+ public void loadAnnotation(String annotation)\r
+ {\r
+ loadAnnotationFrom(getDefaultTargetFrame(), annotation);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)\r
+ {\r
+ if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()\r
+ .getAlignment(), annotation, AppletFormatAdapter.PASTE))\r
+ {\r
+ alf.alignPanel.fontChanged();\r
+ alf.alignPanel.setScrollValues(0, 0);\r
+ }\r
+ else\r
+ {\r
+ alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)\r
+ */\r
+ public String getFeatures(String format)\r
+ {\r
+ return getFeaturesFrom(getDefaultTargetFrame(), format);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,\r
+ * java.lang.String)\r
+ */\r
+ public String getFeaturesFrom(AlignFrame alf, String format)\r
+ {\r
+ return alf.outputFeatures(false, format);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotation()\r
+ */\r
+ public String getAnnotation()\r
+ {\r
+ return getAnnotationFrom(getDefaultTargetFrame());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame\r
+ * )\r
+ */\r
+ public String getAnnotationFrom(AlignFrame alf)\r
+ {\r
+ return alf.outputAnnotations(false);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newView()\r
+ */\r
+ public AlignFrame newView()\r
+ {\r
+ return newViewFrom(getDefaultTargetFrame());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)\r
+ */\r
+ public AlignFrame newView(String name)\r
+ {\r
+ return newViewFrom(getDefaultTargetFrame(), name);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)\r
+ */\r
+ public AlignFrame newViewFrom(AlignFrame alf)\r
+ {\r
+ return alf.newView(null);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,\r
+ * java.lang.String)\r
+ */\r
+ public AlignFrame newViewFrom(AlignFrame alf, String name)\r
+ {\r
+ return alf.newView(name);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public AlignFrame loadAlignment(String text, String title)\r
+ {\r
+ Alignment al = null;\r
+\r
+ String format = new IdentifyFile().Identify(text,\r
+ AppletFormatAdapter.PASTE);\r
+ try\r
+ {\r
+ al = new AppletFormatAdapter().readFile(text,\r
+ AppletFormatAdapter.PASTE, format);\r
+ if (al.getHeight() > 0)\r
+ {\r
+ return new AlignFrame(al, this, title, false);\r
+ }\r
+ } catch (java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)\r
+ */\r
+ public void setMouseoverListener(String listener)\r
+ {\r
+ setMouseoverListener(currentAlignFrame, listener);\r
+ }\r
+\r
+ private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public void setMouseoverListener(AlignFrame af, String listener)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ System.err\r
+ .println("jalview Javascript error: Ignoring empty function for mouseover listener.");\r
+ return;\r
+ }\r
+ }\r
+ jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(\r
+ this, af, listener);\r
+ javascriptListeners.addElement(mol);\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .addStructureViewerListener(mol);\r
+ if (debug)\r
+ {\r
+ System.err.println("Added a mouseover listener for "\r
+ + ((af == null) ? "All frames" : "Just views for "\r
+ + af.getAlignViewport().getSequenceSetId()));\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)\r
+ */\r
+ public void setSelectionListener(String listener)\r
+ {\r
+ setSelectionListener(null, listener);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public void setSelectionListener(AlignFrame af, String listener)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ System.err\r
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");\r
+ return;\r
+ }\r
+ }\r
+ jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(\r
+ this, af, listener);\r
+ javascriptListeners.addElement(mol);\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .addSelectionListener(mol);\r
+ if (debug)\r
+ {\r
+ System.err.println("Added a selection listener for "\r
+ + ((af == null) ? "All frames" : "Just views for "\r
+ + af.getAlignViewport().getSequenceSetId()));\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public void setStructureListener(String listener, String modelSet)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ System.err\r
