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Adding safeguards when requesting chains from structure #1111

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Merged
josemduarte merged 4 commits into from
Mar 20, 2025
+63 −149
Merged

Adding safeguards when requesting chains from structure #1111

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381fedd
Formatting and docs cleanup
josemduarte Mar 19, 2025
743a9fd
More cleanup
josemduarte Mar 19, 2025
c33627f
More cleanup
josemduarte Mar 19, 2025
7217ee8
Safeguards
josemduarte Mar 19, 2025
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More cleanup
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@josemduarte
josemduarte committed Mar 19, 2025
commit c33627f85311f35b5efc947c94cd7439b0db82c5
18 changes: 5 additions & 13 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -243,8 +243,7 @@ public void setStructureIdentifier(StructureIdentifier structureIdentifier) {
/** {@inheritDoc} */
@Override
public void addChain(Chain chain) {
int modelnr = 0 ;
addChain(chain,modelnr);
addChain(chain, 0);
}

/** {@inheritDoc} */
Expand Down Expand Up @@ -293,8 +292,7 @@ public void addModel(List<Chain> modelChains){
/** {@inheritDoc} */
@Override
public void setChains(List<Chain> chains){

setModel(0,chains);
setModel(0, chains);
}

/** {@inheritDoc} */
Expand Down Expand Up @@ -359,7 +357,7 @@ public String toString(){
.append(" authId:")
.append(cha.getName()).append(" ");

if ( cha.getEntityInfo() != null){
if (cha.getEntityInfo() != null){
EntityInfo comp = cha.getEntityInfo();
String molName = comp.getDescription();
if ( molName != null){
Expand Down Expand Up @@ -394,22 +392,16 @@ public String toString(){

@Override
public int size() {
int modelnr = 0 ;

if (!models.isEmpty()) {
return models.get(modelnr).getPolyChains().size();
}
else {
return models.get(0).getPolyChains().size();
} else {
return 0 ;
}

}

@Override
public int size(int modelIdx) { return models.get(modelIdx).size(); }

// some NMR stuff :

@Override
public int nrModels() {
return models.size() ;
Expand Down