$scope.fmTumourSelection = function()

in clns-eTarget/src/main/webapp/js/app.js [1625:1696]
70 lines of code
22 McCabe index (conditional complexity)

	  $scope.fmTumourSelection = function(geneObject, specimenDate, checked, timepoint) {
		    if(checked) {
		      // Add to the table
		      if(geneObject.variation_type=='short_variant'){
		    	  $scope.currentPatient.significantMutations.fmTumour.shortVariant.push(geneObject);
		    	  $scope.currentPatient.significantMutations.latestFmTumour.shortVariant.push(geneObject);
		    	  $scope.addMutationSelection(geneObject.gene_variant_id,'FMTumourSV');
		    	  $scope.currentPatient.significantMutations.summery.push({gene: geneObject.geneName, description: geneObject.result, source: 'FM Tumour', type: 'Short Variant', geneVarientID: geneObject.gene_variant_id, timepoint: timepoint});
		    	  $scope.updateMeetingOutcomeSummary(geneObject.geneName, geneObject.result, specimenDate, true, 'FMTumourSV');
		      }	else if(geneObject.variation_type=='rearrangement'){
		    	  $scope.currentPatient.significantMutations.fmTumour.rearrangement.push(geneObject);
		    	  $scope.currentPatient.significantMutations.latestFmTumour.rearrangement.push(geneObject);
		    	  $scope.addMutationSelection(geneObject.gene_variant_id, 'FMTumourR');
		    	  $scope.currentPatient.significantMutations.summery.push({gene: geneObject.gene1+' - '+geneObject.gene2, description: geneObject.description, source: 'FM Tumour', type: 'Rearrangement', geneVarientID: geneObject.gene_variant_id, timepoint: timepoint});
		    	  $scope.updateMeetingOutcomeSummary(geneObject.gene1, geneObject.gene2, specimenDate, true, 'FMTumourR');
		      } else if(geneObject.variation_type=='copy_number_alteration'){
		    	  $scope.currentPatient.significantMutations.fmTumour.copyNumberAlteration.push(geneObject);
		    	  $scope.currentPatient.significantMutations.latestFmTumour.copyNumberAlteration.push(geneObject);
		    	  $scope.addMutationSelection(geneObject.gene_variant_id, 'FMTumourCNA');
		    	  $scope.currentPatient.significantMutations.summery.push({gene: geneObject.geneName, description: geneObject.type, source: 'FM Tumour', type: 'Copy Number Alteration', geneVarientID: geneObject.gene_variant_id, timepoint: timepoint});
		    	  $scope.updateMeetingOutcomeSummary(geneObject.geneName, geneObject.type, specimenDate, true, 'FMTumourCNA');
		      }
		    } else {
		      // Remove from the table
		      if(geneObject.variation_type=='short_variant'){
		    	  for(var i=0; i<$scope.currentPatient.significantMutations.latestFmTumour.shortVariant.length; i++) {
			        if($scope.currentPatient.significantMutations.latestFmTumour.shortVariant[i].gene_variant_id == geneObject.gene_variant_id) {
			          $scope.currentPatient.significantMutations.latestFmTumour.shortVariant.splice(i, 1);
			        }
				  }
		    	  for(var i=0; i<$scope.currentPatient.significantMutations.fmTumour.shortVariant.length; i++) {
			        if($scope.currentPatient.significantMutations.fmTumour.shortVariant[i].gene_variant_id == geneObject.gene_variant_id) {
			          $scope.currentPatient.significantMutations.fmTumour.shortVariant.splice(i, 1);
			        }
				  }
		    	  $scope.deleteMutationSelection(geneObject.gene_variant_id,'FMTumourSV');
		    	  $scope.updateMeetingOutcomeSummary(geneObject.geneName, geneObject.result, specimenDate, false, 'FMTumourSV');
		      }	else if(geneObject.variation_type=='rearrangement'){
		    	  for(var i=0; i<$scope.currentPatient.significantMutations.fmTumour.rearrangement.length; i++) {
			        if($scope.currentPatient.significantMutations.fmTumour.rearrangement[i].gene_variant_id == geneObject.gene_variant_id) {
			          $scope.currentPatient.significantMutations.fmTumour.rearrangement.splice(i, 1);
			        }
			      }
		    	  for(var i=0; i<$scope.currentPatient.significantMutations.latestFmTumour.rearrangement.length; i++) {
			        if($scope.currentPatient.significantMutations.latestFmTumour.rearrangement[i].gene_variant_id == geneObject.gene_variant_id) {
			          $scope.currentPatient.significantMutations.latestFmTumour.rearrangement.splice(i, 1);
			        }
			      }
		    	  $scope.deleteMutationSelection(geneObject.gene_variant_id,'FMTumourR');
		    	  $scope.updateMeetingOutcomeSummary(geneObject.gene1, geneObject.gene2, specimenDate, false, 'FMTumourR');  
		      }
		      else if(geneObject.variation_type=='copy_number_alteration'){
		    	  for(var i=0; i<$scope.currentPatient.significantMutations.fmTumour.copyNumberAlteration.length; i++) {
			        if($scope.currentPatient.significantMutations.fmTumour.copyNumberAlteration[i].gene_variant_id == geneObject.gene_variant_id) {
			          $scope.currentPatient.significantMutations.fmTumour.copyNumberAlteration.splice(i, 1);
			        }
			      }
		    	  for(var i=0; i<$scope.currentPatient.significantMutations.latestFmTumour.copyNumberAlteration.length; i++) {
			        if($scope.currentPatient.significantMutations.latestFmTumour.copyNumberAlteration[i].gene_variant_id == geneObject.gene_variant_id) {
			          $scope.currentPatient.significantMutations.latestFmTumour.copyNumberAlteration.splice(i, 1);
			        }
			      }
		    	  $scope.deleteMutationSelection(geneObject.gene_variant_id,'FMTumourCNA');
		    	  $scope.updateMeetingOutcomeSummary(geneObject.geneName, geneObject.type, specimenDate, false, 'FMTumourCNA'); 
		      }
		      for(var i=0; i<Object.keys($scope.currentPatient.significantMutations.summery).length; i++) {
		    	  if($scope.currentPatient.significantMutations.summery[i].geneVarientID == geneObject.gene_variant_id) {
		    		  $scope.currentPatient.significantMutations.summery.splice(i,1);
		    	  }
		      }
		    }
		  };