+ String reply = new AppletFormatAdapter().formatSequences(format,\r
+ alf.viewport.getAlignment(), seqlimits);\r
+ return reply;\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\r
+ }\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)\r
+ */\r
+ public void loadAnnotation(String annotation)\r
+ {\r
+ loadAnnotationFrom(getDefaultTargetFrame(), annotation);\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame, 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
+ /* (non-Javadoc)\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
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame, java.lang.String)\r
+ */\r
+ public String getFeaturesFrom(AlignFrame alf, String format)\r
+ {\r
+ return alf.outputFeatures(false, format);\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotation()\r
+ */\r
+ public String getAnnotation()\r
+ {\r
+ return getAnnotationFrom(getDefaultTargetFrame());\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame)\r
+ */\r
+ public String getAnnotationFrom(AlignFrame alf)\r
+ {\r
+ return alf.outputAnnotations(false);\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#newView()\r
+ */\r
+ public AlignFrame newView()\r
+ {\r
+ return newViewFrom(getDefaultTargetFrame());\r
+ }\r
+\r
+ /* (non-Javadoc)\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
+ /* (non-Javadoc)\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
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame, java.lang.String)\r
+ */\r
+ public AlignFrame newViewFrom(AlignFrame alf, String name)\r
+ {\r
+ return alf.newView(name);\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String, 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
+ /* (non-Javadoc)\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
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame, 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
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)\r
+ */\r
+ public void setSelectionListener(String listener)\r
+ {\r
+ setSelectionListener(null, listener);\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame, 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
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String, 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
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui.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
+ public void destroy()\r
+ {\r
+ System.err.println("Applet "+getName()+" destroy().");\r
+ tidyUp();\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.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
+ jsFunctionExec.stopQueue();\r
+ jsFunctionExec.jvlite=null;\r
+ }\r
+ initialAlignFrame=null;\r
+ jsFunctionExec = null;\r
+ javascriptListeners=null;\r
+ StructureSelectionManager.release(this);\r
+ }\r
+ private jalview.javascript.JSFunctionExec jsFunctionExec;\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String, java.lang.String, java.lang.String)\r
+ */\r
+ public void mouseOverStructure(String pdbResNum, String chain,\r
+ String pdbfile)\r
+ {\r
+ try\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .mouseOverStructure(new Integer(pdbResNum).intValue(), chain,\r
+ pdbfile);\r
+ if (debug)\r
+ {\r
+ System.err.println("mouseOver for '" + pdbResNum + "' in chain '"\r
+ + chain + "' in structure '" + pdbfile + "'");\r
+ }\r
+ } catch (NumberFormatException e)\r
+ {\r
+ System.err.println("Ignoring invalid residue number string '"\r
+ + pdbResNum + "'");\r
+ }\r
+ }\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame, java.lang.String, java.lang.String)\r
+ */\r
+ public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn)\r
+ {\r
+ try {\r
+ alf.scrollTo(new Integer(topRow).intValue(), new Integer(leftHandColumn).intValue());\r
+ \r
+ } catch (Exception ex)\r
+ {\r
+ System.err.println("Couldn't parse integer arguments (topRow='"+topRow+"' and leftHandColumn='"+leftHandColumn+"'");\r
+ ex.printStackTrace();\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