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");\r
+ return;\r
+ }\r
+ }\r
+ jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(\r
+ this, listener, separatorListToArray(modelSet));\r
+ javascriptListeners.addElement(mol);\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .addStructureViewerListener(mol);\r
+ if (debug)\r
+ {\r
+ System.err.println("Added a javascript structure viewer listener '"\r
+ + listener + "'");\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui\r
+ * .AlignFrame, java.lang.String)\r
+ */\r
+ public void removeJavascriptListener(AlignFrame af, String listener)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ listener = null;\r
+ }\r
+ }\r
+ boolean rprt = false;\r
+ for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)\r
+ {\r
+ Object lstn = javascriptListeners.elementAt(ms);\r
+ JsCallBack lstner = (JsCallBack) lstn;\r
+ if ((af == null || lstner.getAlignFrame() == af)\r
+ && (listener == null || lstner.getListenerFunction().equals(\r
+ listener)))\r
+ {\r
+ javascriptListeners.removeElement(lstner);\r
+ msSize--;\r
+ if (lstner instanceof SelectionListener)\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeSelectionListener((SelectionListener) lstner);\r
+ }\r
+ else\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeStructureViewerListener(lstner, null);\r
+ }\r
+ rprt = debug;\r
+ if (debug)\r
+ {\r
+ System.err.println("Removed listener '" + listener + "'");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ ms++;\r
+ }\r
+ }\r
+ if (rprt)\r
+ {\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ public void stop()\r
+ {\r
+ System.err.println("Applet " + getName() + " stop().");\r
+ tidyUp();\r
+ }\r
+\r
+ public void destroy()\r
+ {\r
+ System.err.println("Applet " + getName() + " destroy().");\r
+ tidyUp();\r
+ }\r
+\r
+ private void tidyUp()\r
+ {\r
+ removeAll();\r
+ if (currentAlignFrame != null && currentAlignFrame.viewport != null\r
+ && currentAlignFrame.viewport.applet != null)\r
+ {\r
+ AlignViewport av = currentAlignFrame.viewport;\r
+ currentAlignFrame.closeMenuItem_actionPerformed();\r
+ av.applet = null;\r
+ currentAlignFrame = null;\r
+ }\r
+ if (javascriptListeners != null)\r
+ {\r
+ while (javascriptListeners.size() > 0)\r
+ {\r
+ jalview.javascript.JSFunctionExec mol = javascriptListeners\r
+ .elementAt(0);\r
+ javascriptListeners.removeElement(mol);\r
+ if (mol instanceof SelectionListener)\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeSelectionListener((SelectionListener) mol);\r
+ }\r
+ else\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeStructureViewerListener(mol, null);\r
+ }\r
+ mol.jvlite = null;\r
+ }\r
+ }\r
+ if (jsFunctionExec != null)\r
+ {\r
+ jsFunctionExec.stopQueue();\r
+ jsFunctionExec.jvlite = null;\r
+ }\r
+ initialAlignFrame = null;\r
+ jsFunctionExec = null;\r
+ javascriptListeners = null;\r
+ StructureSelectionManager.release(this);\r
+ }\r
+\r
+ private jalview.javascript.JSFunctionExec jsFunctionExec;\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public void mouseOverStructure(final String pdbResNum,\r
+ final String chain, final String pdbfile)\r
+ {\r
+ final StructureSelectionManagerProvider me = this;\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(me)\r
+ .mouseOverStructure(new Integer(pdbResNum).intValue(),\r
+ chain, pdbfile);\r
+ if (debug)\r
+ {\r
+ System.err.println("mouseOver for '" + pdbResNum\r
+ + "' in chain '" + chain + "' in structure '" + pdbfile\r
+ + "'");\r
+ }\r
+ } catch (NumberFormatException e)\r
+ {\r
+ System.err.println("Ignoring invalid residue number string '"\r
+ + pdbResNum + "'");\r
+ }\r
+\r
+ }\r
+ });\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public void scrollViewToIn(final AlignFrame alf, final String topRow,\r
+ final String leftHandColumn)\r
+ {\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ alf.scrollTo(new Integer(topRow).intValue(), new Integer(\r
+ leftHandColumn).intValue());\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ System.err.println("Couldn't parse integer arguments (topRow='"\r
+ + topRow + "' and leftHandColumn='" + leftHandColumn\r
