+\r
+ /**\r
+ * @return the default alignFrame acted on by the public applet methods. May\r
+ * return null with an error message on System.err indicating the\r
+ * fact.\r
+ */\r
+ public AlignFrame getDefaultTargetFrame()\r
+ {\r
+ if (currentAlignFrame != null)\r
+ {\r
+ return currentAlignFrame;\r
+ }\r
+ if (initialAlignFrame != null)\r
+ {\r
+ return initialAlignFrame;\r
+ }\r
+ System.err\r
+ .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * separator used for separatorList\r
+ */\r
+ protected String separator = "" + ((char) 0x00AC); // the default used to be\r
+ // '|' but many sequence\r
+ // IDS include pipes.\r
+\r
+ /**\r
+ * set to enable the URL based javascript execution mechanism\r
+ */\r
+ public boolean jsfallbackEnabled = false;\r
+\r
+ /**\r
+ * parse the string into a list\r
+ * \r
+ * @param list\r
+ * @return elements separated by separator\r
+ */\r
+ public String[] separatorListToArray(String list)\r
+ {\r
+ return separatorListToArray(list, separator);\r
+ }\r
+\r
+ /**\r
+ * parse the string into a list\r
+ * \r
+ * @param list\r
+ * @param separator\r
+ * @return elements separated by separator\r
+ */\r
+ public String[] separatorListToArray(String list, String separator)\r
+ {\r
+ // note separator local variable intentionally masks object field\r
+ int seplen = separator.length();\r
+ if (list == null || list.equals("") || list.equals(separator))\r
+ return null;\r
+ java.util.Vector jv = new Vector();\r
+ int cp = 0, pos;\r
+ while ((pos = list.indexOf(separator, cp)) > cp)\r
+ {\r
+ jv.addElement(list.substring(cp, pos));\r
+ cp = pos + seplen;\r
+ }\r
+ if (cp < list.length())\r
+ {\r
+ String c = list.substring(cp);\r
+ if (!c.equals(separator))\r
+ {\r
+ jv.addElement(c);\r
+ }\r
+ }\r
+ if (jv.size() > 0)\r
+ {\r
+ String[] v = new String[jv.size()];\r
+ for (int i = 0; i < v.length; i++)\r
+ {\r
+ v[i] = (String) jv.elementAt(i);\r
+ }\r
+ jv.removeAllElements();\r
+ if (debug)\r
+ {\r
+ System.err.println("Array from '" + separator\r
+ + "' separated List:\n" + v.length);\r
+ for (int i = 0; i < v.length; i++)\r
+ {\r
+ System.err.println("item " + i + " '" + v[i] + "'");\r
+ }\r
+ }\r
+ return v;\r
+ }\r
+ if (debug)\r
+ {\r
+ System.err.println("Empty Array from '" + separator\r
+ + "' separated List");\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * concatenate the list with separator\r
+ * \r
+ * @param list\r
+ * @return concatenated string\r
+ */\r
+ public String arrayToSeparatorList(String[] list)\r
+ {\r
+ return arrayToSeparatorList(list, separator);\r
+ }\r
+\r
+ /**\r
+ * concatenate the list with separator\r
+ * \r
+ * @param list\r
+ * @param separator\r
+ * @return concatenated string\r
+ */\r
+ public String arrayToSeparatorList(String[] list, String separator)\r
+ {\r
+ StringBuffer v = new StringBuffer();\r
+ if (list != null && list.length > 0)\r
+ {\r
+ for (int i = 0, iSize = list.length; i < iSize; i++)\r
+ {\r
+ if (list[i] != null)\r
+ {\r
+ if (i > 0)\r
+ {\r
+ v.append(separator);\r
+ }\r
+ v.append(list[i]);\r
+ }\r
+ }\r
+ if (debug)\r
+ {\r
+ System.err.println("Returning '" + separator\r
+ + "' separated List:\n");\r
+ System.err.println(v);\r
+ }\r
+ return v.toString();\r
+ }\r
+ if (debug)\r
+ {\r
+ System.err.println("Returning empty '" + separator\r
+ + "' separated List\n");\r
+ }\r
+ return "" + separator;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()\r
+ */\r
+ public String getFeatureGroups()\r
+ {\r
+ String lst = arrayToSeparatorList(getDefaultTargetFrame()\r
+ .getFeatureGroups());\r
+ return lst;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame\r
+ * )\r
+ */\r
+ public String getFeatureGroupsOn(AlignFrame alf)\r
+ {\r
+ String lst = arrayToSeparatorList(alf.getFeatureGroups());\r
+ return lst;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)\r
+ */\r
+ public String getFeatureGroupsOfState(boolean visible)\r
+ {\r
+ return arrayToSeparatorList(getDefaultTargetFrame()\r
