Skip to content

Commit c9b7858

Browse files
andreasprlicandreasprlic
committed
cleaning up some javadoc
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9152 7c6358e6-4a41-0410-a743-a5b2a554c398
1 parent 40ee2b8 commit c9b7858

4 files changed

Lines changed: 26 additions & 26 deletions

File tree

‎biojava3-core/src/main/java/org/biojava3/core/sequence/CDSComparator.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,7 @@ public class CDSComparator implements Comparator<CDSSequence>{
3333
* Used to sort two CDSSequences where Negative Strand makes it tough
3434
* @param o1
3535
* @param o2
36-
* @return
36+
* @return val
3737
*/
3838
public int compare(CDSSequence o1, CDSSequence o2) {
3939
if(o1.getStrand() != o2.getStrand()){

‎biojava3-core/src/main/java/org/biojava3/core/sequence/CDSSequence.java‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -22,20 +22,20 @@
2222
*/
2323
package org.biojava3.core.sequence;
2424

25-
import java.util.logging.Logger;
25+
2626
import org.biojava3.core.sequence.compound.NucleotideCompound;
2727
import org.biojava3.core.sequence.template.CompoundSet;
2828

2929
/**
3030
* Represents a exon or coding sequence in a gene. It has a parent {@link TranscriptSequence}
3131
* where a TranscriptSequence is the child of a GeneSequence
3232
* Not important for protein construction but the phase is used if outputting the gene
33-
* to a gff3 file. {@linkplain http://www.sequenceontology.org/gff3.shtml}
33+
* to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml}
3434
* @author Scooter Willis
3535
*/
3636
public class CDSSequence extends DNASequence {
3737

38-
private static final Logger log = Logger.getLogger(CDSSequence.class.getName());
38+
//private static final Logger log = Logger.getLogger(CDSSequence.class.getName());
3939
Integer phase = 0; // 0, 1, 2
4040
TranscriptSequence parentTranscriptSequence;
4141

@@ -62,15 +62,15 @@ public int getLength() {
6262

6363
/**
6464
*
65-
* @return
65+
* @return get the phase
6666
*/
6767
public Integer getPhase() {
6868
return phase;
6969
}
7070

7171
/**
7272
*
73-
* @return
73+
* @return get the strand
7474
*/
7575
public Strand getStrand() {
7676
return parentTranscriptSequence.getStrand();
@@ -80,9 +80,9 @@ public Strand getStrand() {
8080
* A CDS sequence if negative stranded needs to be reverse complement
8181
* to represent the actual coding sequence. When getting a ProteinSequence
8282
* from a TranscriptSequence this method is callled for each CDSSequence
83-
* {@linkplain http://www.sequenceontology.org/gff3.shtml}
84-
* {@linkplain http://biowiki.org/~yam/bioe131/GFF.ppt}
85-
* @return
83+
* {@link http://www.sequenceontology.org/gff3.shtml}
84+
* {@link http://biowiki.org/~yam/bioe131/GFF.ppt}
85+
* @return coding sequence
8686
*/
8787
public String getCodingSequence() {
8888
String sequence = this.getSequenceAsString(getBioBegin(), getBioEnd(), getStrand());

‎biojava3-core/src/main/java/org/biojava3/core/sequence/DNASequence.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -93,7 +93,7 @@ public DNASequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<N
9393
/**
9494
* Return the RNASequence equivalent of the DNASequence using default Transcription Engine. Not all
9595
* species follow the same rules. If you don't know better use this method
96-
* @return
96+
* @return RNA sequence
9797
*/
9898
public RNASequence getRNASequence() {
9999
return getRNASequence(Frame.getDefaultFrame());
@@ -102,16 +102,16 @@ public RNASequence getRNASequence() {
102102
/**
103103
* Allow a user to pass in a rules engine to do the DNA to RNA translation
104104
* @param engine
105-
* @return
106-
*/
105+
* @return RNA sequence
106+
*/
107107
public RNASequence getRNASequence(TranscriptionEngine engine) {
108108
return getRNASequence(engine, Frame.getDefaultFrame());
109109
}
110110

111111
/**
112112
* Allows the user to pass in the Frame shift.
113113
* @param frame
114-
* @return
114+
* @return rna sequence
115115
*/
116116
public RNASequence getRNASequence(Frame frame) {
117117
return getRNASequence(TranscriptionEngine.getDefault(), frame);
@@ -123,7 +123,7 @@ public RNASequence getRNASequence(TranscriptionEngine engine, Frame frame) {
123123