+ + "')");\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ });\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui\r
+ * .AlignFrame, java.lang.String)\r
+ */\r
+ @Override\r
+ public void scrollViewToRowIn(final AlignFrame alf, final String topRow)\r
+ {\r
+\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ alf.scrollToRow(new Integer(topRow).intValue());\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ System.err.println("Couldn't parse integer arguments (topRow='"\r
+ + topRow + "')");\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ }\r
+ });\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui\r
+ * .AlignFrame, java.lang.String)\r
+ */\r
+ @Override\r
+ public void scrollViewToColumnIn(final AlignFrame alf,\r
+ final String leftHandColumn)\r
+ {\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+\r
+ @Override\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ alf.scrollToColumn(new Integer(leftHandColumn).intValue());\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse integer arguments (leftHandColumn='"\r
+ + leftHandColumn + "')");\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ });\r
+\r
+ }\r
+\r
+ // //////////////////////////////////////////////\r
+ // //////////////////////////////////////////////\r
+\r
+ public static int lastFrameX = 200;\r
+\r
+ public static int lastFrameY = 200;\r
+\r
+ boolean fileFound = true;\r
+\r
+ String file = "No file";\r
+\r
+ Button launcher = new Button("Start Jalview");\r
+\r
+ /**\r
+ * The currentAlignFrame is static, it will change if and when the user\r
+ * selects a new window. Note that it will *never* point back to the embedded\r
+ * AlignFrame if the applet is started as embedded on the page and then\r
+ * afterwards a new view is created.\r
+ */\r
+ public AlignFrame currentAlignFrame = null;\r
+\r
+ /**\r
+ * This is the first frame to be displayed, and does not change. API calls\r
+ * will default to this instance if currentAlignFrame is null.\r
+ */\r
+ AlignFrame initialAlignFrame = null;\r
+\r
+ boolean embedded = false;\r
+\r
+ private boolean checkForJmol = true;\r
+\r
+ private boolean checkedForJmol = false; // ensure we don't check for jmol\r
+\r
+ // every time the app is re-inited\r
+\r
+ public boolean jmolAvailable = false;\r
+\r
+ private boolean alignPdbStructures = false;\r
+\r
+ /**\r
+ * use an external structure viewer exclusively (no jmols or MCViews will be\r
+ * opened by JalviewLite itself)\r
+ */\r
+ public boolean useXtrnalSviewer = false;\r
+\r
+ public static boolean debug = false;\r
+\r
+ static String builddate = null, version = null;\r
+\r
+ private static void initBuildDetails()\r
+ {\r
+ if (builddate == null)\r
+ {\r
+ builddate = "unknown";\r
+ version = "test";\r
+ java.net.URL url = JalviewLite.class\r
+ .getResource("/.build_properties");\r
+ if (url != null)\r
+ {\r
+ try\r
+ {\r
+ BufferedReader reader = new BufferedReader(new InputStreamReader(\r
+ url.openStream()));\r
+ String line;\r
+ while ((line = reader.readLine()) != null)\r
+ {\r
+ if (line.indexOf("VERSION") > -1)\r
+ {\r
+ version = line.substring(line.indexOf("=") + 1);\r
+ }\r
+ if (line.indexOf("BUILD_DATE") > -1)\r
+ {\r
+ builddate = line.substring(line.indexOf("=") + 1);\r
+ }\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ public static String getBuildDate()\r
+ {\r
+ initBuildDetails();\r
+ return builddate;\r
+ }\r
+\r
+ public static String getVersion()\r
+ {\r
+ initBuildDetails();\r
+ return version;\r
+ }\r
+\r
+ // public JSObject scriptObject = null;\r
+\r
+ /**\r
+ * init method for Jalview Applet\r
+ */\r
+ public void init()\r
+ {\r
+ // remove any handlers that might be hanging around from an earlier instance\r
+ try\r
+ {\r
+ if (debug)\r
+ {\r
+ System.err.println("Applet context is '"\r
+ + getAppletContext().getClass().toString() + "'");\r
+ }\r
+ JSObject scriptObject = JSObject.getWindow(this);\r
+ if (debug && scriptObject != null)\r
+ {\r
+ System.err.println("Applet has Javascript callback support.");\r
+ }\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ System.err\r
