-package jalview.bin;
-import jalview.gui.Preferences;
+package jalview.bin;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
-import java.util.Vector;
+
+import jalview.gui.Preferences;
/**
* Collection of all known applet tags from JalviewLite
*
*/
@SuppressWarnings("serial")
-public class AppletParams extends HashMap<String, String>
+public class AppletParams extends HashMap<String, Object>
{
private final static String[] params = { "alignpdbfiles",
"userDefinedColour", "widthScale", "windowHeight", "windowWidth",
"wrap", };
- public AppletParams(Map<String, String> info)
- {
- for (int i = params.length; --i >= 0;)
- {
- put(params[i], info.get(params[i]));
- }
- }
-
public String getParam(String param, String def)
{
- String val = get(param);
- return (val != null ? val : def);
+ Object val = get(param);
+ return (val != null ? val.toString() : def);
}
// <applet
public AppletParams()
{
- // TODO Auto-generated constructor stub
+ }
+
+ public static AppletParams getAppletParams(Map<String, Object> map,
+ List<String> vargs)
+ {
+ AppletParams appletParams = new AppletParams();
+ String resourcePath = getString(map, "resourcePath");
+ if (resourcePath == null)
+ resourcePath = "";
+ if (resourcePath.length() > 0 && !resourcePath.endsWith("/"))
+ {
+ resourcePath += "/";
+ }
+ for (int i = params.length; --i >= 0;)
+ {
+ String prefName = params[i];
+ Object value = map.get(prefName);
+ if (value != null)
+ addParam(vargs, prefName, value, appletParams, resourcePath);
+ }
+ return appletParams;
+ }
+
+ private static String getString(Map<String, Object> map, String key)
+ {
+ Object o = map.get(key);
+ return (o == null ? null : o.toString());
}
public static AppletParams getAppletParams(String[] args,
- Vector<String> vargs)
+ List<String> vargs)
{
AppletParams appletParams = new AppletParams();
- String resourcePath = null;
+ String resourcePath = "";
for (int i = args.length; --i > 0;) // > 0 is correct, not >=0
{
if (args[i].startsWith("name=\"Info.resourcePath\""))
if (arg.startsWith("name="))
{
String prefName = getAttr(arg, "name");
- String appletName = prefName.toLowerCase();
- String argName = prefName;
String value = getAttr(arg, "value");
+ addParam(vargs, prefName, value, appletParams, resourcePath);
+ }
+ }
+ return appletParams;
+ }
- // note that Application arguments ARE case-sensitive, but
- // Applet.getParameter() is not.
+ private static void addParam(List<String> vargs, String prefName,
+ Object value, AppletParams appletParams, String resourcePath)
+ {
- switch (appletName)
- {
+ // note that Application arguments ARE case-sensitive, but
+ // Applet.getParameter() is not.
- case "file":
- argName = "open";
- appletName = null;
- value = resourcePath + value;
- break;
- case "file2":
- argName = "open2";
- prefName = null;
- value = resourcePath + value;
- break;
- 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;
- break;
- case "tree":
- case "treefile":
- // setting appletName to null indicates that we want
- // Jalview.doMain to taken care of this as Jalview args
- argName = "tree";
- appletName = null;
- value = resourcePath + value;
- break;
+ String appletName = prefName.toLowerCase();
+ String argName = prefName;
+ switch (appletName)
+ {
- // non-loading preferences
+ case "file":
+ argName = "open";
+ appletName = null;
+ value = resourcePath + value;
+ break;
+ case "file2":
+ argName = "open2";
+ prefName = null;
+ value = resourcePath + value;
+ break;
+ 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;
+ break;
+ case "tree":
+ case "treefile":
+ // setting appletName to null indicates that we want
+ // Jalview.doMain to taken care of this as Jalview args
+ argName = "tree";
+ appletName = null;
+ value = resourcePath + value;
+ break;
- case "defaultcolour":
- prefName = Preferences.DEFAULT_COLOUR;
- break;
- case "defaultcolournuc":
- prefName = Preferences.DEFAULT_COLOUR_NUC;
- break;
- case "defaultcolourprot":
- prefName = Preferences.DEFAULT_COLOUR_PROT;
- break;
- case "annotationcolour_max":
- prefName = Preferences.ANNOTATIONCOLOUR_MAX;
- break;
- case "annotationcolour_min":
- prefName = Preferences.ANNOTATIONCOLOUR_MIN;
- break;
- case "enablesplitframe":
- prefName = Preferences.ENABLE_SPLIT_FRAME;
- break;
- case "centrecolumnlabels":
- prefName = Preferences.CENTRE_COLUMN_LABELS;
- break;
- case "sortby":
- prefName = Preferences.SORT_ALIGNMENT; // id, etc.
