import jalview.analysis.scoremodels.PIDModel;
import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
-import jalview.util.Platform;
import jalview.util.QuickSort;
import java.util.ArrayList;
* from the first tobesorted position in the alignment. e.g. (a,tb2,b,tb1,c,tb3
* becomes a,tb1,tb2,tb3,b,c)
*/
-public class AlignmentSorter
+public class AlignmentSorter implements ApplicationSingletonI
{
- static AlignmentSorter instance;
+ private AlignmentSorter()
+ {
+ // private singleton
+ }
- public static AlignmentSorter getInstance()
+ private static AlignmentSorter getInstance()
{
+ return (AlignmentSorter) ApplicationSingletonProvider
+ .getInstance(AlignmentSorter.class);
+ }
- // BH 2019.05.08 need to isolate static fields in JavaScript
+ /**
+ * types of feature ordering: Sort by score : average score - or total score -
+ * over all features in region Sort by feature label text: (or if null -
+ * feature type text) - numerical or alphabetical Sort by feature density:
+ * based on counts - ignoring individual text or scores for each feature
+ */
+ public static final String FEATURE_SCORE = "average_score";
- AlignmentSorter i = instance;
- @SuppressWarnings("unused")
- ThreadGroup g = null;
- if (Platform.isJS())
- {
- g = Thread.currentThread().getThreadGroup();
- /**
- * @j2sNative i = g._jalviewScoreModelsInstance;
- *
- */
- }
- if (i == null)
- {
- i = new AlignmentSorter();
+ public static final String FEATURE_LABEL = "text";
- if (Platform.isJS())
- {
- /**
- * @j2sNative g._jalviewScoreModelsInstance = i;
- *
- */
- }
- else
- {
- instance = i;
- }
- }
- return i;
- }
+ public static final String FEATURE_DENSITY = "density";
/*
* todo: refactor searches to follow a basic pattern: (search property, last
}
/**
- * types of feature ordering: Sort by score : average score - or total score -
- * over all features in region Sort by feature label text: (or if null -
- * feature type text) - numerical or alphabetical Sort by feature density:
- * based on counts - ignoring individual text or scores for each feature
- */
- public static String FEATURE_SCORE = "average_score";
-
- public static String FEATURE_LABEL = "text";
-
- public static String FEATURE_DENSITY = "density";
-
- /**
* Sort sequences by feature score or density, optionally restricted by
* feature types, feature groups, or alignment start/end positions.
* <p>