+ .println("Warning: No JalviewLite javascript callbacks available.");\r
+ if (debug)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ /**\r
+ * turn on extra applet debugging\r
+ */\r
+ String dbg = getParameter("debug");\r
+ if (dbg != null)\r
+ {\r
+ debug = dbg.toLowerCase().equals("true");\r
+ }\r
+ if (debug)\r
+ {\r
+\r
+ System.err.println("JalviewLite Version " + getVersion());\r
+ System.err.println("Build Date : " + getBuildDate());\r
+\r
+ }\r
+ String externalsviewer = getParameter("externalstructureviewer");\r
+ if (externalsviewer != null)\r
+ {\r
+ useXtrnalSviewer = externalsviewer.trim().toLowerCase()\r
+ .equals("true");\r
+ }\r
+ /**\r
+ * if true disable the check for jmol\r
+ */\r
+ String chkforJmol = getParameter("nojmol");\r
+ if (chkforJmol != null)\r
+ {\r
+ checkForJmol = !chkforJmol.equals("true");\r
+ }\r
+ /**\r
+ * get the separator parameter if present\r
+ */\r
+ String sep = getParameter("separator");\r
+ if (sep != null)\r
+ {\r
+ if (sep.length() > 0)\r
+ {\r
+ separator = sep;\r
+ if (debug)\r
+ {\r
+ System.err.println("Separator set to '" + separator + "'");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ throw new Error(\r
+ "Invalid separator parameter - must be non-zero length");\r
+ }\r
+ }\r
+ int r = 255;\r
+ int g = 255;\r
+ int b = 255;\r
+ String param = getParameter("RGB");\r
+\r
+ if (param != null)\r
+ {\r
+ try\r
+ {\r
+ r = Integer.parseInt(param.substring(0, 2), 16);\r
+ g = Integer.parseInt(param.substring(2, 4), 16);\r
+ b = Integer.parseInt(param.substring(4, 6), 16);\r
+ } catch (Exception ex)\r
+ {\r
+ r = 255;\r
+ g = 255;\r
+ b = 255;\r
+ }\r
+ }\r
+ param = getParameter("label");\r
+ if (param != null)\r
+ {\r
+ launcher.setLabel(param);\r
+ }\r
+\r
+ setBackground(new Color(r, g, b));\r
+\r
+ file = getParameter("file");\r
+\r
+ if (file == null)\r
+ {\r
+ // Maybe the sequences are added as parameters\r
+ StringBuffer data = new StringBuffer("PASTE");\r
+ int i = 1;\r
+ while ((file = getParameter("sequence" + i)) != null)\r
+ {\r
+ data.append(file.toString() + "\n");\r
+ i++;\r
+ }\r
+ if (data.length() > 5)\r
+ {\r
+ file = data.toString();\r
+ }\r
+ }\r
+\r
+ final JalviewLite jvapplet = this;\r
+ if (getParameter("embedded") != null\r
+ && getParameter("embedded").equalsIgnoreCase("true"))\r
+ {\r
+ // Launch as embedded applet in page\r
+ embedded = true;\r
+ LoadingThread loader = new LoadingThread(file, jvapplet);\r
+ loader.start();\r
+ }\r
+ else if (file != null)\r
+ {\r
+ if (getParameter("showbutton") == null\r
+ || !getParameter("showbutton").equalsIgnoreCase("false"))\r
+ {\r
+ // Add the JalviewLite 'Button' to the page\r
+ add(launcher);\r
+ launcher.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ LoadingThread loader = new LoadingThread(file, jvapplet);\r
+ loader.start();\r
+ }\r
+ });\r
+ }\r
+ else\r
+ {\r
+ // Open jalviewLite immediately.\r
+ LoadingThread loader = new LoadingThread(file, jvapplet);\r
+ loader.start();\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // jalview initialisation with no alignment. loadAlignment() method can\r
+ // still be called to open new alignments.\r
+ file = "NO FILE";\r
+ fileFound = false;\r
+ // callInitCallback();\r
+ }\r
+ }\r
+\r
+ private void callInitCallback()\r
+ {\r
+ String initjscallback = getParameter("oninit");\r
+ if (initjscallback == null)\r
+ {\r
+ return;\r
+ }\r
+ initjscallback = initjscallback.trim();\r
+ if (initjscallback.length() > 0)\r
+ {\r
+ JSObject scriptObject = null;\r
+ try\r
+ {\r
+ scriptObject = JSObject.getWindow(this);\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+ ;\r
+ if (scriptObject != null)\r
+ {\r
+ try\r
+ {\r
+ // do onInit with the JS executor thread\r
+ new JSFunctionExec(this).executeJavascriptFunction(true,\r
+ initjscallback, null, "Calling oninit callback '"\r
+ + initjscallback + "'.");\r
+ } catch (Exception e)\r
+ {\r
+ System.err.println("Exception when executing _oninit callback '"\r
+ + initjscallback + "'.");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ else\r
+ {\r
+ System.err.println("Not executing _oninit callback '"\r
