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author
Sebastian Bittrich
committed
removes star imports
1 parent f410aa5 commit 0b59a10

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7 files changed

+168
-13
lines changed

7 files changed

+168
-13
lines changed

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileConsumerImplTest.java‎

Lines changed: 18 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,19 @@
11
package org.biojava.nbio.structure.test.io.cif;
22

3-
import org.biojava.nbio.structure.*;
4-
import org.biojava.nbio.structure.io.*;
3+
import org.biojava.nbio.structure.Atom;
4+
import org.biojava.nbio.structure.Chain;
5+
import org.biojava.nbio.structure.DBRef;
6+
import org.biojava.nbio.structure.Group;
7+
import org.biojava.nbio.structure.GroupType;
8+
import org.biojava.nbio.structure.PDBHeader;
9+
import org.biojava.nbio.structure.Structure;
10+
import org.biojava.nbio.structure.io.BcifFileReader;
11+
import org.biojava.nbio.structure.io.CifFileReader;
12+
import org.biojava.nbio.structure.io.FileParsingParameters;
13+
import org.biojava.nbio.structure.io.LocalPDBDirectory;
14+
import org.biojava.nbio.structure.io.MMCIFFileReader;
15+
import org.biojava.nbio.structure.io.MMTFFileReader;
16+
import org.biojava.nbio.structure.io.PDBFileParser;
517
import org.biojava.nbio.structure.io.cif.CifFileConverter;
618
import org.junit.Ignore;
719
import org.junit.Test;
@@ -21,7 +33,10 @@
2133
import java.util.regex.Pattern;
2234
import java.util.zip.GZIPInputStream;
2335

24-
import static org.junit.Assert.*;
36+
import static org.junit.Assert.assertNotNull;
37+
import static org.junit.Assert.assertEquals;
38+
import static org.junit.Assert.assertTrue;
39+
import static org.junit.Assert.fail;
2540

2641
public class CifFileConsumerImplTest {
2742
private static boolean headerOnly;

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileSupplierImplTest.java‎

Lines changed: 12 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,17 @@
11
package org.biojava.nbio.structure.test.io.cif;
22

3-
import org.biojava.nbio.structure.*;
3+
import org.biojava.nbio.structure.AminoAcidImpl;
4+
import org.biojava.nbio.structure.Atom;
5+
import org.biojava.nbio.structure.AtomImpl;
6+
import org.biojava.nbio.structure.Chain;
7+
import org.biojava.nbio.structure.ChainImpl;
8+
import org.biojava.nbio.structure.Element;
9+
import org.biojava.nbio.structure.EntityInfo;
10+
import org.biojava.nbio.structure.Group;
11+
import org.biojava.nbio.structure.ResidueNumber;
12+
import org.biojava.nbio.structure.Structure;
13+
import org.biojava.nbio.structure.StructureImpl;
14+
import org.biojava.nbio.structure.StructureTools;
415
import org.biojava.nbio.structure.io.cif.CifFileConverter;
516
import org.junit.Test;
617
import org.rcsb.cif.CifReader;

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/BcifFileReader.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,7 @@ public BcifFileReader() {
2828
}
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3030
/**
31-
* Constructs a new BcifFileReader, initializing the extensions member variable.
31+
* Constructs a new B`FileReader, initializing the extensions member variable.
3232
* The path is initialized to the given path, both autoFetch and splitDir are initialized to false.
3333
*/
3434
public BcifFileReader(String path) {

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

Lines changed: 45 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,50 @@
11
package org.biojava.nbio.structure.io.cif;
22

