Skip to content

Handling some nulls in PdbId creation #1020

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
josemduarte merged 3 commits into from
Feb 1, 2022
Merged

Handling some nulls in PdbId creation #1020

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
c84cf73
Handling some nulls in PdbId creation, #1019
josemduarte Jan 31, 2022
93d299c
More readable
josemduarte Feb 1, 2022
0fe0e26
Make sure there's no ambiguity in constructor to call
josemduarte Feb 1, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -117,8 +117,8 @@ public SubstructureIdentifier(String id) {
* Create a new identifier based on a set of ranges.
*
* If ranges is empty, includes all residues.
* @param pdbId
* @param ranges
* @param pdbId a pdb id, can't be null
* @param ranges the ranges
*/
public SubstructureIdentifier(String pdbId, List<ResidueRange> ranges) {
this(new PdbId(pdbId), ranges);
Expand Down
2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@ public SubstructureIdentifier toCanonical() throws StructureException{
String path = url.getPath();
pdbId = guessPDBID(path.substring(path.lastIndexOf("/") + 1));
}
return new SubstructureIdentifier(new PdbId(pdbId), ranges);
return new SubstructureIdentifier((pdbId==null?(PdbId)null:new PdbId(pdbId)), ranges);
}

@Override
Expand Down
4 changes: 3 additions & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,9 @@ public void finalizeStructure() {
@Override
public void initStructure(int totalNumBonds, int totalNumAtoms, int totalNumGroups,
int totalNumChains, int totalNumModels, String modelId) {
structure.setPdbId(new PdbId(modelId));
if (modelId != null) {
structure.setPdbId(new PdbId(modelId));
}
allAtoms = new Atom[totalNumAtoms];
}

Expand Down
6 changes: 4 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopDomain.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -138,8 +138,10 @@ public PdbId getPdbId() {
*/
@Deprecated
public void setPdbId(String pdbId) {
if(pdbId == null) this.pdbId = null;
this.pdbId = new PdbId(pdbId);
if (pdbId == null)
this.pdbId = null;
Copy link
Member

@aalhossary aalhossary Jan 31, 2022

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Good catch! Thank you.

else
this.pdbId = new PdbId(pdbId);
}


Expand Down