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Commit 82d3fd82 authored by Davide Lagoa's avatar Davide Lagoa
Browse files

transyt debugger improved

parent 5969a426
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Showing with 136 additions and 593 deletions
src/main/java/pt/uminho/ceb/biosystems/transyt/service/kbase/ModelSEEDCompoundsFileReader.java
View file @ 82d3fd82
......@@ -8,10 +8,6 @@ import java.util.Set;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.ReactionContainer;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.TcNumberContainer;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.Enumerators.TypeOfTransporter;
public class ModelSEEDCompoundsFileReader {
/**
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/reactions/TransportReactionsBuilder.java
View file @ 82d3fd82
......@@ -448,14 +448,14 @@ public class TransportReactionsBuilder {
boolean isChild = false;
String reaction = reactionContainer.getReaction();
String reaction = reactionContainer.getReaction() + " "; //important for correct following replacements
reactionBase = reactionContainer.getReaction();
reactionMetaCyc = reactionContainer.getReaction();
reactionModelSeed = reactionContainer.getReaction();
reactionBiGG = reactionContainer.getReaction();
reactionKEGG = reactionContainer.getReaction();
String formulasReaction = reactionContainer.getReaction();
reactionBase = reaction;
reactionMetaCyc = reaction;
reactionModelSeed = reaction;
reactionBiGG = reaction;
reactionKEGG = reaction;
String formulasReaction = reaction;
boolean go = true;
......@@ -473,12 +473,16 @@ public class TransportReactionsBuilder {
if(reactionContainer.getTransportType().equals(TypeOfTransporter.PEPdependent)) { //PEP dependent
reaction = reaction.replaceAll(replace + "\\s+\\(", childNames.get(id) + " \\(");
reactionBase = reactionBase.replaceAll(replace + "\\s+\\(", metabolites.get(id) + " \\(");
replace = replace + "\\s+\\(";
reaction = reaction.replaceAll(replace, childNames.get(id) + " \\(");
reactionBase = reactionBase.replaceAll(replace, metabolites.get(id) + " \\(");
}
else {
reaction = reaction.replace(replace, childNames.get(id));
reactionBase = reactionBase.replace(replace, metabolites.get(id));
replace = replace + " ";
reaction = reaction.replace(replace, childNames.get(id) + " ");
reactionBase = reactionBase.replace(replace, metabolites.get(id) + " ");
}
String repl = "";
......@@ -489,9 +493,9 @@ public class TransportReactionsBuilder {
repl = mappingModelSeed.get(entryID);
if(reactionContainer.getTransportType().equals(TypeOfTransporter.PEPdependent))
reactionModelSeed = reactionModelSeed.replaceAll(replace + "\\s+\\(", repl + " \\(");
reactionModelSeed = reactionModelSeed.replaceAll(replace, repl + " \\(");
else
reactionModelSeed = reactionModelSeed.replace(replace, repl);
reactionModelSeed = reactionModelSeed.replace(replace, repl + " ");
}
else {
reactionModelSeed = null;
......@@ -500,9 +504,9 @@ public class TransportReactionsBuilder {
if(mappingBiGG.containsKey(entryID) && reactionBiGG != null) {
repl = mappingBiGG.get(entryID);
if(reactionContainer.getTransportType().equals(TypeOfTransporter.PEPdependent))
reactionBiGG = reactionBiGG.replaceAll(replace + "\\s+\\(", repl + " \\(");
reactionBiGG = reactionBiGG.replaceAll(replace, repl + " \\(");
else
reactionBiGG = reactionBiGG.replace(replace, repl);
reactionBiGG = reactionBiGG.replace(replace, repl+ " ");
}
else {
reactionBiGG = null;
......@@ -511,9 +515,9 @@ public class TransportReactionsBuilder {
if(mappingKEGG.containsKey(entryID) && reactionKEGG != null) {
repl = mappingKEGG.get(entryID);
if(reactionContainer.getTransportType().equals(TypeOfTransporter.PEPdependent))
reactionKEGG = reactionKEGG.replaceAll(replace + "\\s+\\(", repl + " \\(");
reactionKEGG = reactionKEGG.replaceAll(replace, repl + " \\(");
else
reactionKEGG = reactionKEGG.replace(replace, repl);
reactionKEGG = reactionKEGG.replace(replace, repl+ " ");
}
else {
reactionKEGG = null;
......@@ -522,9 +526,9 @@ public class TransportReactionsBuilder {
if(mappingMetaCyc.containsKey(entryID) && reactionMetaCyc != null) {
repl = mappingMetaCyc.get(entryID);
if(reactionContainer.getTransportType().equals(TypeOfTransporter.PEPdependent))
reactionMetaCyc = reactionMetaCyc.replaceAll(replace + "\\s+\\(", repl + " \\(");
reactionMetaCyc = reactionMetaCyc.replaceAll(replace, repl + " \\(");
else
reactionMetaCyc = reactionMetaCyc.replace(replace, repl);
reactionMetaCyc = reactionMetaCyc.replace(replace, repl + " ");
}
else {
reactionMetaCyc = null;
......@@ -539,11 +543,11 @@ public class TransportReactionsBuilder {