3-
import org.rcsb.cif.model.generated.*;
3+
import org.rcsb.cif.model.generated.AtomSite;
4+
import org.rcsb.cif.model.generated.AtomSites;
5+
import org.rcsb.cif.model.generated.AuditAuthor;
6+
import org.rcsb.cif.model.generated.Cell;
7+
import org.rcsb.cif.model.generated.ChemComp;
8+
import org.rcsb.cif.model.generated.ChemCompBond;
9+
import org.rcsb.cif.model.generated.DatabasePDBRemark;
10+
import org.rcsb.cif.model.generated.DatabasePDBRev;
11+
import org.rcsb.cif.model.generated.DatabasePDBRevRecord;
12+
import org.rcsb.cif.model.generated.Entity;
13+
import org.rcsb.cif.model.generated.EntityPoly;
14+
import org.rcsb.cif.model.generated.EntityPolySeq;
15+
import org.rcsb.cif.model.generated.EntitySrcGen;
16+
import org.rcsb.cif.model.generated.EntitySrcNat;
17+
import org.rcsb.cif.model.generated.Exptl;
18+
import org.rcsb.cif.model.generated.PdbxAuditRevisionHistory;
19+
import org.rcsb.cif.model.generated.PdbxChemCompIdentifier;
20+
import org.rcsb.cif.model.generated.PdbxDatabaseStatus;
21+
import org.rcsb.cif.model.generated.PdbxEntityDescriptor;
22+
import org.rcsb.cif.model.generated.PdbxEntitySrcSyn;
23+
import org.rcsb.cif.model.generated.PdbxMolecule;
24+
import org.rcsb.cif.model.generated.PdbxMoleculeFeatures;
25+
import org.rcsb.cif.model.generated.PdbxNonpolyScheme;
26+
import org.rcsb.cif.model.generated.PdbxReferenceEntityLink;
27+
import org.rcsb.cif.model.generated.PdbxReferenceEntityList;
28+
import org.rcsb.cif.model.generated.PdbxReferenceEntityPolyLink;
29+
import org.rcsb.cif.model.generated.PdbxStructAssembly;
30+
import org.rcsb.cif.model.generated.PdbxStructAssemblyGen;
31+
import org.rcsb.cif.model.generated.PdbxStructModResidue;
32+
import org.rcsb.cif.model.generated.PdbxStructOperList;
33+
import org.rcsb.cif.model.generated.Refine;
34+
import org.rcsb.cif.model.generated.Struct;
35+
import org.rcsb.cif.model.generated.StructAsym;
36+
import org.rcsb.cif.model.generated.StructConf;
37+
import org.rcsb.cif.model.generated.StructConn;
38+
import org.rcsb.cif.model.generated.StructConnType;
39+
import org.rcsb.cif.model.generated.StructKeywords;
40+
import org.rcsb.cif.model.generated.StructNcsOper;
41+
import org.rcsb.cif.model.generated.StructRef;
42+
import org.rcsb.cif.model.generated.StructRefSeq;
43+
import org.rcsb.cif.model.generated.StructRefSeqDif;
44+
import org.rcsb.cif.model.generated.StructSheetRange;
45+
import org.rcsb.cif.model.generated.StructSite;
46+
import org.rcsb.cif.model.generated.StructSiteGen;
47+
import org.rcsb.cif.model.generated.Symmetry;
448

549
/**
650
* Defines a rather generic interface which allows to populate some data structure with data parsed from a CIF file.

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

Lines changed: 75 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,34 @@
11
package org.biojava.nbio.structure.io.cif;
22

3-
import org.biojava.nbio.structure.*;
4-
import org.biojava.nbio.structure.io.*;
3+
import org.biojava.nbio.structure.AminoAcid;
4+
import org.biojava.nbio.structure.AminoAcidImpl;
5+
import org.biojava.nbio.structure.Atom;
6+
import org.biojava.nbio.structure.AtomImpl;
7+
import org.biojava.nbio.structure.Chain;
8+
import org.biojava.nbio.structure.ChainImpl;
9+
import org.biojava.nbio.structure.DBRef;
10+
import org.biojava.nbio.structure.Element;
11+
import org.biojava.nbio.structure.EntityInfo;
12+
import org.biojava.nbio.structure.EntityType;
13+
import org.biojava.nbio.structure.Group;
14+
import org.biojava.nbio.structure.GroupType;
15+
import org.biojava.nbio.structure.HetatomImpl;
16+
import org.biojava.nbio.structure.NucleotideImpl;
17+
import org.biojava.nbio.structure.PDBCrystallographicInfo;
18+
import org.biojava.nbio.structure.PDBHeader;
19+
import org.biojava.nbio.structure.ResidueNumber;
20+
import org.biojava.nbio.structure.SeqMisMatch;
21+
import org.biojava.nbio.structure.SeqMisMatchImpl;
22+
import org.biojava.nbio.structure.Site;
23+
import org.biojava.nbio.structure.Structure;
24+
import org.biojava.nbio.structure.StructureException;
25+
import org.biojava.nbio.structure.StructureImpl;
26+
import org.biojava.nbio.structure.StructureTools;
27+
import org.biojava.nbio.structure.io.BondMaker;
28+
import org.biojava.nbio.structure.io.ChargeAdder;
29+
import org.biojava.nbio.structure.io.EntityFinder;
30+
import org.biojava.nbio.structure.io.FileParsingParameters;
31+
import org.biojava.nbio.structure.io.SeqRes2AtomAligner;
532
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
633
import org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord;
734
import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
@@ -13,7 +40,51 @@
1340
import org.rcsb.cif.model.FloatColumn;
1441
import org.rcsb.cif.model.IntColumn;
1542
import org.rcsb.cif.model.StrColumn;
16-
import org.rcsb.cif.model.generated.*;
43+
import org.rcsb.cif.model.generated.AtomSite;
44+
import org.rcsb.cif.model.generated.AtomSites;
45+
import org.rcsb.cif.model.generated.AuditAuthor;
46+
import org.rcsb.cif.model.generated.Cell;
47+
import org.rcsb.cif.model.generated.ChemComp;
48+
import org.rcsb.cif.model.generated.ChemCompBond;
49+
import org.rcsb.cif.model.generated.DatabasePDBRemark;
50+
import org.rcsb.cif.model.generated.DatabasePDBRev;
51+
import org.rcsb.cif.model.generated.DatabasePDBRevRecord;
52+
import org.rcsb.cif.model.generated.Entity;
53+
import org.rcsb.cif.model.generated.EntityPoly;
54+
import org.rcsb.cif.model.generated.EntityPolySeq;
55+
import org.rcsb.cif.model.generated.EntitySrcGen;
56+
import org.rcsb.cif.model.generated.EntitySrcNat;
57+
import org.rcsb.cif.model.generated.Exptl;
58+
import org.rcsb.cif.model.generated.PdbxAuditRevisionHistory;
59+
import org.rcsb.cif.model.generated.PdbxChemCompIdentifier;
60+
import org.rcsb.cif.model.generated.PdbxDatabaseStatus;
61+
import org.rcsb.cif.model.generated.PdbxEntityDescriptor;
62+
import org.rcsb.cif.model.generated.PdbxEntitySrcSyn;
63+
import org.rcsb.cif.model.generated.PdbxMolecule;
64+
import org.rcsb.cif.model.generated.PdbxMoleculeFeatures;
65+
import org.rcsb.cif.model.generated.PdbxNonpolyScheme;
66+
import org.rcsb.cif.model.generated.PdbxReferenceEntityLink;
67+
import org.rcsb.cif.model.generated.PdbxReferenceEntityList;
68+
import org.rcsb.cif.model.generated.PdbxReferenceEntityPolyLink;
69+
import org.rcsb.cif.model.generated.PdbxStructAssembly;
70+
import org.rcsb.cif.model.generated.PdbxStructAssemblyGen;
71+
import org.rcsb.cif.model.generated.PdbxStructModResidue;
72+
import org.rcsb.cif.model.generated.PdbxStructOperList;
73+
import org.rcsb.cif.model.generated.Refine;
74+
import org.rcsb.cif.model.generated.Struct;
75+
import org.rcsb.cif.model.generated.StructAsym;
76+
import org.rcsb.cif.model.generated.StructConf;
77+
import org.rcsb.cif.model.generated.StructConn;
78+
import org.rcsb.cif.model.generated.StructConnType;
79+
import org.rcsb.cif.model.generated.StructKeywords;
80+
import org.rcsb.cif.model.generated.StructNcsOper;
81+
import org.rcsb.cif.model.generated.StructRef;
82+
import org.rcsb.cif.model.generated.StructRefSeq;
83+
import org.rcsb.cif.model.generated.StructRefSeqDif;
84+
import org.rcsb.cif.model.generated.StructSheetRange;
85+
import org.rcsb.cif.model.generated.StructSite;
86+
import org.rcsb.cif.model.generated.StructSiteGen;
87+
import org.rcsb.cif.model.generated.Symmetry;
1788
import org.slf4j.Logger;
1889
import org.slf4j.LoggerFactory;
1990

