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@@ -36,7 +36,7 @@
/**
*
* @author Scooter Willis
* @author Scooter Willis
*/
public class GeneFeatureHelper {
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@@ -418,7 +418,7 @@ static public void addGmodGFF3GeneFeatures(Map<String, ChromosomeSequence> chrom
String startCodonName = "";
String stopCodonName = "";
FeatureList startCodonList = mRNAChildren.selectByType("five_prime_UTR");
if (startCodonList != null && startCodonList.size() > 0) {
if (startCodonList != null && !startCodonList.isEmpty()) {
startCodon = startCodonList.get(0);
if (strand == Strand.NEGATIVE) {
startCodonBegin = startCodon.location().bioEnd();
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@@ -430,7 +430,7 @@ static public void addGmodGFF3GeneFeatures(Map<String, ChromosomeSequence> chrom
FeatureList stopCodonList = mRNAChildren.selectByType("three_prime_UTR");
if (stopCodonList != null && stopCodonList.size() > 0) {
if (stopCodonList != null && !stopCodonList.isEmpty()) {
stopCodon = stopCodonList.get(0);
if (strand == Strand.NEGATIVE) {
stopCodonEnd = stopCodon.location().bioStart();
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@@ -577,7 +577,7 @@ static public void addGlimmerGFF3GeneFeatures(Map<String, ChromosomeSequence> ch
String startCodonName = "";
String stopCodonName = "";
FeatureList startCodonList = gene.selectByAttribute("Note", "initial-exon");
if (startCodonList != null && startCodonList.size() > 0) {
if (startCodonList != null && !startCodonList.isEmpty()) {
startCodon = startCodonList.get(0);
if (strand == Strand.NEGATIVE) {
startCodonBegin = startCodon.location().bioEnd();
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@@ -589,7 +589,7 @@ static public void addGlimmerGFF3GeneFeatures(Map<String, ChromosomeSequence> ch
FeatureList stopCodonList = gene.selectByAttribute("Note", "final-exon");
if (stopCodonList != null && stopCodonList.size() > 0) {
if (stopCodonList != null && !stopCodonList.isEmpty()) {
stopCodon = stopCodonList.get(0);
if (strand == Strand.NEGATIVE) {
stopCodonEnd = stopCodon.location().bioStart();
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@@ -723,7 +723,7 @@ static public void addGeneMarkGTFGeneFeatures(Map<String, ChromosomeSequence> ch
String startCodonName = "";
String stopCodonName = "";
FeatureList startCodonList = transcriptFeature.selectByType("start_codon");
if (startCodonList != null && startCodonList.size() > 0) {
if (startCodonList != null && !startCodonList.isEmpty()) {
startCodon = startCodonList.get(0);
if (strand == Strand.POSITIVE) {
startCodonBegin = startCodon.location().bioStart();
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@@ -735,7 +735,7 @@ static public void addGeneMarkGTFGeneFeatures(Map<String, ChromosomeSequence> ch
FeatureList stopCodonList = transcriptFeature.selectByType("stop_codon");
if (stopCodonList != null && stopCodonList.size() > 0) {
if (stopCodonList != null && !stopCodonList.isEmpty()) {
stopCodon = stopCodonList.get(0);
if (strand == Strand.POSITIVE) {
stopCodonEnd = stopCodon.location().bioEnd();
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