String previousFormula = formulasReaction;
if(reactionContainer.getTransportType().equals(TypeOfTransporter.PEPdependent))
formulasReaction = formulasReaction.replaceAll(replace + "\\s+\\(",
formulasReaction = formulasReaction.replaceAll(replace,
formulas.get(entryID).concat("@") + " \\(");
else
formulasReaction = formulasReaction.replaceAll(replace,
formulas.get(entryID).concat("@")); //@ is added to control if replacements are really happening bacause some names might be like the formula
formulasReaction = formulasReaction.replace(replace,
formulas.get(entryID).concat("@") + " "); //@ is added to control if replacements are really happening bacause some names might be like the formula
if(formulasReaction.equals(previousFormula))
formulasReaction = null;
......@@ -553,7 +557,7 @@ public class TransportReactionsBuilder {
childNames.get(id).equalsIgnoreCase(ReactionContainer.LIGHT_NAME)) ||
childNames.get(id).equalsIgnoreCase(ReactionContainer.ELECTRON_NAME)) {
formulasReaction = formulasReaction.replace(replace, "");
formulasReaction = formulasReaction.replace(replace, " ");
}
else {
formulasReaction = null;
......@@ -590,8 +594,6 @@ public class TransportReactionsBuilder {
String reactantIDs = reactionIDsSplit[0];
String productIDs = reactionIDsSplit[1];
boolean print = false;
// if(tcNumber.equals("3.A.1.7.1")) {
//
// System.out.println(reaction);
......@@ -615,9 +617,9 @@ public class TransportReactionsBuilder {
// System.out.println(formulasReaction);
// System.out.println(reactant + " <<>> " + product);
// System.out.println(reactantIDs + " <<>> " + productIDs);
// System.out.println(formulasReaction);
System.out.println(reactant + " <<>> " + product);
System.out.println(reactantIDs + " <<>> " + productIDs);
System.out.println(formulasReaction);
if((reactant.contains("ATP") && product.contains("ADP")) || (reactant.contains("GTP") && product.contains("GDP"))) {
......@@ -668,6 +670,8 @@ public class TransportReactionsBuilder {
// System.out.println(reactionContainer.getDirectionRegex());
// System.out.println();
boolean print = false;
boolean balanced = isEquationBalanced(formulasReaction, reactionContainer.getDirectionRegex(), print);
// System.out.println("balanced: " + balanced);
......@@ -677,12 +681,6 @@ public class TransportReactionsBuilder {
// System.out.println(reactionKEGG);
// System.out.println();
// if(idsReaction.contains("META:BUTYRIC_ACID=MetaCyc (out) + META:CO-A=MetaCyc (in) + META:ATP=MetaCyc (in) $IRREV$ META:BU"))
// System.out.println(balanced);
// if(tcNumber.equals("3.A.1.7.1"))
// System.out.println("balanceada " + "\t" + balanced);
boolean sugarPEPcorrect = true;
if(balanced && reactionContainer.getTransportType().equals(TypeOfTransporter.PEPdependent)) {
......@@ -1021,6 +1019,7 @@ public class TransportReactionsBuilder {
if(print) {
System.out.println(reactantsCounts);
System.out.println(productsCounts);
System.out.println();
}
if(reactantsCounts.equals(productsCounts))
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/transyt/TransyTestMain.java
View file @ 82d3fd82
......@@ -63,7 +63,7 @@ public class TransyTestMain {
logger.info("Scraper and database service option selected!");
Retriever.runRetriever(true);
Retriever.runRetriever(true, true, null);
// WriteByMetabolitesID.start(properties);
break;
......@@ -72,7 +72,7 @@ public class TransyTestMain {
logger.info("Database service option selected!");
WriteByMetabolitesID.start(properties);
WriteByMetabolitesID.start(properties, true);
break;
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/transyt/TransytMain.java
View file @ 82d3fd82
......@@ -23,7 +23,7 @@ public class TransytMain {
// Integer taxID = Integer.valueOf(args[0]);
logger.info("############################################ TranSyT - v0.0.12.4-SNAPSHOT ############################################");
logger.info("############################################ TranSyT - v0.0.12.6-SNAPSHOT ############################################");
String command = args[0];
......@@ -40,8 +40,8 @@ public class TransytMain {
logger.info("Scraper and database service option selected!");
Retriever.runRetriever(useCache);
WriteByMetabolitesID.start(new Properties());
Retriever.runRetriever(useCache, false, null);
WriteByMetabolitesID.start(new Properties(), false);
break;
......@@ -49,7 +49,7 @@ public class TransytMain {
logger.info("Database service option selected!");
WriteByMetabolitesID.start(new Properties());
WriteByMetabolitesID.start(new Properties(), false);
break;
......
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