@@ -1168,7 +1239,7 @@ public void finish() {
11681239
setStructNcsOps();
11691240
setCrystallographicInfoMetadata();
11701241

1171-
Map<String,List<SeqMisMatch>> misMatchMap = new HashMap<>();
1242+
Map<String, List<SeqMisMatch>> misMatchMap = new HashMap<>();
11721243
for (int rowIndex = 0; rowIndex < structRefSeqDif.getRowCount(); rowIndex++) {
11731244
SeqMisMatch seqMisMatch = new SeqMisMatchImpl();
11741245
seqMisMatch.setDetails(structRefSeqDif.getDetails().get(rowIndex));

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

Lines changed: 13 additions & 2 deletions
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@@ -1,11 +1,22 @@
11
package org.biojava.nbio.structure.io.cif;
22

3-
import org.biojava.nbio.structure.*;
3+
import org.biojava.nbio.structure.Atom;
4+
import org.biojava.nbio.structure.Chain;
5+
import org.biojava.nbio.structure.Element;
6+
import org.biojava.nbio.structure.EntityType;
7+
import org.biojava.nbio.structure.Group;
8+
import org.biojava.nbio.structure.GroupType;
9+
import org.biojava.nbio.structure.Structure;
410
import org.biojava.nbio.structure.xtal.CrystalCell;
511
import org.biojava.nbio.structure.xtal.SpaceGroup;
612
import org.rcsb.cif.model.Category;
713
import org.rcsb.cif.model.CifFile;
8-
import org.rcsb.cif.model.builder.*;
14+
import org.rcsb.cif.model.builder.BlockBuilder;
15+
import org.rcsb.cif.model.builder.CategoryBuilder;
16+
import org.rcsb.cif.model.builder.CifBuilder;
17+
import org.rcsb.cif.model.builder.FloatColumnBuilder;
18+
import org.rcsb.cif.model.builder.IntColumnBuilder;
19+
import org.rcsb.cif.model.builder.StrColumnBuilder;
920

1021
import java.util.ArrayList;
1122
import java.util.LinkedHashMap;

‎biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java‎

Lines changed: 4 additions & 1 deletion
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@@ -24,7 +24,10 @@
2424
import java.util.Objects;
2525
import java.util.zip.GZIPInputStream;
2626

27-
import static org.junit.Assert.*;
27+
import static org.junit.Assert.assertEquals;
28+
import static org.junit.Assert.assertNotNull;
29+
import static org.junit.Assert.assertSame;
30+
import static org.junit.Assert.assertTrue;
2831

2932
public class CifFileConsumerImplTest {
3033
/**

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