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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
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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30 changes: 15 additions & 15 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
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Original file line number Diff line number Diff line change
Expand Up @@ -178,10 +178,10 @@ public interface Structure extends Cloneable, Serializable {
/**
* Return number of chains of model.
*
* @param modelnr an int specifying the number of the Model that should be used
* @param modelIdx an int specifying the index of the Model that should be used
* @return an int representing the number of Chains in this Model
*/
int size(int modelnr);
int size(int modelIdx);

/**
* Return the number of models .
Expand Down Expand Up @@ -232,10 +232,10 @@ public interface Structure extends Cloneable, Serializable {
* Retrieve all Chains belonging to a model .
* @see #getChains(int modelnr)
*
* @param modelnr an int
* @param modelIdx the model index
* @return a List object containing the Chains of Model nr. modelnr
*/
List<Chain> getModel(int modelnr);
List<Chain> getModel(int modelIdx);

/**
* Retrieve all chains for the first model.
Expand All @@ -261,17 +261,17 @@ public interface Structure extends Cloneable, Serializable {
* Retrieve all chains of a model.
* @see #getModel
*
* @param modelnr an int
* @param modelIdx the model index
* @return a List object containing the Chains of Model nr. modelnr
*/
List<Chain> getChains(int modelnr);
List<Chain> getChains(int modelIdx);

/**
* Set the chains for a model
* @param chains the chains for a model
* @param modelnr the number of the model
* @param modelIdx the model index
*/
void setChains( int modelnr, List<Chain> chains);
void setChains(int modelIdx, List<Chain> chains);

/**
* Return all polymeric chains for the first model
Expand Down Expand Up @@ -315,7 +315,7 @@ public interface Structure extends Cloneable, Serializable {

/**
* Return all water chains for the given model index
* @param modelIdx
* @param modelIdx the model index
* @return
* @since 5.0
*/
Expand All @@ -332,9 +332,9 @@ public interface Structure extends Cloneable, Serializable {
* Add a new chain to the model specified by the given index
*
* @param chain a Chain object
* @param modelnr an int specifying to which model the Chain should be added
* @param modelIdx an int specifying to which model the Chain should be added
*/
void addChain(Chain chain, int modelnr);
void addChain(Chain chain, int modelIdx);

/**
* Retrieve a chain by its index within the Structure .
Expand All @@ -348,10 +348,10 @@ public interface Structure extends Cloneable, Serializable {
* Retrieve a chain by its indices within the Structure and model.
*
* @param chainIndex the index of the desired chain in the structure
* @param modelnr the model the desired chain is in
* @param modelIdx the model index
* @return a Chain object
*/
Chain getChainByIndex(int modelnr, int chainIndex);
Chain getChainByIndex(int modelIdx, int chainIndex);

/**
* Check if a chain with the chainId aymId is contained in this structure.
Expand Down Expand Up @@ -394,11 +394,11 @@ public interface Structure extends Cloneable, Serializable {
* considers only model nr X. count starts with 0.
* @param authId the chain name of the chain to use
* @param pdbResnum the PDB residue number of the requested group
* @param modelnr the number of the model to use
* @param modelIdx the model index
* @return Group the requested Group
* @throws StructureException
*/
Group findGroup(String authId, String pdbResnum, int modelnr) throws StructureException;
Group findGroup(String authId, String pdbResnum, int modelIdx) throws StructureException;

/**
* Retrieve a Chain (polymeric, non-polymeric or water) based on
Expand Down
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