124124
/**
125125
* Get the GC count in the DNA Sequence
126-
* @return
126+
* @return GC count
127127
*/
128128
public int getGCCount() {
129129
return SequenceMixin.countGC(this);

‎biojava3-core/src/main/java/org/biojava3/core/sequence/GeneSequence.java‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -70,7 +70,7 @@ public GeneSequence(ChromosomeSequence parentSequence, int begin, int end, Stran
7070

7171
/**
7272
* The parent ChromosomeSequence which contains the actual DNA sequence data
73-
* @return
73+
* @return Chromosome sequence
7474
*/
7575
public ChromosomeSequence getParentChromosomeSequence() {
7676
return chromosomeSequence;
@@ -142,15 +142,15 @@ public void setStrand(Strand strand) {
142142
/**
143143
* Get the transcript sequence by accession
144144
* @param accession
145-
* @return
145+
* @return the transcript
146146
*/
147147
public TranscriptSequence getTranscript(String accession) {
148148
return transcriptSequenceHashMap.get(accession);
149149
}
150150

151151
/**
152152
* Get the collection of transcription sequences assigned to this gene
153-
* @return
153+
* @return transcripts
154154
*/
155155
public LinkedHashMap<String, TranscriptSequence> getTranscripts() {
156156
return transcriptSequenceHashMap;
@@ -159,7 +159,7 @@ public LinkedHashMap<String, TranscriptSequence> getTranscripts() {
159159
/**
160160
* Remove the transcript sequence from the gene
161161
* @param accession
162-
* @return
162+
* @return transcriptsequence
163163
*/
164164
public TranscriptSequence removeTranscript(String accession) {
165165

@@ -172,7 +172,7 @@ public TranscriptSequence removeTranscript(String accession) {
172172
* @param accession
173173
* @param begin
174174
* @param end
175-
* @return
175+
* @return transcript sequence
176176
* @throws Exception If the accession id is already used
177177
*/
178178
public TranscriptSequence addTranscript(AccessionID accession, int begin, int end) throws Exception {
@@ -188,7 +188,7 @@ public TranscriptSequence addTranscript(AccessionID accession, int begin, int en
188188
/**
189189
* Remove the intron by accession
190190
* @param accession
191-
* @return
191+
* @return intron sequence
192192
*/
193193
public IntronSequence removeIntron(String accession) {
194194
for (IntronSequence intronSequence : intronSequenceList) {
@@ -206,7 +206,7 @@ public IntronSequence removeIntron(String accession) {
206206
* @param accession
207207
* @param begin
208208
* @param end
209-
* @return
209+
* @return intron sequence
210210
*/
211211
public IntronSequence addIntron(AccessionID accession, int begin, int end) throws Exception {
212212
if (intronSequenceHashMap.containsKey(accession.getID())) {
@@ -223,7 +223,7 @@ public IntronSequence addIntron(AccessionID accession, int begin, int end) throw
223223
/**
224224
* Remove the exon sequence
225225
* @param accession
226-
* @return
226+
* @return exon sequence
227227
*/
228228
public ExonSequence removeExon(String accession) {
229229
for (ExonSequence exonSequence : exonSequenceList) {
@@ -250,7 +250,7 @@ public ExonSequence removeExon(String accession) {
250250
* @param accession
251251
* @param begin
252252
* @param end
253-
* @return
253+
* @return exon sequence
254254
*/
255255
public ExonSequence addExon(AccessionID accession, int begin, int end) throws Exception {
256256
if (exonSequenceHashMap.containsKey(accession.getID())) {
@@ -266,15 +266,15 @@ public ExonSequence addExon(AccessionID accession, int begin, int end) throws Ex
266266

267267
/**
268268
* Get the exons as an ArrayList
269-
* @return
269+
* @return exons
270270
*/
271271
public ArrayList<ExonSequence> getExonSequences() {
272272
return exonSequenceList;
273273
}
274274

275275
/**
276276
* Get the introns as an ArrayList
277-
* @return
277+
* @return introns
278278
*/
279279
public ArrayList<IntronSequence> getIntronSequences() {
280280
return intronSequenceList;
@@ -283,7 +283,7 @@ public ArrayList<IntronSequence> getIntronSequences() {
283283
/**
284284
* Try to give method clarity where you want a DNASequence coding in the 5' to 3' direction
285285
* Returns the DNASequence representative of the 5' and 3' reading based on strand
286-
* @return
286+
* @return dna sequence
287287
*/
288288
public DNASequence getSequence5PrimeTo3Prime() {
289289
String sequence = getSequenceAsString(this.getBioBegin(), this.getBioEnd(), this.getStrand());

0 commit comments

Comments
 (0)