- case "debug":
- value = checkTF(value);
- break;
- case "embedded":
- value = checkTF(value);
- break;
- case "showbutton":
- value = checkTF(value);
- break;
- case "showannotation":
- prefName = Preferences.SHOW_ANNOTATIONS;
- value = checkTF(value);
- break;
- case "showconsensus":
- prefName = Preferences.SHOW_CONSENSUS_LOGO;
- value = checkTF(value);
- break;
- case "showconsensushistogram":
- prefName = Preferences.SHOW_CONSENSUS_HISTOGRAM;
- value = checkTF(value);
- break;
- case "showconservation":
- prefName = Preferences.SHOW_CONSERVATION;
- value = checkTF(value);
- break;
- case "showgroupconsensus":
- prefName = Preferences.SHOW_GROUP_CONSENSUS;
- value = checkTF(value);
- break;
- case "showgroupconservation":
- prefName = Preferences.SHOW_GROUP_CONSERVATION;
- value = checkTF(value);
- break;
- case "showoccupancy":
- prefName = Preferences.SHOW_OCCUPANCY;
- value = checkTF(value);
- break;
- case "showquality":
- prefName = Preferences.SHOW_QUALITY;
- value = checkTF(value);
- break;
- case "showsequencelogo":
- prefName = Preferences.SHOW_CONSENSUS_LOGO;
- value = checkTF(value);
- break;
- case "showfeaturegroups":
- value = checkTF(value);
- break;
- case "showfeaturesettings":
- value = checkTF(value);
- break;
- case "showfullid":
- value = checkTF(value);
- break;
- case "showtreebootstraps":
- value = checkTF(value);
- break;
- case "showtreedistances":
- value = checkTF(value);
- break;
- case "showunconserved":
- prefName = Preferences.SHOW_UNCONSERVED;
- value = checkTF(value);
- break;
- case "showunlinkedtreenodes":
- value = checkTF(value);
- break;
- default:
- if (appletName.startsWith("pdbfile")
- || appletName.startsWith("sequence") && Character.isDigit(
- appletName.charAt(appletName.length() - 1)))
- {
- // could be pdbFile2, for example
- prefName = argName = null;
- value = resourcePath + value;
- break;
- }
- // or one of the app preference names
- break;
- }
- // put name and value into application args
- if (value != null && argName != null)
- {
- vargs.add(argName);
- if (value != "true")
- {
- vargs.add(value);
- }
- }
- if (value == null)
- {
- value = "false";
- }
- System.out.println("AppletParams propName=" + prefName + " argName="
- + argName + " appletName="
- + appletName + " value=" + value);
- if (appletName != null)
- {
- appletParams.put(appletName, value);
- }
- if (prefName != null)
- {
- Cache.setPropertyNoSave(prefName, value);
- }
+ // TRUE/FALSE
+
+ case "debug":
+ value = checkTF(value);
+ break;
+ case "embedded":
+ value = checkTF(value);
+ break;
+ case "showbutton":
+ value = checkTF(value);
+ break;
+ case "showannotation":
+ prefName = Preferences.SHOW_ANNOTATIONS;
+ value = checkTF(value);
+ break;
+ case "showconsensus":
+ prefName = Preferences.SHOW_CONSENSUS_LOGO;
+ value = checkTF(value);
+ break;
+ case "showconsensushistogram":
+ prefName = Preferences.SHOW_CONSENSUS_HISTOGRAM;
+ value = checkTF(value);
+ break;
+ case "showconservation":
+ prefName = Preferences.SHOW_CONSERVATION;
+ value = checkTF(value);
+ break;
+ case "showgroupconsensus":
+ prefName = Preferences.SHOW_GROUP_CONSENSUS;
+ value = checkTF(value);
+ break;
+ case "showgroupconservation":
+ prefName = Preferences.SHOW_GROUP_CONSERVATION;
+ value = checkTF(value);
+ break;
+ case "showoccupancy":
+ prefName = Preferences.SHOW_OCCUPANCY;
+ value = checkTF(value);
+ break;
+ case "showquality":
+ prefName = Preferences.SHOW_QUALITY;
+ value = checkTF(value);
+ break;
+ case "showsequencelogo":
+ prefName = Preferences.SHOW_CONSENSUS_LOGO;
+ value = checkTF(value);
+ break;
+ case "showfeaturegroups":
+ value = checkTF(value);
+ break;
+ case "showfeaturesettings":
+ value = checkTF(value);
+ break;
+ case "showfullid":
+ value = checkTF(value);
+ break;
+ case "showtreebootstraps":
+ value = checkTF(value);
+ break;
+ case "showtreedistances":
+ value = checkTF(value);
+ break;
+ case "showunconserved":
+ prefName = Preferences.SHOW_UNCONSERVED;
+ value = checkTF(value);
+ break;
+ case "showunlinkedtreenodes":
+ value = checkTF(value);
+ break;
+ default:
+ if (appletName.startsWith("pdbfile")
+ || appletName.startsWith("sequence") && Character
+ .isDigit(appletName.charAt(appletName.length() - 1)))
+ {
+ // could be pdbFile2, for example
+ prefName = argName = null;
+ value = resourcePath + value;
+ break;