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sbittrichsbittrich
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detach mmcif.model.DatabasePdbrevRecord
- replaced by DatabasePdbRevRecord
1 parent 633021b commit e3bad37

3 files changed

Lines changed: 56 additions & 16 deletions

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/DatabasePdbRevRecord.java‎

Lines changed: 43 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,43 @@
1+
package org.biojava.nbio.structure;
2+
3+
import java.io.Serializable;
4+
5+
public class DatabasePdbRevRecord implements Serializable {
6+
private static final long serialVersionUID = -791924804009516791L;
7+
private String rev_num;
8+
private String type;
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private String details;
10+
11+
public String getRev_num() {
12+
return rev_num;
13+
}
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15+
public void setRev_num(String rev_num) {
16+
this.rev_num = rev_num;
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}
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public String getType() {
20+
return type;
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}
22+
23+
public void setType(String type) {
24+
this.type = type;
25+
}
26+
27+
public String getDetails() {
28+
return details;
29+
}
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31+
public void setDetails(String details) {
32+
this.details = details;
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}
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35+
@Override
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public String toString() {
37+
return "DatabasePdbrevRecord{" +
38+
"rev_num='" + rev_num + '\'' +
39+
", type='" + type + '\'' +
40+
", details='" + details + '\'' +
41+
'}';
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}
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}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java‎

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,6 @@
2020
*/
2121
package org.biojava.nbio.structure;
2222

23-
import org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord;
2423
import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
2524
import org.slf4j.Logger;
2625
import org.slf4j.LoggerFactory;
@@ -77,7 +76,7 @@ public class PDBHeader implements PDBRecord {
7776

7877
private Map<Integer,BioAssemblyInfo> bioAssemblies ;
7978

80-
List<DatabasePdbrevRecord> revisionRecords;
79+
List<DatabasePdbRevRecord> revisionRecords;
8180

8281
public PDBHeader(){
8382

@@ -663,11 +662,11 @@ public int getNrBioAssemblies() {
663662
return this.bioAssemblies.size();
664663
}
665664

666-
public List<DatabasePdbrevRecord> getRevisionRecords() {
665+
public List<DatabasePdbRevRecord> getRevisionRecords() {
667666
return revisionRecords;
668667
}
669668

670-
public void setRevisionRecords(List<DatabasePdbrevRecord> revisionRecords) {
669+
public void setRevisionRecords(List<DatabasePdbRevRecord> revisionRecords) {
671670
this.revisionRecords = revisionRecords;
672671
}
673672

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java‎

Lines changed: 10 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@
77
import org.biojava.nbio.structure.Chain;
88
import org.biojava.nbio.structure.ChainImpl;
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import org.biojava.nbio.structure.DBRef;
10+
import org.biojava.nbio.structure.DatabasePdbRevRecord;
1011
import org.biojava.nbio.structure.Element;
1112
import org.biojava.nbio.structure.EntityInfo;
1213
import org.biojava.nbio.structure.EntityType;
@@ -30,7 +31,6 @@
3031
import org.biojava.nbio.structure.io.FileParsingParameters;
3132
import org.biojava.nbio.structure.io.SeqRes2AtomAligner;
3233
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
33-
import org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord;
3434
import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
3535
import org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder;
3636
import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
@@ -97,8 +97,6 @@
9797
import java.util.stream.Collectors;
9898
import java.util.stream.IntStream;
9999

100-
// TODO detach the impl from the redundant mmCIF impl
101-
102100
/**
103101
* An implementation of a CifFileConsumer for BioJava. Will process the information provided by a CifFile instance and
104102
* use it to build up a {@link Structure} object. The implementation is for the most part really close to that in
@@ -144,7 +142,7 @@ class CifFileConsumerImpl implements CifFileConsumer<Structure> {
144142
private Map<String, String> asymId2authorId;
145143
private Matrix4d parsedScaleMatrix;
146144

147-
private FileParsingParameters params;
145+
private final FileParsingParameters params;
148146

149147
public CifFileConsumerImpl(FileParsingParameters params) {
150148
this.params = params;
@@ -624,7 +622,7 @@ public void consumeDatabasePDBrev(DatabasePDBRev databasePDBrev) {
624622

625623
@Override
626624
public void consumeDatabasePDBrevRecord(DatabasePDBRevRecord databasePDBrevRecord) {
627-
List<DatabasePdbrevRecord> revRecords = pdbHeader.getRevisionRecords();
625+
List<DatabasePdbRevRecord> revRecords = pdbHeader.getRevisionRecords();
628626
if (revRecords == null) {
629627
revRecords = new ArrayList<>();
630628
pdbHeader.setRevisionRecords(revRecords);
@@ -633,10 +631,10 @@ public void consumeDatabasePDBrevRecord(DatabasePDBRevRecord databasePDBrevRecor
633631
revRecords.addAll(convert(databasePDBrevRecord));
634632
}
635633

636-
private List<DatabasePdbrevRecord> convert(DatabasePDBRevRecord databasePDBrevRecord) {
637-
List<DatabasePdbrevRecord> revRecords = new ArrayList<>();
634+
private List<DatabasePdbRevRecord> convert(DatabasePDBRevRecord databasePDBrevRecord) {
635+
List<DatabasePdbRevRecord> revRecords = new ArrayList<>();
638636
for (int rowIndex = 0; rowIndex < databasePDBrevRecord.getRowCount(); rowIndex++) {
639-
DatabasePdbrevRecord revRecord = new DatabasePdbrevRecord();
637+
DatabasePdbRevRecord revRecord = new DatabasePdbRevRecord();
640638
revRecord.setDetails(databasePDBrevRecord.getDetails().get(rowIndex));
641639
revRecord.setRev_num(databasePDBrevRecord.getRevNum().getStringData(rowIndex));
642640
revRecord.setType(databasePDBrevRecord.getType().get(rowIndex));
@@ -1297,14 +1295,14 @@ private void addEntity(int asymRowIndex, String entityId, String pdbxDescription
12971295
} catch (NumberFormatException e) {
12981296
logger.warn("Could not parse mol_id from string {}. Will use 0 for creating Entity", entityId);
12991297
}
1300-
1298+
13011299
int entityRowIndex = IntStream.range(0, entity.getRowCount())
13021300
.filter(i -> entity.getId().get(i).equals(entityId))
13031301
.findFirst()
13041302
.orElse(-1);
1305-
1303+
13061304
EntityInfo entityInfo = structure.getEntityById(eId);
1307-
1305+
13081306
if (entityInfo == null) {
13091307
entityInfo = new EntityInfo();
13101308
entityInfo.setMolId(eId);
@@ -1320,7 +1318,7 @@ private void addEntity(int asymRowIndex, String entityId, String pdbxDescription
13201318
}
13211319
addAncilliaryEntityData(asymRowIndex, entityInfo);
13221320
structure.addEntityInfo(entityInfo);
1323-
logger.debug("Adding Entity with entity id {} from _entity, with name: {}", eId,
1321+
logger.debug("Adding Entity with entity id {} from _entity, with name: {}", eId,
13241322
entityInfo.getDescription());
13251323
}
13261324
}

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