args for excluded tags

Author: cgoina

colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/AbstractGradientScoresArgs.java

@@ -35,11 +35,16 @@ class AbstractGradientScoresArgs extends AbstractColorDepthMatchArgs {
             variableArity = true)
     List<String> maskDatasets = new ArrayList<>();
 
-    @Parameter(names = {"--masks-tags"}, description = "Tags associated with the mask of the match to be scored",
+    @Parameter(names = {"--mask-tags", "--masks-tags"}, description = "Tags associated with the mask of the match to be scored",
             listConverter = ListValueAsFileArgConverter.class,
             variableArity = true)
     List<String> maskTags = new ArrayList<>();
 
+    @Parameter(names = {"--mask-excluded-tags", "--masks-excluded-tags"}, description = "Tags that should not be associated with the mask of the match to be scored",
+            listConverter = ListValueAsFileArgConverter.class,
+            variableArity = true)
+    List<String> maskExcludedTags = new ArrayList<>();
+
     @Parameter(names = {"--masks-terms"}, description = "Terms associated with the mask of the match to be scored",
             listConverter = ListValueAsFileArgConverter.class,
             variableArity = true)
@@ -64,11 +69,16 @@ class AbstractGradientScoresArgs extends AbstractColorDepthMatchArgs {
             variableArity = true)
     List<String> targetDatasets = new ArrayList<>();
 
-    @Parameter(names = {"--targets-tags"}, description = "Tags associated with the target of the match to be scored",
+    @Parameter(names = {"--target-tags", "--targets-tags"}, description = "Tags associated with the target of the match to be scored",
             listConverter = ListValueAsFileArgConverter.class,
             variableArity = true)
     List<String> targetTags = new ArrayList<>();
 
+    @Parameter(names = {"--target-excluded-tags", "--targetss-excluded-tags"}, description = "Tags that should not be associated with the target of the match to be scored",
+            listConverter = ListValueAsFileArgConverter.class,
+            variableArity = true)
+    List<String> targetExcludedTags = new ArrayList<>();
+
     @Parameter(names = {"--targets-published-names"}, description = "Selected target names",
             listConverter = ListValueAsFileArgConverter.class,
             variableArity = true)

colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/CalculateGradientScoresCmd.java

@@ -251,6 +251,7 @@ List<CDMatchEntity<M, T>> startAllGradientScores() {
                                 .addMipIDs(args.masksMIPIDs)
                                 .addDatasets(args.maskDatasets)
                                 .addTags(args.maskTags)
+                                .addExcludedTags(args.maskExcludedTags)
                                 .addAnnotations(args.maskAnnotations)
                                 .addExcludedAnnotations(args.excludedMaskAnnotations)
                                 .addProcessingTags(args.getMasksProcessingTags())
@@ -332,6 +333,7 @@ List<GroupedItems<M, CDMatchEntity<M, T>>> getCDMatchesForMaskMipID(NeuronMatche
                         .addMipIDs(args.targetsMIPIDs)
                         .addDatasets(args.targetDatasets)
                         .addTags(args.targetTags)
+                        .addExcludedTags(args.targetExcludedTags)
                         .addAnnotations(args.targetAnnotations)
                         .addExcludedAnnotations(args.excludedTargetAnnotations)
                         .addProcessingTags(args.getTargetsProcessingTags()),