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Fix issue s1319 Declarations should use Java collection interfaces on biojava-core
1 parent b33d74c commit 1ae6b52

36 files changed

+172
-146
lines changed

‎biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -43,6 +43,7 @@
4343
import java.util.ArrayList;
4444
import java.util.LinkedHashMap;
4545
import java.util.List;
46+
import java.util.Map;
4647

4748
public class TestDNAAlignment {
4849

@@ -75,7 +76,7 @@ public void testDNAAlignment() {
7576
private static List<DNASequence> getDNAFASTAFile() throws Exception {
7677

7778
InputStream inStream = TestDNAAlignment.class.getResourceAsStream(String.format("/dna-fasta.txt"));
78-
LinkedHashMap<String, DNASequence> fastas = FastaReaderHelper.readFastaDNASequence(inStream);
79+
Map<String, DNASequence> fastas = FastaReaderHelper.readFastaDNASequence(inStream);
7980

8081
List<DNASequence> sequences = new ArrayList<DNASequence>();
8182

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -27,6 +27,7 @@
2727
import java.util.NoSuchElementException;
2828

2929
import org.biojava.nbio.core.sequence.template.Sequence;
30+
import java.util.Map;
3031

3132
/**
3233
* This class models a search result.
@@ -46,7 +47,7 @@ public abstract class Result implements Iterable<Hit>{
4647
private String reference;
4748
private String dbFile;
4849

49-
private HashMap<String,String> programSpecificParameters;
50+
private Map<String, String> programSpecificParameters;
5051

5152
private int iterationNumber;
5253
private String queryID;
@@ -56,7 +57,7 @@ public abstract class Result implements Iterable<Hit>{
5657
private List<Hit> hits;
5758
private int hitCounter = -1;
5859

59-
public Result(String program, String version, String reference, String dbFile, HashMap<String, String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence) {
60+
public Result(String program, String version, String reference, String dbFile, Map<String, String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence) {
6061
this.program = program;
6162
this.version = version;
6263
this.reference = reference;

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -28,6 +28,7 @@
2828
import java.util.List;
2929
import java.util.ServiceLoader;
3030
import java.util.NoSuchElementException;
31+
import java.util.Map;
3132

3233
/**
3334
* Designed by Paolo Pavan.
@@ -39,7 +40,7 @@
3940
*/
4041

4142
public class SearchIO implements Iterable<Result>{
42-
static private HashMap<String,ResultFactory> extensionFactoryAssociation;
43+
static private Map<String, ResultFactory> extensionFactoryAssociation;
4344

4445
final private ResultFactory factory;
4546
final private File file;

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResult.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -25,6 +25,7 @@
2525
import java.util.HashMap;
2626
import java.util.List;
2727
import org.biojava.nbio.core.sequence.template.Sequence;
28+
import java.util.Map;
2829

2930
/**
3031
* This class models a Blast/Blast plus result.
@@ -39,7 +40,7 @@
3940
*
4041
*/
4142
public class BlastResult extends Result{
42-
public BlastResult(String program, String version, String reference, String dbFile, HashMap<String, String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence) {
43+
public BlastResult(String program, String version, String reference, String dbFile, Map<String, String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence) {
4344
super(program, version, reference, dbFile, programSpecificParameters, iterationNumber, queryID, queryDef, queryLength, hits, querySequence);
4445
}
4546

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,7 @@
2424
import java.util.HashMap;
2525
import java.util.List;
2626
import org.biojava.nbio.core.sequence.template.Sequence;
27+
import java.util.Map;
2728

2829
/**
2930
* Designed by Paolo Pavan.
@@ -39,7 +40,7 @@ public class BlastResultBuilder {
3940
private String version;
4041
private String reference;
4142
private String dbFile;
42-
private HashMap<String, String> programSpecificParameters;
43+
private Map<String, String> programSpecificParameters;
4344
private int iterationNumber;
4445
private String queryID;
4546
private String queryDef;
@@ -70,7 +71,7 @@ public BlastResultBuilder setDbFile(String dbFile) {
7071
return this;
7172
}
7273

