/*\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 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, boolean autoenabledisplay)\r
+ {\r
+ return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);\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
if (protocol == jalview.io.AppletFormatAdapter.PASTE)\r
{\r
- newAlignFrame.setTitle("Sequences from "\r
- + applet.getDocumentBase());\r
+ newAlignFrame.setTitle("Sequences from " + applet.getDocumentBase());\r
}\r
\r
newAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
}\r
}\r
\r
+\r
+ /*\r
+ * Try to load T-Coffee score file\r
+ */\r
+ String sScoreFile = applet.getParameter("scoreFile");\r
+ if( sScoreFile != null && !"".equals(sScoreFile) ) {\r
+ try {\r
+ if (debug) {\r
+ System.err.println("Attempting to load T-COFFEE score file from the scoreFile parameter");\r
+ }\r
+ if (!newAlignFrame.loadScoreFile(sScoreFile)) {\r
+ System.err.println("Failed to parse T-COFFEE parameter as a valid score file ('"+sScoreFile+"')");\r
+ }\r
+ }catch( Exception e ) {\r
+ System.err.printf("Cannot read score file: '%s'. Cause: %s \n", sScoreFile, e.getMessage());\r
+ }\r
+ }\r
+ \r
+\r
// ///////////////////////////\r
// modify display of features\r
// we do this before any features have been loaded, ensuring any hidden groups are hidden when features first displayed\r