- break;
- case "normalisesequencelogo":
- prefName = Preferences.NORMALISE_CONSENSUS_LOGO;
- break;
- case "relaxedidmatch":
- prefName = Preferences.RELAXEDSEQIDMATCHING;
- break;
- case "scaleproteinascdna":
- prefName = Preferences.SCALE_PROTEIN_TO_CDNA;
- break;
- case "userdefinedcolour":
- argName = "colour";
- prefName = Preferences.USER_DEFINED_COLOURS;
- break;
- case "wrap":
- prefName = Preferences.WRAP_ALIGNMENT;
- break;
+ // non-loading preferences
- // implemented; not tested:
+ case "defaultcolour":
+ prefName = Preferences.DEFAULT_COLOUR;
+ break;
+ case "defaultcolournuc":
+ prefName = Preferences.DEFAULT_COLOUR_NUC;
+ break;
+ case "defaultcolourprot":
+ prefName = Preferences.DEFAULT_COLOUR_PROT;
+ break;
+ case "annotationcolour_max":
+ prefName = Preferences.ANNOTATIONCOLOUR_MAX;
+ break;
+ case "annotationcolour_min":
+ prefName = Preferences.ANNOTATIONCOLOUR_MIN;
+ break;
+ case "enablesplitframe":
+ prefName = Preferences.ENABLE_SPLIT_FRAME;
+ break;
+ case "centrecolumnlabels":
+ prefName = Preferences.CENTRE_COLUMN_LABELS;
+ break;
+ case "sortby":
+ prefName = Preferences.SORT_ALIGNMENT; // id, etc.
+ break;
+ case "normalisesequencelogo":
+ prefName = Preferences.NORMALISE_CONSENSUS_LOGO;
+ break;
+ case "relaxedidmatch":
+ prefName = Preferences.RELAXEDSEQIDMATCHING;
+ break;
+ case "scaleproteinascdna":
+ prefName = Preferences.SCALE_PROTEIN_TO_CDNA;
+ break;
+ case "userdefinedcolour":
+ argName = "colour";
+ prefName = Preferences.USER_DEFINED_COLOURS;
+ break;
+ case "wrap":
+ prefName = Preferences.WRAP_ALIGNMENT;
+ break;
- case "oninit":
- prefName = null;
- break;
- case "annotations":
- value = resourcePath + value;
- argName = null;
- break;
- case "hidefeaturegroups":
- // TODO
- break;
- case "pdbseq":
- argName = prefName = null;
- break;
- case "sortbytree":
- prefName = Preferences.SORT_BY_TREE;
- value = checkTF(value);
- appletName = null; // taken care of by Jalview
- break;
- case "format":
- break;
- case "alignpdbfiles":
- argName = prefName = null;
- break;
- case "separator":
- break;
+ // implemented; not tested:
- // TODO: probably not relevant?
+ case "oninit":
+ prefName = null;
+ break;
+ case "annotations":
+ value = resourcePath + value;
+ argName = null;
+ break;
+ case "hidefeaturegroups":
+ // TODO
+ break;
+ case "pdbseq":
+ argName = prefName = null;
+ break;
+ case "sortbytree":
+ prefName = Preferences.SORT_BY_TREE;
+ value = checkTF(value);
+ appletName = null; // taken care of by Jalview
+ break;
+ case "format":
+ break;
+ case "alignpdbfiles":
+ argName = prefName = null;
+ break;
+ case "separator":
+ break;
- case "rgb":
- prefName = null; // TODO no background for application?
- break;
- case "externalstructureviewer":
- break;
- case "application_url":
- break;
- case "automaticscrolling":
- break;
- case "heightscale":
- break;
- case "jalviewhelpurl":
- break;
- case "label":
- break;
- case "linklabel_":
- prefName = "linkLabel_";
- break;
- case "linklabel_1":
- prefName = "linkLabel_1";
- break;
- case "linkurl_":
- prefName = "linkURL_";
- break;
+ // TODO: probably not relevant?
- // unknown:
+ case "rgb":
+ prefName = null; // TODO no background for application?
+ break;
+ case "externalstructureviewer":
+ break;
+ case "application_url":
+ break;
+ case "automaticscrolling":
+ break;
+ case "heightscale":
+ break;
+ case "jalviewhelpurl":
+ break;
+ case "label":
+ break;
+ case "linklabel_":
+ prefName = "linkLabel_";
+ break;
+ case "linklabel_1":
+ prefName = "linkLabel_1";
+ break;
+ case "linkurl_":
+ prefName = "linkURL_";
+ break;
- case "nojmol":
- case "normaliselogo":
- case "resolvetocodebase":
- case "uppercase":
- case "widthscale":
- case "windowheight":
- case "windowwidth":
- argName = prefName = null;
- break;
+ // unknown:
- // TRUE/FALSE
+ case "nojmol":
+ case "normaliselogo":
+ case "resolvetocodebase":
+ case "uppercase":
+ case "widthscale":
+ case "windowheight":
+ case "windowwidth":
+ argName = prefName = null;
+ break;
- 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;
}
+ // 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.toString());
+ }
+ }
+ 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.toString());
}
- return appletParams;
}
/**
* @param value
* @return "true" or null
*/
- private static String checkTF(String value)
+ private static String checkTF(Object value)
{
- return (value.toLowerCase() == "true" ? "true" : null);
+ return (("" + value).toLowerCase() == "true" ? "true" : null);
}
/**
git://source.jalview.org / jalview.git / blobdiff