import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
+ AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
assertNotNull("Couldn't read supplied alignment data.", al);
System.out.println("Output file in '" + ioformat + "':\n"
+ outputfile + "\n<<EOF\n");
// test for consistency in io
- Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+ AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
AppletFormatAdapter.PASTE, ioformat);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
an_new.displayCharacter.trim())
|| !("" + an_or.secondaryStructure).trim().equals(
("" + an_new.secondaryStructure).trim())
- || (an_or.description != an_new.description && (an_or.description == null
- || an_new.description == null || !an_or.description
- .equals(an_new.description))))
+ || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
+ .trim().length() == 0)
+ || (an_new.description == null && an_or.description
+ .trim().length() == 0) || an_or.description
+ .trim().equals(an_new.description.trim()))))
{
System.err.println("Annotation Element Mismatch\nElement " + i
+ " in original: " + annot_or.annotations[i].toString()