+ .getFeatureGroupsOfState(visible));\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui\r
+ * .AlignFrame, boolean)\r
+ */\r
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)\r
+ {\r
+ return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.\r
+ * AlignFrame, java.lang.String, boolean)\r
+ */\r
+ public void setFeatureGroupStateOn(final AlignFrame alf,\r
+ final String groups, boolean state)\r
+ {\r
+ final boolean st = state;// !(state==null || state.equals("") ||\r
+ // state.toLowerCase().equals("false"));\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ alf.setFeatureGroupState(separatorListToArray(groups), st);\r
+ }\r
+ });\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,\r
+ * boolean)\r
+ */\r
+ public void setFeatureGroupState(String groups, boolean state)\r
+ {\r
+ setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getSeparator()\r
+ */\r
+ public String getSeparator()\r
+ {\r
+ return separator;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)\r
+ */\r
+ public void setSeparator(String separator)\r
+ {\r
+ if (separator == null || separator.length() < 1)\r
+ {\r
+ // reset to default\r
+ separator = "" + ((char) 0x00AC);\r
+ }\r
+ this.separator = separator;\r
+ if (debug)\r
+ {\r
+ System.err.println("Default Separator now: '" + separator + "'");\r
+ }\r
+ }\r
+\r
+ /**\r
+ * get boolean value of applet parameter 'name' and return default if\r
+ * parameter is not set\r
+ * \r
+ * @param name\r
+ * name of paremeter\r
+ * @param def\r
+ * the value to return otherwise\r
+ * @return true or false\r
+ */\r
+ public boolean getDefaultParameter(String name, boolean def)\r
+ {\r
+ String stn;\r
+ if ((stn = getParameter(name)) == null)\r
+ {\r
+ return def;\r
+ }\r
+ if (stn.toLowerCase().equals("true"))\r
+ {\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,\r
+ * java.lang.String, java.lang.String, java.lang.String)\r
+ */\r
+ public boolean addPdbFile(AlignFrame alFrame, String sequenceId,\r
+ String pdbEntryString, String pdbFile)\r
+ {\r
+ return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);\r
+ }\r
+\r
+ protected void setAlignPdbStructures(boolean alignPdbStructures)\r
+ {\r
+ this.alignPdbStructures = alignPdbStructures;\r
+ }\r
+\r
+ public boolean isAlignPdbStructures()\r
+ {\r
+ return alignPdbStructures;\r
+ }\r
+\r
+ public void start()\r
+ {\r
+ // callInitCallback();\r
+ }\r
+\r
+ private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();\r
+\r
+ private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();\r
+\r
+ public void setJsMessageSet(String messageclass, String viewId,\r
+ String[] colcommands)\r
+ {\r
+ Hashtable<String, String[]> msgset = jsmessages.get(messageclass);\r
+ if (msgset == null)\r
+ {\r
+ msgset = new Hashtable<String, String[]>();\r
+ jsmessages.put(messageclass, msgset);\r
+ }\r
+ msgset.put(viewId, colcommands);\r
+ long[] l = new long[colcommands.length];\r
+ for (int i = 0; i < colcommands.length; i++)\r
+ {\r
+ l[i] = colcommands[i].hashCode();\r
+ }\r
+ jshashes.put(messageclass + "|" + viewId, l);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public String getJsMessage(String messageclass, String viewId)\r
+ {\r
+ Hashtable<String, String[]> msgset = jsmessages.get(messageclass);\r
+ if (msgset != null)\r
+ {\r
+ String[] msgs = msgset.get(viewId);\r
+ if (msgs != null)\r
+ {\r
+ for (int i = 0; i < msgs.length; i++)\r
+ {\r
+ if (msgs[i] != null)\r
+ {\r
+ String m = msgs[i];\r
+ msgs[i] = null;\r
+ return m;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return "";\r
+ }\r
+\r
+ public boolean isJsMessageSetChanged(String string, String string2,\r
+ String[] colcommands)\r
+ {\r
+ long[] l = jshashes.get(string + "|" + string2);\r
+ if (l == null && colcommands != null)\r
+ {\r
+ return true;\r
+ }\r
+ for (int i = 0; i < colcommands.length; i++)\r
+ {\r
+ if (l[i] != colcommands[i].hashCode())\r
