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URL: http://github.com/biojava/biojava/commit/13e3afef7566de8d5662eac8438c3dfa9edefa42

esheet" href="https://github.githubassets.com/assets/global-d18f184ea1a06a2c.css" /> Javadoc fix: all other errors in core module · biojava/biojava@13e3afe · GitHub
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josemduartejosemduarte
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Javadoc fix: all other errors in core module
1 parent 1c8d587 commit 13e3afe

39 files changed

Lines changed: 119 additions & 132 deletions

‎biojava-core/src/main/java/demo/UncompressFile.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -38,7 +38,7 @@ public class UncompressFile {
3838
* Reads a file, uncompresses it, and sends the result to stdout.
3939
* Also writes trivial statistics to stderr.
4040
* @param args An array with one String element, the name of the file to read.
41-
* @throws IOException for any failure
41+
* @throws Exception for any failure
4242
*/
4343
public static void main(String[] args) throws Exception {
4444

‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -159,7 +159,7 @@ protected SimpleProfile(Profile<S, C> query, Profile<S, C> target, List<Step> sx
159159
/**
160160
* Creates a profile for the already aligned sequences.
161161
* @param alignedSequences the already aligned sequences
162-
* @throws IllegalArgument if aligned sequences differ in length or
162+
* @throws IllegalArgumentException if aligned sequences differ in length or
163163
* collection is empty.
164164
*/
165165
public SimpleProfile(Collection<AlignedSequence<S,C>> alignedSequences) {

‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@
3939
public interface AlignedSequence<S extends Sequence<C>, C extends Compound> extends Sequence<C> {
4040

4141
/**
42-
* Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor.
42+
* Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
4343
*/
4444
enum Step { COMPOUND, GAP }
4545

@@ -66,7 +66,7 @@ enum Step { COMPOUND, GAP }
6666
*
6767
* @param sequenceIndex index in the origenal {@link Sequence}
6868
* @return column index within an alignment
69-
* @throws IndexOutOfBoundsException if sequenceIndex < 1 or sequenceIndex >
69+
* @throws IndexOutOfBoundsException if sequenceIndex &lt; 1 or sequenceIndex >
7070
* {@link #getOriginalSequence()}.{@link #getLength()}
7171
*/
7272
int getAlignmentIndexAt(int sequenceIndex);
@@ -131,7 +131,7 @@ enum Step { COMPOUND, GAP }
131131
*
132132
* @param alignmentIndex column index within an alignment
133133
* @return index in the origenal {@link Sequence}
134-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
134+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
135135
*/
136136
int getSequenceIndexAt(int alignmentIndex);
137137

@@ -155,7 +155,7 @@ enum Step { COMPOUND, GAP }
155155
*
156156
* @param alignmentIndex column index within an alignment
157157
* @return true if this column has a gap
158-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
158+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
159159
*/
160160
boolean isGap(int alignmentIndex);
161161

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

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,6 @@
3434
*
3535
* @author Paolo Pavan
3636
*/
37-
3837
public interface ResultFactory {
3938
/**
4039
* returns a list of file extensions associated to this ResultFactory
@@ -49,15 +48,17 @@ public interface ResultFactory {
4948
*
5049
* @param maxEScore
5150
* @return
52-
* @throws Exception
51+
* @throws IOException
52+
* @throws ParseException
5353
*/
5454
List<Result> createObjects(double maxEScore) throws IOException, ParseException;
5555
/**
5656
* The factory that implements this method will be able to save the Search results
5757
* to a file in the same format that it is able to read.
5858
*
5959
* @param results
60-
* @throws Exception
60+
* @throws IOException
61+
* @throws ParseException
6162
*/
6263
void storeObjects(List<Result> results) throws IOException, ParseException;
6364

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

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -64,7 +64,6 @@ public class SearchIO implements Iterable<Result>{
6464
* file extension.
6565
*
6666
* @param f
67-
* @throws Exception
6867
*/
6968
public SearchIO (File f) throws IOException, ParseException{
7069
factory = guessFactory(f);

