/**\r
* Load the (T-Coffee) score file from the specified url \r
* \r
- * @param url The absolute path from where download and read the score file\r
+ * @param source File/URL/T-COFFEE score file contents\r
* @throws IOException \r
+ * @return true if alignment was annotated with data from source\r
*/\r
- public void loadScoreFile( URL url ) throws IOException {\r
- // TODO: refactor to string/standard jalview data importer\r
- TCoffeeScoreFile file = TCoffeeScoreFile.load( new InputStreamReader( url.openStream() ) );\r
- if( file == null ) {\r
- // TODO: raise a dialog box here rather than bomb out.\r
- \r
- throw new RuntimeException("The file provided does not match the T-Coffee scores file format");\r
+ public boolean loadScoreFile( String source ) throws IOException {\r
+\r
+ TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));\r
+ if( !file.isValid()) {\r
+ // TODO: raise dialog for gui\r
+ System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());\r
+ System.err.println("Origin was:\n"+source);\r
+ return false;\r
}\r
\r
/*\r
AlignmentI aln; \r
if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {\r
// TODO: raise a dialog box here rather than bomb out.\r
- throw new RuntimeException("The scores matrix does not match the alignment dimensions");\r
+ System.err.println("The scores matrix does not match the alignment dimensions");\r
\r
}\r
\r
// TODO add parameter to indicate if matching should be done\r
if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
{\r
- tcoffeeColour.setEnabled(true);\r
+ alignPanel.fontChanged();\r
+ tcoffeeColour.setEnabled(true);\r
// switch to this color\r
changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+ return true;\r
+ } else {\r
+ System.err.println("Problems resolving T-Coffee scores:");\r
+ if (file.getWarningMessage()!=null) {\r
+ System.err.println(file.getWarningMessage());\r
+ }\r
}\r
+ return false;\r
}\r
\r
\r