*/
package jalview.io.packed;
+import java.util.Locale;
+
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
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
{
* 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());
+ .valueOf(type.toUpperCase(Locale.ROOT));
if (jtype != null)
{
final FileParse fp;
fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
} catch (Exception e)
{
- System.err.println("Couldn't handle datasource of type " + jtype
- + " using URI " + file);
+ jalview.bin.Console
+ .errPrintln("Couldn't handle datasource of type " + jtype
+ + " using URI " + file);
e.printStackTrace();
return;
}
}
else
{
- System.out.println("Couldn't parse source type token '"
- + type.toUpperCase() + "'");
+ jalview.bin.Console.outPrintln("Couldn't parse source type token '"
+ + type.toUpperCase(Locale.ROOT) + "'");
}
}
if (i < args.length)
System.out.print("\n");
}
- System.out.println("Now trying to parse set:");
+ jalview.bin.Console.outPrintln("Now trying to parse set:");
JalviewDataset context;
Object[] newdm;
ParsePackedSet pps;
.getAlignment(context = new JalviewDataset(), dp);
} catch (Exception e)
{
- System.out.println("Test failed for these arguments.\n");
+ jalview.bin.Console.outPrintln("Test failed for these arguments.\n");
e.printStackTrace(System.out);
return;
}
{
for (Object o : newdm)
{
- System.out.println("Will need to create an " + o.getClass());
+ jalview.bin.Console
+ .outPrintln("Will need to create an " + o.getClass());
}
// now test uniquify/deuniquify stuff
{
if (context.getLastAlignmentSet().isModified())
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Initial alignment set was modified and any associated views should be updated.");
}
}