Jalview.processAllAppletElements = function(PageInfo) {
- var applets = document.getElementsByTagName("applet") || document.getElementsByTagName("jvapplet");
+ var applets = document.getElementsByTagName("applet");
var apps=[];
for (var i = 0; i < applets.length; i++)
apps[i] = applets[i];
Jalview.processAppletElement = function(element, UserInfo) {
- // This code is specifically for processing the <applet> or <jvapplet> tag.
-
- // To set Jalview application tags, use Info.args="......."
-
- // To set preferences, use "jalview_" prefix with all-upper-case names:
-
- //Info.jalview_SCREEN_X= 10,Info.jalview_SCREEN_Y= 10;
- //Info.jalview_EMBEDDED= true;
- //Info.jalview_SCREEN_WIDTH = 400;
- //Info.jalview_SCREEN_HEIGHT = 100;
-
-var text = element.outerHTML;
-var code = element.getAttribute("code");
-var parent = element.parentElement;
-if (code != "jalview.bin.JalviewLite" && text.indexOf("<applet") == 0) {
- return;
-}
+ var code = element.getAttribute("code");
+ var parent = element.parentElement;
+ if (code != "jalview.bin.JalviewLite") {
+ return;
+ }
var Info = {
- code: null,
- main: "jalview.bin.Jalview",
- core: "NONE",
- resourcePath: "examples",
- readyFunction: null,
- serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
- j2sPath: 'swingjs/j2s',
- console:'sysout',
- startButton:'Start Jalview',
- hideDesktop:true,
- embedInternalFrames:false,
- idPrefix:'%ID%',
- allowjavascript: true
+ code: null,
+ main: "jalview.bin.Jalview",
+ core: "NONE",
+ resourcePath: "examples",
+ readyFunction: null,
+ serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
+ j2sPath: 'swingjs/j2s',
+ console:'sysout',
+ startButton:'Start Jalview',
+ hideDesktop:true,
+ embedInternalFrames:false,
+ idPrefix:'%ID%',
+ allowJavascript: true,
}
- var args = Info.args = text.replace(/[\n\t]/g, " ").replace("<jvapplet","<applet").split("<param ");
+ var text = element.outerHTML;
+ var args = Info.args = text.replace(/[\n\t]/g, " ").split("<param ");
- // overwrite default parameters with UserInfo (global JalviewInfo):
+ // overwrite default parameters with UserInfo (global JalviewInfo):
if (UserInfo) {
for (var i in UserInfo) {
Info[i] = UserInfo[i];
}
}
-
// generate name/value pairs for parameters in Applet tag
Info.j2sAppletID = Info.j2sAppletID
|| element.getAttribute("id")
|| Info.idPrefix.replace(/%ID%/g, "jalview" + ++Jalview.jvid);
+ //Info.jalview_SCREEN_X= 10,Info.jalview_SCREEN_Y= 10;
+ //Info.jalview_EMBEDDED= true;
+ //Info.jalview_SCREEN_WIDTH = 400;
+ //Info.jalview_SCREEN_HEIGHT = 100;
+
var addParam = function(key,value) {
args.push("name=\"" + key + "\" value=\"" + value + "\"");
}
-
-
+
+
for (var i in Info) {
var v = ("" + Info[i] || "null").replace(/\"/g,"'");
addParam("Info." + i, v);
}
-
-
+
+
element.JalviewInfo = Info;
var btn = document.createElement("button");
btn.appletElement = element;
parent.replaceChild(btn, element);
$(btn).click(Jalview.doStartJalview);
} else {
- parent.removeElement(element);
+ parent.removeChild(element);
Jalview.doStartJalview({target:btn});
}
}
Jalview.doStartJalview = function(e) {
+ e.target.disabled = true;
var element = e.target.appletElement;
-var parent = e.target.jvparent;
+ var parent = e.target.jvparent;
var Info = element.JalviewInfo;
var id = Info.j2sAppletID;
var d = document.createElement("div");
d.style.display = "none";
d.style.width = d.style.height = "0px";
}
- SwingJS.getApplet(id, Info);
- document.title = id;
- e.target.style.visibility="hidden";
+ if (Info.allowJavascript) {
+ if (Info.readyFunction) {
+ var c = Info.readyFunction;
+ Info.readyFunction = function(a){
+ Jalview._setAPI(a);
+ c.apply(null, arguments);
+ }
+ } else {
+ Info.readyFunction = function(a) {Jalview._setAPI(a)};
+ }
+ }
+ var app = SwingJS.getApplet(id, Info);
}
+Jalview._setAPI = function(app) {
+
+ // Create a map of nonqualified methods to qualified methods
+ // based on parameter type.
