- public static void setAppletDefaults()
- {
-
- // http://www.jalview.org/old/v2_8/examples/appletParameters.html
-
- // showConservation true or false Default is true.
- // showQuality true or false Default is true.
- // showConsensus true or false Default is true.
- // showFeatureSettings true or false Shows the feature settings window when
- // startin
- // showTreeBootstraps true or false (default is true) show or hide branch
- // bootstraps
- // showTreeDistances true or false (default is true) show or hide branch
- // lengths
- // showUnlinkedTreeNodes true or false (default is false) indicate if
- // unassociated nodes should be highlighted in the tree view
- // showUnconserved true of false (default is false) When true, only gaps and
- // symbols different to the consensus sequence ions of the alignment
- // showGroupConsensus true of false (default is false) When true, shows
- // consensus annotation row for any groups on the alignment. (since 2.7)
- // showGroupConservation true of false (default is false) When true, shows
- // amino-acid property conservation annotation row for any groups on the
- // showConsensusHistogram true of false (default is true) When true, shows
- // the percentage occurence of the consensus symbol for each column as a
- // showSequenceLogo true of false (default is false) When true, shows a
- // sequence logo above the consensus sequence (overlaid above the Consensus
-
- Cache.setPropertyNoSave(SHOW_CONSERVATION, "true");
- Cache.setPropertyNoSave(SHOW_QUALITY, "false");
- Cache.setPropertyNoSave(SHOW_CONSENSUS, "true");
- Cache.setPropertyNoSave(SHOW_UNCONSERVED, "false");
- Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, "false");
- Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, "false");
-
- // TODO -- just a start here
- }
-