public Object[] getAlignment(JalviewDataset context,
Iterable<DataProvider> files) throws Exception
{
- List<Object> rslt = new ArrayList<Object>();
+ List<Object> rslt = new ArrayList<>();
if (context == null)
{
context = new JalviewDataset();
// if not, create one.
if (context.featureColours == null)
{
- context.featureColours = new HashMap<String, FeatureColourI>();
+ context.featureColours = new HashMap<>();
}
try
{
jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
context.updateSetModified(ff.parse(context.getLastAlignment(),
- context.featureColours, false, context.relaxedIdMatching));
+ context.featureColours, false,
+ context.relaxedIdMatching));
} catch (Exception e)
{
errmsg = ("Failed to parse the Features file associated with the alignment.");
* would be created.
*
* @param args
+ * @j2sIgnore
*/
public static void main(String args[])
{
// make data providers from the set of keys/files
int i = 0;
- List<DataProvider> dp = new ArrayList<DataProvider>();
+ List<DataProvider> dp = new ArrayList<>();
while ((i + 1) < args.length)
{
String type = args[i++];
final String file = args[i++];
- final JvDataType jtype = DataProvider.JvDataType.valueOf(type
- .toUpperCase());
+ final JvDataType jtype = DataProvider.JvDataType
+ .valueOf(type.toUpperCase());
if (jtype != null)
{
final FileParse fp;
ParsePackedSet pps;
try
{
- newdm = (pps = new ParsePackedSet()).getAlignment(
- context = new JalviewDataset(), dp);
+ newdm = (pps = new ParsePackedSet())
+ .getAlignment(context = new JalviewDataset(), dp);
} catch (Exception e)
{
System.out.println("Test failed for these arguments.\n");
{
if (context.getLastAlignmentSet().isModified())
{
- System.err
- .println("Initial alignment set was modified and any associated views should be updated.");
+ System.err.println(
+ "Initial alignment set was modified and any associated views should be updated.");
}
}
}