Change default GENE##X/ARRAY##X to "ROW##X/COL##X"

[Robert Leach]

People might not be working with genes & arrays or might even load them in the opposite orientations, so I think that when we auto-generate row & column labels, we should change them to generic "row" and "col" instead of gene/array in the strings.

E.g. Change this default:

GENE1X GENE2X GENE3X ...

to:

ROW1X ROW2X ROW3X ...

[Christopher Keil]

Let's do this when all current branches are merged. In the process of updates I have already changed a bunch of method, variable and class names. Going to adapt this in the UI as well.

[Christopher Keil]

We have brought up and talked about this issue in at least 2 previous CCB meetings, so I will set this to open and begin work.

[Christopher Keil]

Final adaptations for changing axis IDs from old GENE/ ARRY to new ROW/ COL

Changed the access modifier of the static variables describing axis ID names in ClusterController so that they can actually be accessed by other classes. Changed the axis ID name references in HierCluster to set the correct labels to be used in ClusterFileGenerator and when generating the tree file (atr/ gtr) in HierCluster. Adapted regex for recognizing common labels in PreviewLoader to look for the new axis prefixes.

Resolves: #214 See also: #321

→ <<cset 4d56024a2e70>>

[Christopher Keil]

Final adaptations for changing axis IDs from old GENE/ ARRY to new ROW/ COL

Changed the access modifier of the static variables describing axis ID names in ClusterController so that they can actually be accessed by other classes. Changed the axis ID name references in HierCluster to set the correct labels to be used in ClusterFileGenerator and when generating the tree file (atr/ gtr) in HierCluster. Adapted regex for recognizing common labels in PreviewLoader to look for the new axis prefixes.

Resolves: #214 See also: #321

→ <<cset 4d56024a2e70>>

[Anastasia Baryshnikova]

This seems to be working, but the name of the ROWX column and the COLX row is still GID and AID (reminiscent of the GENEX and ARRAYX naming system). Is that how we'd like to leave it? Or should we changed it to RID and CID?

[Robert Leach]

Removing milestone: General interface (automated comment)