG to make sure this works. + +We need to review the operations in the XML-xremote interface, **RS to do this. + +We will need the xremote mechanism to dynanically add whole columns. This will involve +operations to do at least: + +- adding the column name into our column list so it appears in the correct position +in the columns. + +- adding the style for the column to our set of styles _before_ we are given the column +itself. + +- adding a whole column with data. + + + + +ZMap Display: + +- transcripts now display the CDS but not start/end not found. This data should be +dumped in GFF and available. **RS to check this out. + +- separate scale window...not done but not a priority. + +- 3-frame translation, not done **RS to code this. + +- reverse complement, not done **EG to investigate, will users be prepared to put up +with the hit of refetching the data or should we fudge it locally. Check how acedb does +this now, I think Simon changed it not to cache data so much. + +- DNA highlighting - EG thinks he may have broken it in moving the code for +the DNA into ordinary feature group. **RS to check. + +- mulitple feature types in a single column needs checking to see if it is still +working. **EG to do this. + +- blixem needs to be checked to see it still works. **EG to do this. + + +- methods and columns and things: we had a useful dicussion about these and came +up with: + + - we need to publish a list of "reservered" style/method names for + columns that are either derived dynamically or special in some way, + e.g. dna, genefinder output, 3-frame translation. The user can create + styles with these names and their style will be applied to these specific + datasets (if available, e.g. the dna may not be available). The user + cannot use these names for their own columns/data, they are reserved. + + +In addition the rules concerning display will be tightened to be: + +- if any column is not in the columns list it will not be displayed. + +- if a column is in the columns list but there is no style for it, it will not be +displayed. + +i.e. columns without styles will be removed from the columns list and will +not be displayed. + + + +g_dataset problem: + +To recap: + +the glib g_dataset code grinds almost to a halt while we are processing the GFF +from the server. We've not been able to profile this well within our threaded +environment sadly. What we do know is that it seems to spend a lot of time in +a free routine so it maybe a problem with glibs chunk routines for allocating +blocks of memory. It may also be, as Roy suggests, that its having to search +longer and longer lists of blocks... + +solution is to write a small program that uses the GFF parser to read in a file, +this should be simple, in a single threaded program and see where the problem is. + +A temporary solution is to try and reduce the enormous number of homols being +displayed. + + + +Styles, Features and canvas item drawing....: + +this is an old chestnut...what decides how a feature is drawn ? Is it only +the style ? Is it the feature type (e.g. allele etc.) ? In acedb the feature +type was the thing that decide it. We wanted to generalise this but there +is a problem in that if the style is the only thing its hard to make pop-up +menus and other things that are specific to certain feature types unless +you add a feature type field to the method/style which means that now the +style is the feature...and in any case the feature just contain exons etc +so it is the feature as well...it just doesn't really work... + +So this is our sytem which is a blend... + + +Feature drawn shape Style + + +BASIC => read shape from style read shape as basic box, + splice markers (for genefinder) + constant shapes (for alleles) + + +TRANSCRIPT => usual transcript shape read for colours + + +ALIGNMENT => usual align shape read for colours + + +This works because there three basic feature types should be enough to allow popup menus etc +to work well but then we can avoid having endless types fields for alleles etc by having a +drawing type in the style which will sort all this out. + +So in otherwords, the feature type decides what type of main shape the feature will be +drawn as, but the style allows tailoring of the basic feature types. + + + +