import jalview.api.AlignmentViewPanel;
import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.ViewBasedAnalysisI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.ScoreMatrixFile;
/*
* delegate parsing to ScoreMatrixFile
*/
- FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
+ FileParse fp = new FileParse(resourcePath,
+ DataSourceType.CLASSLOADER);
ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
registerScoreModel(sm);
return sm;
} catch (IOException e)
{
- System.err.println("Error reading " + resourcePath + ": "
- + e.getMessage());
+ System.err.println(
+ "Error reading " + resourcePath + ": " + e.getMessage());
}
return null;
}
public ScoreModelI getScoreModel(String name, AlignmentViewPanel avp)
{
ScoreModelI model = models.get(name);
- if (model instanceof ViewBasedAnalysisI)
- {
- try
- {
- model = model.getClass().newInstance();
- ((ViewBasedAnalysisI) model).configureFromAlignmentView(avp);
- } catch (IllegalAccessException | InstantiationException e)
- {
- System.err.println("Error creating score model " + name + ": "
- + e.getMessage());
- return null;
- }
- }
- return model;
+ return model == null ? null : model.getInstance(avp);
}
public void registerScoreModel(ScoreModelI sm)