Add additional nblock regions based on configured regions to call.
    Identifies user defined regions which we should not be analyzing.
183580
def _add_config_regions(nblock_regions, ref_regions, data):
    
    input_regions_bed = dd.get_variant_regions(data)
    if input_regions_bed:
        input_regions = pybedtools.BedTool(input_regions_bed)
        # work around problem with single region not subtracted correctly.
        if len(input_regions) == 1:
            str_regions = str(input_regions[0]).strip()
            input_regions = pybedtools.BedTool("%s\n%s" % (str_regions, str_regions),
                                               from_string=True)
        input_nblock = ref_regions.subtract(input_regions, nonamecheck=True)
        if input_nblock == ref_regions:
            raise ValueError("Input variant_region file (%s) "
                             "excludes all genomic regions. Do the chromosome names "
                             "in the BED file match your genome (chr1 vs 1)?" % input_regions_bed)
        all_intervals = _combine_regions([input_nblock, nblock_regions], ref_regions)
    else:
        all_intervals = nblock_regions
    if "noalt_calling" in dd.get_tools_on(data) or "altcontigs" in dd.get_exclude_regions(data):
        from bcbio.heterogeneity import chromhacks
        remove_intervals = ref_regions.filter(lambda r: not chromhacks.is_nonalt(r.chrom))
        all_intervals = _combine_regions([all_intervals, remove_intervals], ref_regions)
    return all_intervals.merge()
500274
public void setCallingRegions(java.util.Collection<String> callingRegions) {
        if (callingRegions == null) {
            this.callingRegions = null;
            return;
        }

        this.callingRegions = new java.util.ArrayList<String>(callingRegions);
    }
686352
def ignored_regions(source):
    
    return [(match.start(), match.end()) for match in _str.finditer(source)]
950855
private void updateRegion() {
		actMessagePanel.setVisible(false);

		if (rbtACT.isSelected()) {
			actMessagePanel.setVisible(true);
			regionFields.setVisible(true);
			regionSelector.setOptions(new String[]{null, "Belconnen", "City", "Woden"});
			regionSelector.setVisible(true);
		} else if (rbtNSW.isSelected()) {
			regionFields.setVisible(true);
			regionSelector.setOptions(
					new String[]{null, "Hunter", "Riverina", "Southern Tablelands"});
			regionSelector.setVisible(true);
		} else if (rbtVIC.isSelected()) {
			regionFields.setVisible(true);
			regionSelector.setOptions(
					new String[]{null, "Gippsland", "Melbourne", "Mornington Peninsula"});
			regionSelector.setVisible(true);
		} else {
			regionSelector.setOptions(new Object[]{null});
			regionSelector.setVisible(false);
			regionFields.setVisible(false);
		}
	}
92200
def _get_regions(self):
        """"""
        if self._specs_in[_REGIONS_STR] == 'all':
            return [_get_all_objs_of_type(
                Region, getattr(self._obj_lib, 'regions', self._obj_lib)
            )]
        else:
            return [set(self._specs_in[_REGIONS_STR])]
831796
private int combineSubsetBlocks(Mode[] mode_type, int[] mode_length, int index_point) {
        /* bring together same type blocks */
        if (index_point > 1) {
            for (int i = 1; i < index_point; i++) {
                if (mode_type[i - 1] == mode_type[i]) {
                    /* bring together */
                    mode_length[i - 1] = mode_length[i - 1] + mode_length[i];
                    /* decrease the list */
                    for (int j = i + 1; j < index_point; j++) {
                        mode_length[j - 1] = mode_length[j];
                        mode_type[j - 1] = mode_type[j];
                    }
                    index_point--;
                    i--;
                }
            }
        }
        return index_point;
    }
1047918
public void setRegions(java.util.Collection<Region> regions) {
        if (regions == null) {
            this.regions = null;
            return;
        }

        this.regions = new com.amazonaws.internal.SdkInternalList<Region>(regions);
    }
40875
protected void addRangeBounds(BandData band, CellReference[] crefs) {
        if (templateBounds.containsKey(band.getName()))
            return;
        Bounds bounds = new Bounds(crefs[0].getRow(), crefs[0].getCol(), crefs[crefs.length - 1].getRow(), crefs[crefs.length - 1].getCol());
        templateBounds.put(band.getName(), bounds);
    }
540435
def do_region(self, x, y, w, h):
        """"""
        if (x is None):
            self.logger.debug("region: full (nop)")
        else:
            self.logger.debug("region: (%d,%d,%d,%d)" % (x, y, w, h))
            self.image = self.image.crop((x, y, x + w, y + h))
            self.width = w
            self.height = h
676144
def add_pseudo_parameter_values(self):
        
        if 'AWS::Region' not in self.parameter_values:
            self.parameter_values['AWS::Region'] = boto3.session.Session().region_name
1069589
function Region(config) {
  this.config = config;
  this.appLimit = new RateLimit(this.config.rateLimitTypeApplication, 1, this.config);
  this.methodLimits = {};
  this.liveRequests = 0;
}
271644
def child_regions(self):
        """"""
        start, end = self.get_range()
        block = self._trigger.next()
        ref_lvl = self.scope_level
        while block.blockNumber() <= end and block.isValid():
            lvl = TextBlockHelper.get_fold_lvl(block)
            trigger = TextBlockHelper.is_fold_trigger(block)
            if lvl == ref_lvl and trigger:
                yield FoldScope(block)
            block = block.next()
969604
public boolean regionMatches(char []cb, int offset, int length)
  {
    int pos = getIndex();

    char ch = current();
    for (int i = 0; i < length; i++) {
      if (cb[i + offset] != ch) {
        setIndex(pos);
        return false;
      }
      ch = next();
    }

    return true;
  }
948301
def merge_regions(self, id1, id2):
        
        region2 = self.region_by_identifier(id2)
        self[region2] = id1
148942
protected void selectBoundaryCorners() {
		List<Point2D_F64> layout = detector.getLayout();

		Polygon2D_F64 hull = new Polygon2D_F64();
		UtilPolygons2D_F64.convexHull(layout,hull);
		UtilPolygons2D_F64.removeAlmostParallel(hull,0.02);

		boundaryIndexes = new int[hull.size()];
		for (int i = 0; i < hull.size(); i++) {
			Point2D_F64 h = hull.get(i);
			boolean matched = false;
			for (int j = 0; j < layout.size(); j++) {
				if( h.isIdentical(layout.get(j),1e-6)) {
					matched = true;
					boundaryIndexes[i] = j;
					break;
				}
			}
			if( !matched )
				throw new RuntimeException("Bug!");
		}

	}
19881
def add_regional_client(self, region_name):
        
        if region_name not in self._regional_clients:
            session = boto3.session.Session(region_name=region_name, botocore_session=self.config.botocore_session)
            client = session.client("kms", config=self._user_agent_adding_config)
            self._register_client(client, region_name)
            self._regional_clients[region_name] = client
526008
def _update_terminal_region(self, tree, terminal_regions, leaf, X, y,
                                residual, pred, sample_weight):
        """"""