- "ANNOTATIONCOLOUR_MAX", "ANNOTATIONCOLOUR_MIN", "annotations",
+ Preferences.ANNOTATIONCOLOUR_MAX, Preferences.ANNOTATIONCOLOUR_MIN,
+ "annotations",
"APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
"debug", "defaultColour", "defaultColourNuc", "defaultColourProt",
"embedded", "enableSplitFrame", "externalstructureviewer", "features",
"APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
"debug", "defaultColour", "defaultColourNuc", "defaultColourProt",
"embedded", "enableSplitFrame", "externalstructureviewer", "features",
- String key = getAttr(arg, "name");
+ String prefName = getAttr(arg, "name");
+ String appletName = prefName.toLowerCase();
+ String argName = prefName;
- case "alignpdbfiles":
- break;
- case "annotationcolour_max":
- name = "ANNOTATIONCOLOUR_MAX";
- break;
- case "annotationcolour_min":
- name = "ANNOTATIONCOLOUR_MIN";
- break;
- case "annotations":
- value = checkTF(value);
+
+ case "file":
+ argName = "open";
+ appletName = null;
+ value = resourcePath + value;
- case "automaticscrolling":
- name = "automaticScrolling";
+ case "features":
+ case "jnetfile":
+ case "jpredfile":
+ case "pdbfile":
+ case "scorefile":
+ case "sequence":
+ // setting argName to null indicates that we want
+ // JalviewAppLoader to take care of this.
+ prefName = argName = null;
+ value = resourcePath + value;
+ 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
- System.out.println("AppletParams name=" + name + " value=" + value);
- Cache.setPropertyNoSave(name, value);
- if (key != null)
+ System.out.println("AppletParams propName=" + prefName + " argName="
+ + argName + " appletName="
+ + appletName + " value=" + value);
+ if (appletName != null)
+ {
+ appletParams.put(appletName, value);
+ }
+ if (prefName != null)