+ var cl = Class.forName$S("jalview.bin.Jalview");
+ if (!cl.$clazz$.getInstance$) {
+ System.err.println(app.__Info.main + " has no getInstance() method; interface creation skipped.");
+ return;
+ }
+ var instance = app._instance = cl.$clazz$.getInstance$();
+ var apply = function(args, methods) {
+ return methods[args.length].apply(instance, args);
+ }
+ var getMap = function(cl) {
+ var methods = cl.getMethods$();
+ var p = cl.$clazz$.prototype;
+ var map = {};
+ for (var i = 0, n = methods.length; i < n; i++) {
+ var qname = methods[i].name;
+ if (cl.$clazz$[qname])
+ continue; // static method
+ var s = qname.split("$");
+ var name = s[0];
+ if (!name)
+ continue; // $init$, $cinit$
+ if (app[name]) {
+ name += "$";
+ System.err.println(app._id + "." + name + " is " + qname);
+ };
+ (m = map[name])||(m = map[name] = []);
+ var j = p[qname].length;
+ if (m[j]) {
+ System.err.println(app._id + ".instance." + qname + " must be called directly.");
+ app[qname] = p[qname];
+ } else {
+ System.out.println(app._id + "." + name + "(" + j + ") aliases " + app._id + ".instance." + qname);
+ m[j] = p[qname];
+ }
+ }
+ return map;
+ }
+ var getFunc = function(map,i) {
+ return function(){return apply(arguments,map[i])};
+ }
+ var map = getMap(Clazz._4Name(app.__Info.main));
+ var n = 0;
+ for (var i in map) {
+ n++;
+ app[i] = getFunc(map,i);
+ }
+ System.err.println(app._id + " contains " + n + " JavaScript interface methods");
+}
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.gff.SequenceOntologyFactory;
+import jalview.javascript.JalviewLiteJsApi;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
* @author $author$
* @version $Revision$
*/
-public class Jalview implements ApplicationSingletonI
+public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
{
public static Jalview getInstance()
new JalviewAppLoader(true).load(app);
}
+ @Override
+ public String getSelectedSequences()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequences(String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesFrom(jalview.appletgui.AlignFrame alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesFrom(jalview.appletgui.AlignFrame alf,
+ String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void highlight(String sequenceId, String position,
+ String alignedPosition)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void highlightIn(jalview.appletgui.AlignFrame alf,
+ String sequenceId, String position, String alignedPosition)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void select(String sequenceIds, String columns)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void select(String sequenceIds, String columns, String sep)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void selectIn(jalview.appletgui.AlignFrame alf, String sequenceIds,
+ String columns)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void selectIn(jalview.appletgui.AlignFrame alf, String sequenceIds,
+ String columns, String sep)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignment(String format,
+ String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignmentFrom(
+ jalview.appletgui.AlignFrame alf, String format, String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentOrder()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(jalview.appletgui.AlignFrame alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(jalview.appletgui.AlignFrame alf,
+ String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String orderBy(String order, String undoName)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String orderBy(String order, String undoName, String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String orderAlignmentBy(jalview.appletgui.AlignFrame alf,
+ String order, String undoName, String sep)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignment(String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentFrom(jalview.appletgui.AlignFrame alf,
+ String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignment(String format, String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAlignmentFrom(jalview.appletgui.AlignFrame alf,
+ String format, String suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void loadAnnotation(String annotation)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void loadAnnotationFrom(jalview.appletgui.AlignFrame alf,
+ String annotation)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void loadFeatures(String features, boolean autoenabledisplay)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean loadFeaturesFrom(jalview.appletgui.AlignFrame alf,
+ String features, boolean autoenabledisplay)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public String getFeatures(String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeaturesFrom(jalview.appletgui.AlignFrame alf,
+ String format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAnnotation()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAnnotationFrom(jalview.appletgui.AlignFrame alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public jalview.appletgui.AlignFrame newView()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public jalview.appletgui.AlignFrame newView(String name)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public jalview.appletgui.AlignFrame newViewFrom(
+ jalview.appletgui.AlignFrame alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public jalview.appletgui.AlignFrame newViewFrom(
+ jalview.appletgui.AlignFrame alf, String name)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public jalview.appletgui.AlignFrame loadAlignment(String text,
+ String title)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setMouseoverListener(String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setMouseoverListener(jalview.appletgui.AlignFrame af,
+ String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setSelectionListener(String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setSelectionListener(jalview.appletgui.AlignFrame af,
+ String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setStructureListener(String listener, String modelSet)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void removeJavascriptListener(jalview.appletgui.AlignFrame af,
+ String listener)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseOverStructure(String pdbResNum, String chain,
+ String pdbfile)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean addPdbFile(jalview.appletgui.AlignFrame alFrame,
+ String sequenceId, String pdbEntryString, String pdbFile)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public void scrollViewToIn(jalview.appletgui.AlignFrame alf,
+ String topRow, String leftHandColumn)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void scrollViewToRowIn(jalview.appletgui.AlignFrame alf,
+ String topRow)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void scrollViewToColumnIn(jalview.appletgui.AlignFrame alf,
+ String leftHandColumn)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getFeatureGroups()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeatureGroupsOn(jalview.appletgui.AlignFrame alf)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFeatureGroupsOfStateOn(jalview.appletgui.AlignFrame alf,
+ boolean visible)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setFeatureGroupStateOn(jalview.appletgui.AlignFrame alf,
+ String groups, boolean state)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setFeatureGroupState(String groups, boolean state)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getSeparator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setSeparator(String separator)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getJsMessage(String messageclass, String viewId)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff