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External Language Bridge APIs

Overview

src/api/rpython/ contains the Java bridge surface intended to be called from Python or R wrappers.

Current Classes

Class Role
API4R Compatibility-oriented tree utility bridge
EvolTreeManipulator Base utility API for extracting node names from Newick trees
RlangInterfaceEGPS R-facing desktop bridge for launching eGPS and opening the two primary GUI modules
ModernTreeViewPyLauncher Python-facing launcher for starting eGPS and importing Modern Tree View from a VOICE config file
PathwayFamilyBrowserPyLauncher Python-facing launcher for starting eGPS and importing Pathway Family Browser from a VOICE config file
TestJFrame Local helper/test UI bridge

Preferred Methods

Class Preferred methods
API4R extractNodeNames(...), describe()
EvolTreeManipulator extractNodeNames(...), describe()
RlangInterfaceEGPS launchDesktop(), showPayloadAndReturnLength(...), openModernTreeView(...), openPathwayFamilyBrowser(...)
ModernTreeViewPyLauncher launchFromConfigFile(...)
PathwayFamilyBrowserPyLauncher launchFromConfigFile(...)
TestJFrame showDemoWindow(...), renderDemoImageAsPng(...)

Boundary

Only public bridge entry points and small bridge helpers should live here. Internal visualization implementation classes stay in their subsystem packages unless they are promoted into real external APIs.

Maintenance Rules

  1. New R/Python-facing Java bridge classes belong under src/api/rpython.
  2. Keep the package focused on entry points and lightweight helpers.
  3. If a wrapper depends on a class here, document it in docs/current/external_language_api.md.