+ {\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ private Vector jsExecQueue = new Vector();\r
+\r
+ public Vector getJsExecQueue()\r
+ {\r
+ return jsExecQueue;\r
+ }\r
+\r
+ public void setExecutor(JSFunctionExec jsFunctionExec2)\r
+ {\r
+ jsFunctionExec = jsFunctionExec2;\r
+ }\r
+\r
+ /**\r
+ * return the given colour value parameter or the given default if parameter\r
+ * not given\r
+ * \r
+ * @param colparam\r
+ * @param defcolour\r
+ * @return\r
+ */\r
+ public Color getDefaultColourParameter(String colparam, Color defcolour)\r
+ {\r
+ String colprop = getParameter(colparam);\r
+ if (colprop == null || colprop.trim().length() == 0)\r
+ {\r
+ return defcolour;\r
+ }\r
+ Color col = jalview.schemes.ColourSchemeProperty\r
+ .getAWTColorFromName(colprop);\r
+ if (col == null)\r
+ {\r
+ try\r
+ {\r
+ col = new jalview.schemes.UserColourScheme(colprop).findColour('A');\r
+ } catch (Exception ex)\r
+ {\r
+ System.err.println("Couldn't parse '" + colprop\r
+ + "' as a colour for " + colparam);\r
+ col = null;\r
+ }\r
+ }\r
+ return (col == null) ? defcolour : col;\r
+\r
+ }\r
+\r
+ public void openJalviewHelpUrl()\r
+ {\r
+ String helpUrl = getParameter("jalviewhelpurl");\r
+ if (helpUrl == null || helpUrl.trim().length() < 5)\r
+ {\r
+ helpUrl = "http://www.jalview.org/help.html";\r
+ }\r
+ showURL(helpUrl, "HELP");\r
+ }\r
+\r
+ /**\r
+ * form a complete URL given a path to a resource and a reference location on\r
+ * the same server\r
+ * \r
+ * @param url\r
+ * - an absolute path on the same server as localref or a document\r
+ * located relative to localref\r
+ * @param localref\r
+ * - a URL on the same server as url\r
+ * @return a complete URL for the resource located by url\r
+ */\r
+ private String resolveUrlForLocalOrAbsolute(String url, URL localref)\r
+ {\r
+ String codebase = localref.toString();\r
+ if (url.indexOf("/") == 0)\r
+ {\r
+ url = codebase.substring(0, codebase.length()\r
+ - localref.getFile().length())\r
+ + url;\r
+ }\r
+ else\r
+ {\r
+ url = localref + url;\r
+ }\r
+ return url;\r
+ }\r
+\r
+ /**\r
+ * open a URL in the browser - resolving it according to relative refs and\r
+ * coping with javascript: protocol if necessary.\r
+ * \r
+ * @param url\r
+ * @param target\r
+ */\r
+ public void showURL(String url, String target)\r
+ {\r
+ try\r
+ {\r
+ if (url.indexOf(":") == -1)\r
+ {\r
+ // TODO: verify (Bas Vroling bug) prepend codebase or server URL to\r
+ // form valid URL\r
+ // Should really use docbase, not codebase.\r
+ URL prepend;\r
+ url = resolveUrlForLocalOrAbsolute(\r
+ url,\r
+ prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()\r
+ : getCodeBase());\r
+ if (debug)\r
+ {\r
+ System.err\r
+ .println("Show url (prepended "\r
+ + prepend\r
+ + " - toggle resolvetocodebase if code/docbase resolution is wrong): "\r
+ + url);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (debug)\r
+ {\r
+ System.err.println("Show url: " + url);\r
+ }\r
+ }\r
+ if (url.indexOf("javascript:") == 0)\r
+ {\r
+ // no target for the javascript context\r
+ getAppletContext().showDocument(new java.net.URL(url));\r
+ }\r
+ else\r
+ {\r
+ getAppletContext().showDocument(new java.net.URL(url), target);\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * bind structures in a viewer to any matching sequences in an alignFrame (use\r
+ * sequenceIds to limit scope of search to specific sequences)\r
+ * \r
+ * @param alFrame\r
+ * @param viewer\r
+ * @param sequenceIds\r
+ * @return TODO: consider making an exception structure for indicating when\r
+ * binding fails public SequenceStructureBinding\r
+ * addStructureViewInstance( AlignFrame alFrame, Object viewer, String\r
+ * sequenceIds) {\r
+ * \r
+ * if (sequenceIds != null && sequenceIds.length() > 0) { return\r
+ * alFrame.addStructureViewInstance(viewer,\r
+ * separatorListToArray(sequenceIds)); } else { return\r
+ * alFrame.addStructureViewInstance(viewer, null); } // return null; }\r
+ */\r