+ + initjscallback + "' - no scripting allowed.");\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Initialises and displays a new java.awt.Frame\r
+ * \r
+ * @param frame\r
+ * java.awt.Frame to be displayed\r
+ * @param title\r
+ * title of new frame\r
+ * @param width\r
+ * width if new frame\r
+ * @param height\r
+ * height of new frame\r
+ */\r
+ public static void addFrame(final Frame frame, String title, int width,\r
+ int height)\r
+ {\r
+ frame.setLocation(lastFrameX, lastFrameY);\r
+ lastFrameX += 40;\r
+ lastFrameY += 40;\r
+ frame.setSize(width, height);\r
+ frame.setTitle(title);\r
+ frame.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ if (frame instanceof AlignFrame)\r
+ {\r
+ AlignViewport vp = ((AlignFrame) frame).viewport;\r
+ ((AlignFrame) frame).closeMenuItem_actionPerformed();\r
+ if (vp.applet.currentAlignFrame == frame)\r
+ {\r
+ vp.applet.currentAlignFrame = null;\r
+ }\r
+ vp.applet = null;\r
+ vp = null;\r
+\r
+ }\r
+ lastFrameX -= 40;\r
+ lastFrameY -= 40;\r
+ if (frame instanceof EmbmenuFrame)\r
+ {\r
+ ((EmbmenuFrame) frame).destroyMenus();\r
+ }\r
+ frame.setMenuBar(null);\r
+ frame.dispose();\r
+ }\r
+\r
+ public void windowActivated(WindowEvent e)\r
+ {\r
+ if (frame instanceof AlignFrame)\r
+ {\r
+ ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;\r
+ if (debug)\r
+ {\r
+ System.err.println("Activated window " + frame);\r
+ }\r
+ }\r
+ // be good.\r
+ super.windowActivated(e);\r
+ }\r
+ /*\r
+ * Probably not necessary to do this - see TODO above. (non-Javadoc)\r
+ * \r
+ * @see\r
+ * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent\r
+ * )\r
+ * \r
+ * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==\r
+ * frame) { currentAlignFrame = null; if (debug) {\r
+ * System.err.println("Deactivated window "+frame); } }\r
+ * super.windowDeactivated(e); }\r
+ */\r
+ });\r
+ frame.setVisible(true);\r
+ }\r
+\r
+ /**\r
+ * This paints the background surrounding the "Launch Jalview button" <br>\r
+ * <br>\r
+ * If file given in parameter not found, displays error message\r
+ * \r
+ * @param g\r
+ * graphics context\r
+ */\r
+ public void paint(Graphics g)\r
+ {\r
+ if (!fileFound)\r
+ {\r
+ g.setColor(new Color(200, 200, 200));\r
+ g.setColor(Color.cyan);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ g.setColor(Color.red);\r
+ g.drawString("Jalview can't open file", 5, 15);\r
+ g.drawString("\"" + file + "\"", 5, 30);\r
+ }\r
+ else if (embedded)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.setFont(new Font("Arial", Font.BOLD, 24));\r
+ g.drawString("Jalview Applet", 50, getSize().height / 2 - 30);\r
+ g.drawString("Loading Data...", 50, getSize().height / 2);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * get all components associated with the applet of the given type\r
+ * \r
+ * @param class1\r
+ * @return\r
+ */\r
+ public Vector getAppletWindow(Class class1)\r
+ {\r
+ Vector wnds = new Vector();\r
+ Component[] cmp = getComponents();\r
+ if (cmp != null)\r
+ {\r
+ for (int i = 0; i < cmp.length; i++)\r
+ {\r
+ if (class1.isAssignableFrom(cmp[i].getClass()))\r
+ {\r
+ wnds.addElement(cmp);\r
+ }\r
+ }\r
+ }\r
+ return wnds;\r
+ }\r
+\r
+ class LoadJmolThread extends Thread\r
+ {\r
+ private boolean running = false;\r
+\r
+ public void run()\r
+ {\r
+ if (running || checkedForJmol)\r
+ {\r
+ return;\r
+ }\r
+ running = true;\r
+ if (checkForJmol)\r
+ {\r
+ try\r
+ {\r
+ if (!System.getProperty("java.version").startsWith("1.1"))\r
+ {\r
+ Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");\r
+ jmolAvailable = true;\r
+ }\r
+ if (!jmolAvailable)\r
+ {\r
+ System.out\r
+ .println("Jmol not available - Using MCview for structures");\r
+ }\r
+ } catch (java.lang.ClassNotFoundException ex)\r
+ {\r
+ }\r
+ }\r
+ else\r
+ {\r
+ jmolAvailable = false;\r
+ if (debug)\r
+ {\r
+ System.err\r
+ .println("Skipping Jmol check. Will use MCView (probably)");\r
+ }\r
+ }\r
+ checkedForJmol = true;\r
+ running = false;\r
+ }\r
+\r
+ public boolean notFinished()\r
+ {\r
+ return running || !checkedForJmol;\r
+ }\r
+ }\r
+\r
+ class LoadingThread extends Thread\r