73-
public BlastResultBuilder setProgramSpecificParameters(HashMap<String, String> programSpecificParameters) {
74+
public BlastResultBuilder setProgramSpecificParameters(Map<String, String> programSpecificParameters) {
7475
this.programSpecificParameters = programSpecificParameters;
7576
return this;
7677
}

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,7 @@
3737
import org.biojava.nbio.core.sequence.template.Sequence;
3838
import org.slf4j.Logger;
3939
import org.slf4j.LoggerFactory;
40+
import java.util.Map;
4041

4142
/**
4243
* Designed by Paolo Pavan.
@@ -71,7 +72,7 @@ private enum PARSING_CONSISTENCY {
7172

7273
// data imported private:
7374
int queryIdNumber = 0;
74-
HashMap<String,String> queryIdMapping = new HashMap<>();
75+
Map<String, String> queryIdMapping = new HashMap<>();
7576
String programName=null, queryName = null, databaseFile = null;
7677
private String queryId ;
7778
private String subjectId ;

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -90,9 +90,9 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
9090
// create mappings between sequences and blast id
9191
mapIds();
9292

93-
ArrayList<Result> resultsCollection;
94-
ArrayList<Hit> hitsCollection;
95-
ArrayList<Hsp> hspsCollection;
93+
List<Result> resultsCollection;
94+
List<Hit> hitsCollection;
95+
List<Hsp> hspsCollection;
9696

9797
try {
9898
// select top level elements
@@ -102,7 +102,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
102102
String dbFile = XMLHelper.selectSingleElement(blastDoc.getDocumentElement(),"BlastOutput_db").getTextContent();
103103

104104
logger.info("Query for hits in "+ targetFile);
105-
ArrayList<Element> IterationsList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]");
105+
List<Element> IterationsList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]");
106106
logger.info(IterationsList.size() + " results");
107107

108108
resultsCollection = new ArrayList<>();
@@ -129,7 +129,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
129129

130130

131131
Element iterationHitsElement = XMLHelper.selectSingleElement(element, "Iteration_hits");
132-
ArrayList<Element> hitList = XMLHelper.selectElements(iterationHitsElement, "Hit");
132+
List<Element> hitList = XMLHelper.selectElements(iterationHitsElement, "Hit");
133133

134134
hitsCollection = new ArrayList<>();
135135
for (Element hitElement : hitList) {
@@ -146,7 +146,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
146146
));
147147

148148
Element hithspsElement = XMLHelper.selectSingleElement(hitElement, "Hit_hsps");
149-
ArrayList<Element> hspList = XMLHelper.selectElements(hithspsElement, "Hsp");
149+
List<Element> hspList = XMLHelper.selectElements(hithspsElement, "Hsp");
150150

151151
hspsCollection = new ArrayList<>();
152152
for (Element hspElement : hspList) {
@@ -195,7 +195,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
195195

196196
@Override
197197
public List<String> getFileExtensions(){
198-
ArrayList<String> extensions = new ArrayList<>(1);
198+
List<String> extensions = new ArrayList<>(1);
199199
extensions.add("blastxml");
200200
return extensions;
201201
}

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -29,6 +29,7 @@
2929
import org.biojava.nbio.core.sequence.template.SequenceReader;
3030

3131
import java.util.LinkedHashMap;
32+
import java.util.Map;
3233

3334
/**
3435
* A ChromosomeSequence is a DNASequence but keeps track of geneSequences
@@ -37,7 +38,7 @@
3738
public class ChromosomeSequence extends DNASequence {
3839

3940
private int chromosomeNumber;
40-
private LinkedHashMap<String, GeneSequence> geneSequenceHashMap = new LinkedHashMap<>();
41+
private Map<String, GeneSequence> geneSequenceHashMap = new LinkedHashMap<>();
4142

4243
/**
4344
* Empty constructor used by tools that need a proper Bean that allows the actual
@@ -106,7 +107,7 @@ public void setChromosomeNumber(int chromosomeNumber) {
106107
* @return
107108
*/
108109

