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Ordered promoters

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Added code to check order of tandem promoters, so that the roadblocking effect is in the correct promoter
This commit is contained in:
Pedro Fontanarrosa 2020-01-18 19:13:00 -03:00
parent e0b7c2a22f
commit 7c2074fbfb
2 changed files with 28 additions and 5 deletions
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12
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
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@ -2307,12 +2307,16 @@ public class BioModel extends CoreObservable{
* @return the string
*/
//TODO PEDRO createCelloProductionKineticLaw
public static String createCelloProductionKineticLaw(Reaction reaction, HashMap<String, List<String>> celloParameters, HashMap<String, HashMap <String, String>> promoterInteractions, List <String> promoters) {
public static String createCelloProductionKineticLaw(Reaction reaction, HashMap<String, List<String>> celloParameters, HashMap<String, HashMap <String, String>> promoterInteractions, List <String> promoters, List<String> ordered_promoters) {
String kineticLaw = "";
//boolean activated = false;
String promoter = "";
int promoterCnt = 0;
if(ordered_promoters.size() == 2) {
promoters = ordered_promoters;
}
for (Object it : promoters.toArray()) {
promoter = it.toString();
promoterCnt++;
@ -2406,7 +2410,7 @@ public class BioModel extends CoreObservable{
in_parentesis = "(" + numerator + "/(" + denominator + ") +" + ymin + ")";
// This adds roadblocking effects if this promoter is the downstream one of tandem promoters.
if(promoters.toArray().length == 2 && promoterCnt == 2) {
if(ordered_promoters.get(1).equals(promoter)) {
String top = "";
String bottom = "";
@ -2496,7 +2500,7 @@ public class BioModel extends CoreObservable{
in_parentesis = "(" + numerator + "/(" + denominator + ") +" + ymin + ")";
// This adds roadblocking effects if this promoter is the downstream one of tandem promoters.
if(promoters.toArray().length == 2 && promoterCnt == 2) {
if(ordered_promoters.get(1).equals(promoter)) {
String top = "";
String bottom = "";
@ -2559,7 +2563,7 @@ public class BioModel extends CoreObservable{
in_parentesis = "(" + numerator + ")";
// This adds roadblocking effects if this promoter is the downstream one of tandem promoters.
if(promoters.toArray().length == 2 && promoterCnt == 2) {
if(ordered_promoters.get(1).equals(promoter)) {
String roadblock = "";
String delta_function = "";