GUI - allow user control of null value display colours

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What steps will reproduce the problem?
1.  Run a cluster analysis with a def query that excludes some set of groups, 
or that results in a null value for some set of groups (given calculations for 
each node).  

What is the expected output? What do you see instead?

These cells are all displayed as black.  It would be more useful if users could 
select the colours each of these receives.  This would allow differentiation 
between, for example, groups not in the tree and groups which have undef.

Original issue reported on code.google.com by shawnlaffan on 23 Jan 2012 at 3:11

• Blocking: GUI - Improve pan, zoom, etc. controls #353

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This issue was updated by revision r867.

Change default shade for groups not in the tree.  Now using a light grey.  

Original comment by shawnlaffan on 23 Jan 2012 at 3:12

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Add 1.0 milestone

Original comment by shawnlaffan on 14 Nov 2013 at 4:36

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Add issue 353 as a blocker, as those changes need to land on the trunk before 
this can be implemented (without major shenanigans).

Original comment by shawnlaffan on 18 Apr 2014 at 11:09

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• Now blocked on: GUI - Improve pan, zoom, etc. controls #353

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See also issue 311 which is related.  

Original comment by shawnlaffan on 18 Apr 2014 at 11:19

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Original comment by shawnlaffan on 26 Aug 2014 at 5:50

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• Now blocking: GUI - Improve pan, zoom, etc. controls #353

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Original comment by shawnlaffan on 26 Aug 2014 at 5:51

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Branch was created in r2937

Original comment by shawnlaffan on 20 Oct 2014 at 3:57

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[GoogleCodeExporter]

There is more than one type of null value to deal with.

1.  The value failed the def query so was not included in the analysis.  
Cluster outputs currently display these as grey, spatial outputs display them 
as white.  

2.  The calculation was run but the index value was undef.  This is currently 
white for both types of output.

Original comment by shawnlaffan on 20 Oct 2014 at 4:00

• Changed state: Started
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[GoogleCodeExporter]

This issue was updated by revision r2938.

Initial work.  Mostly cleanup and trying to differentiate between conditions.  
Add new method Biodiverse::Spatial::group_passed_def_query so we can identify 
which groups passed and colour accordingly.  We could one day plot and update 
these separately if speed becomes an issue.
Need to aim to do most of the work in Outputs.pm since the calls are mainly 
ending up on the analysis objects.

Original comment by shawnlaffan on 20 Oct 2014 at 6:03

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This issue was updated by revision r2939.

Unify the colouring for the cells which failed the def query or are absent 
(excluded) from the results.  
Still need to allow user control over the colour.

Original comment by shawnlaffan on 20 Oct 2014 at 10:39

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This issue was updated by revision r2940.

Add menu options to change the excluded cell colour (these are typically groups 
which failed a def query).
ALso fixes a long standing issue where the cluster plots did not update the 
tree properly.  This was due to the grid being updated after the dendrogram, so 
presumably there is an interaction in there somewhere.  

Original comment by shawnlaffan on 20 Oct 2014 at 10:51

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[GoogleCodeExporter]

The dendrogram uses COLOUR_LIST_UNDEF for undef values.
It also has colours for cells that are outside the current selection, so there 
are two cases for clusters: 
1. Node is selected but value is undef
2. Node is not selected

Spatial analyses have only "value is undef".

Original comment by shawnlaffan on 20 Oct 2014 at 11:16

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This issue was updated by revision r2941.

Rename some constants to be more meaningful (prefix is now COLOUR instead of 
CELL).

Original comment by shawnlaffan on 21 Oct 2014 at 1:33

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This issue was updated by revision r2942.

Allow user control over cells with undef list values.
Also make the colour selector use the currently set colour if provided.

Original comment by shawnlaffan on 21 Oct 2014 at 3:54

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This issue was updated by revision r2943.

A bit of tweaking to make the hue/sat/grey menus consistent between the spatial 
and clustering tabs.  
Also use any existing cell outline colour in its colour selector.

Original comment by shawnlaffan on 21 Oct 2014 at 4:26

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This issue was updated by revision r2944.

Make sure we recolour the branches and cells when we change the colour mode.  
Do this by adding "all_elements => 1" to each relevant recolour call.
(This doesn't strictly fit in this issue, but it needs to go somewhere).  

Original comment by shawnlaffan on 21 Oct 2014 at 4:36

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This issue was updated by revision r2945.

Merge revisions across to the trunk

Original comment by shawnlaffan on 21 Oct 2014 at 4:46

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This issue was updated by revision r2946.

Delete branch

Original comment by shawnlaffan on 21 Oct 2014 at 4:47

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Mark as fixed. 

The colours for the non-selected cells in clustering plots, and the index cell 
for the SpatialMatrix plot, can be done under their own issues.  

Original comment by shawnlaffan on 21 Oct 2014 at 4:48

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