109-
public LinkedHashMap<String, GeneSequence> getGeneSequences() {
110+
public Map<String, GeneSequence> getGeneSequences() {
110111
return geneSequenceHashMap;
111112
}
112113

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java‎

Lines changed: 10 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -32,6 +32,8 @@
3232
import java.util.ArrayList;
3333
import java.util.Collections;
3434
import java.util.LinkedHashMap;
35+
import java.util.Map;
36+
import java.util.List;
3537

3638
/**
3739
*
@@ -41,11 +43,11 @@ public class GeneSequence extends DNASequence {
4143

4244
private final static Logger logger = LoggerFactory.getLogger(GeneSequence.class);
4345

44-
private final LinkedHashMap<String, TranscriptSequence> transcriptSequenceHashMap = new LinkedHashMap<>();
45-
private final LinkedHashMap<String, IntronSequence> intronSequenceHashMap = new LinkedHashMap<>();
46-
private final LinkedHashMap<String, ExonSequence> exonSequenceHashMap = new LinkedHashMap<>();
47-
private final ArrayList<IntronSequence> intronSequenceList = new ArrayList<>();
48-
private final ArrayList<ExonSequence> exonSequenceList = new ArrayList<>();
46+
private final Map<String, TranscriptSequence> transcriptSequenceHashMap = new LinkedHashMap<>();
47+
private final Map<String, IntronSequence> intronSequenceHashMap = new LinkedHashMap<>();
48+
private final Map<String, ExonSequence> exonSequenceHashMap = new LinkedHashMap<>();
49+
private final List<IntronSequence> intronSequenceList = new ArrayList<>();
50+
private final List<ExonSequence> exonSequenceList = new ArrayList<>();
4951
boolean intronAdded = false; // need to deal with the problem that typically introns are not added when validating the list and adding in introns as the regions not included in exons
5052
private Strand strand = Strand.UNDEFINED;
5153
private ChromosomeSequence chromosomeSequence;
@@ -179,7 +181,7 @@ public TranscriptSequence getTranscript(String accession) {
179181
* Get the collection of transcription sequences assigned to this gene
180182
* @return transcripts
181183
*/
182-
public LinkedHashMap<String, TranscriptSequence> getTranscripts() {
184+
public Map<String, TranscriptSequence> getTranscripts() {
183185
return transcriptSequenceHashMap;
184186
}
185187

@@ -294,15 +296,15 @@ public ExonSequence addExon(AccessionID accession, int begin, int end) {
294296
* Get the exons as an ArrayList. Modifying this list will not modify the underlying collection
295297
* @return exons
296298
*/
297-
public ArrayList<ExonSequence> getExonSequences() {
299+
public List<ExonSequence> getExonSequences() {
298300
return new ArrayList<>(exonSequenceList);
299301
}
300302

301303
/**
302304
* Get the introns as an ArrayList. Modifying this list will not modify the underlying collection
303305
* @return introns
304306
*/
305-
public ArrayList<IntronSequence> getIntronSequences() {
307+
public List<IntronSequence> getIntronSequences() {
306308
return new ArrayList<>(intronSequenceList);
307309
}
308310

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -42,6 +42,7 @@
4242
import java.util.LinkedHashMap;
4343
import java.util.List;
4444
import org.biojava.nbio.core.sequence.features.Qualifier;
45+
import java.util.Map;
4546

4647
/**
4748
* The representation of a ProteinSequence
@@ -163,7 +164,7 @@ private DNASequence getRawParentSequence(String accessId) throws IOException {
163164
= new FastaReader<>(is,
164165
new PlainFastaHeaderParser<DNASequence, NucleotideCompound>(),
165166
new DNASequenceCreator(AmbiguityDNACompoundSet.getDNACompoundSet()));
166-
LinkedHashMap<String, DNASequence> seq = parentReader.process();
167+
Map<String, DNASequence> seq = parentReader.process();
167168

168169
DNASequence parentSeq = null;
169170
if (seq.size() == 1) {

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