doc/dev-client.md, doc/vidjil-format.md: bikeshedding, reformulations

doc/dev-client.md

@@ -72,12 +72,6 @@ as well with the locus selection.
   - Other objects: `Report`, `Shortcut`
     Extends functionalities but requires elements from the full `index.html`.
 
-### Clone types
-By default, 3 types of clone is created: constant, distribution and other.
-
-* `Constant` clone: correspond to real clone describe into the vidjil file, individually. They are limited to the top clones of a sample (100x by sample).
-* `Other`, or smaller clones: corresponding to the sum of each clones of a given locus, with size dynamically computed to take into account the current filter and viewable constant clones. 
-* `Distributions` clones: correspond to the values given into the distributions data of the vidjil file. They are generated by a function of the model (`loadAllDistribClones`) that automatically agregate data of distributions for each samples. It agregate information on each clones that cannon't be view or show in the interface. It is particularry usefull to simmulate a genescan view in the interface for example.
 
 ### Clone attributes
 
@@ -113,19 +107,37 @@ Each clone that has values on the current axes will be displayed in the 'scatter
 
 Each clone that has a sequence will be displayed in the bottom 'segmenter' panel.
 
-### Clone creation 
+### Creation of common clones
+
+Three types of clone are now created combining some of the attributes
+In the following example, `data` is an map specifying values for a clone (locus, segments, number of reads, ...).
+
 
-Here are commands and set of attributes for each common type:
+* `Constant` clone: actual individual clones,
+described into an item of the `clones` list in the `.vidjil` file
 
 ```javascript
 // Constant
 new Clone(data, model, index, C_SIZE_CONSTANT | C_CLUSTERIZABLE | C_INTERACTABLE | C_IN_SCATTERPLOT);
+```
+
+* `Other`, or smaller clones: corresponding to the sum of each clones of a given locus, with size dynamically computed to take into account the current filter and viewable constant clones.
+
+```javascript
 // Other
 new Clone(data, model, index, C_SIZE_OTHER);
+```
+
+* `Distribution` clones correspond to `distributions` lists of the `.vidjil` file. 
+See "distributions" in `vidjil-format.md`.
+They are aggregate information on clones that won't be shown individually in the client,
+and are useful to display views such a "simulated Genescan".
+They are generated by `model.loadAllDistribClones()`, that agregates such data for each sample. 
+
+```javascript
 // Distributions
 new Clone(data, model, index, C_SIZE_DISTRIB | C_INTERACTABLE | C_IN_SCATTERPLOT );
 ```
-The data contain the set of values specify for a clone (locus, segments, number of reads, ...).
 
 
 ## Integrating the client

doc/vidjil-format.md

@@ -385,16 +385,18 @@ Distributions can be on several axes, like both V/J (here seg3/seg5).
    }
 ```
 
-Distributions are easily computed by the tool `fuse.py` of vidjil. You need to specify a list of distributions waited in the command line. For the example show, the command is:
+Distributions from a `.vidjil` files can be computed by `tools/fuse.py`, 
+giving the desired list of distributions
+through the `-d` option. For the above example, run:
 
 ```bash
 python fuse.py -d lenSeqAverage -d seg3,seg5 sample_42.vidjil
 ```
-To get the list of available axis, run `fuse.py` with option `-l`:
-```bash
-python fuse.py -l
-```
-Some axis should be added after release. If you want to be able to had new one, you need to modify the function `get_values` in the `fuse.py` script. The new axis should also be added in the client to be taken into account (XXX see axis.js doc XXX).
+
+The command `fuse.py -l` yields the list of available axes,
+but currently only `lenSeqAverage` and `seq3,seq5` are supported.
+Adding axes can be done trough in `get_values()` in `tools/fuse.py`.
+Note that axes should also be added to `browser/js/axes.js` to be displayed in the client.
 
 
 ## `germlines` list \[optional\]\[work in progress, to be documented\]