/*\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
* \r
boolean seqlimits = suffix.equalsIgnoreCase("true");\r
if (alf.viewport.getSelectionGroup() != null)\r
{\r
+ // JBPNote: getSelectionAsNewSequence behaviour has changed - this\r
+ // method now returns a full copy of sequence data\r
+ // TODO consider using getSequenceSelection instead here\r
String reply = new AppletFormatAdapter().formatSequences(format,\r
new Alignment(alf.viewport.getSelectionAsNewSequence()),\r
seqlimits);\r
/*\r
* (non-Javadoc)\r
* \r
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)\r
+ */\r
+ public void loadFeatures(String features, boolean autoenabledisplay)\r
+ {\r
+ loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public boolean loadFeaturesFrom(AlignFrame alf, String features,\r
+ boolean autoenabledisplay)\r
+ {\r
+ return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,\r
+ autoenabledisplay);\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
}\r
\r
- String param = applet.getParameter("features");\r
+ /*\r
+ * Try to load T-Coffee score file\r
+ */\r
+ String sScoreFile = applet.getParameter("scoreFile");\r
+ if (sScoreFile != null && !"".equals(sScoreFile))\r
+ {\r
+ try\r
+ {\r
+ if (debug)\r
+ {\r
+ System.err\r
+ .println("Attempting to load T-COFFEE score file from the scoreFile parameter");\r
+ }\r
+ if (!newAlignFrame.loadScoreFile(sScoreFile))\r
+ {\r
+ System.err\r
+ .println("Failed to parse T-COFFEE parameter as a valid score file ('"\r
+ + sScoreFile + "')");\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err.printf("Cannot read score file: '%s'. Cause: %s \n",\r
+ sScoreFile, e.getMessage());\r
+ }\r
+ }\r
+\r
+ // ///////////////////////////\r
+ // modify display of features\r
+ // we do this before any features have been loaded, ensuring any hidden\r
+ // groups are hidden when features first displayed\r
+ //\r
+ // hide specific groups\r
+ //\r
+ String param = applet.getParameter("hidefeaturegroups");\r
+ if (param != null)\r
+ {\r
+ newAlignFrame.setFeatureGroupState(separatorListToArray(param),\r
+ false);\r
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, false);\r
+ }\r
+ // show specific groups\r
+ param = applet.getParameter("showfeaturegroups");\r
+ if (param != null)\r
+ {\r
+ newAlignFrame.setFeatureGroupState(separatorListToArray(param),\r
+ true);\r
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, true);\r
+ }\r
+ // and now load features\r
+ param = applet.getParameter("features");\r
if (param != null)\r
{\r
param = setProtocolState(param);\r
protocols);\r
\r
}\r
- // ///////////////////////////\r
- // modify display of features\r
- //\r
- // hide specific groups\r
- param = applet.getParameter("hidefeaturegroups");\r
- if (param != null)\r
- {\r
- applet.setFeatureGroupStateOn(newAlignFrame, param, false);\r
- }\r
- // show specific groups\r
- param = applet.getParameter("showfeaturegroups");\r
- if (param != null)\r
- {\r
- applet.setFeatureGroupStateOn(newAlignFrame, param, true);\r
- }\r
}\r
else\r
{\r