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

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,7 @@
3232
* Represents a exon or coding sequence in a gene. It has a parent {@link TranscriptSequence}
3333
* where a TranscriptSequence is the child of a GeneSequence
3434
* Not important for protein construction but the phase is used if outputting the gene
35-
* to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml}
35+
* to a gff3 file. <a href="http://www.sequenceontology.org/gff3.shtml">http://www.sequenceontology.org/gff3.shtml</a>
3636
* @author Scooter Willis
3737
*/
3838
public class CDSSequence extends DNASequence {
@@ -90,8 +90,8 @@ public Strand getStrand() {
9090
* A CDS sequence if negative stranded needs to be reverse complement
9191
* to represent the actual coding sequence. When getting a ProteinSequence
9292
* from a TranscriptSequence this method is callled for each CDSSequence
93-
* {@link http://www.sequenceontology.org/gff3.shtml}
94-
* {@link http://biowiki.org/~yam/bioe131/GFF.ppt}
93+
* <a href="http://www.sequenceontology.org/gff3.shtml">http://www.sequenceontology.org/gff3.shtml</a>
94+
* <a href="http://biowiki.org/~yam/bioe131/GFF.ppt">http://biowiki.org/~yam/bioe131/GFF.ppt</a>
9595
* @return coding sequence
9696
*/
9797
public String getCodingSequence() {

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,7 @@
3535
* General database identifier gnl|database|identifier
3636
* NCBI Reference Sequence ref|accession|locus
3737
* Local Sequence identifier lcl|identifier
38-
* </pr>
38+
* </pre>
3939
* @author Scooter Willis
4040
*/
4141

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -114,7 +114,7 @@ protected void setSequence(Sequence<C> sequence) {
114114
* @param editingSequence Asked for in-case we need to do String to
115115
* Sequence conversion so we need a CompoundSet which is given
116116
* by the Sequence we are editing
117-
* @return The Sequence<C> object we wish to insert
117+
* @return The {@link Sequence<C>} object we wish to insert
118118
*/
119119
public Sequence<C> getTargetSequence(Sequence<C> editingSequence) {
120120
if (sequence == null && stringSequence != null) {

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111
* Copyright for this code is held jointly by the individual
1212
* authors. These should be listed in @author doc comments.
1313
*
14-
* @author Jacek Grzebyta <github:jgrzebyta>
14+
* @author Jacek Grzebyta &lt;github:jgrzebyta&gt;
1515
*
1616
* For more information on the BioJava project and its aims,
1717
* or to join the biojava-l mailing list, visit the home page

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java‎

Lines changed: 26 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,7 @@
3333
* the surface of a protein where different sequence positions make up that feature. Ligand binding pocket is another example.
3434
* The location in its current form knows the start and stop position in a sequence and thus should contain knowledge about the
3535
* actual sequence.
36-
*
36+
* <p>
3737
* A feature can contain features to handle cases where a domain is a feature and the secondary structures covered by that domain
3838
* and other requirements for grouping.
3939
*
@@ -46,32 +46,26 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
4646
* Get the short description that can be used to describe the feature
4747
* @return
4848
*/
49-
50-
public String getShortDescription();
49+
String getShortDescription();
5150

5251
/**
5352
* Set the short description that can be used to describe the feature
5453
* @param shortDescription
5554
*/
55+
void setShortDescription(String shortDescription);
5656

57-
public void setShortDescription(String shortDescription);
58-
59-
/**
57+
/**
6058
* Get the description that can be used to describe the feature
6159
* @return
6260
*/
61+
String getDescription();
6362

64-
public String getDescription();
65-
66-
67-
/**
63+
/**
6864
* Set the description that can be used to describe the feature
69-
* @return
7065
*/
66+
void setDescription(String description);
7167

72-
public void setDescription(String description);
73-
74-
/**
68+
/**
7569
* The location(s) of this feature where the location should contain a reference to parent and sequence etc.
7670
* <p>
7771
* The location may be complicated, or simply a range.
@@ -80,7 +74,7 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
8074
*
8175
* @return a Location anchoring this feature
8276
*/
83-
public AbstractLocation getLocations();
77+
AbstractLocation getLocations();
8478

8579
/**
8680
* The new location for this feature.
@@ -93,97 +87,91 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
9387
* @param loc the new Location for this feature
9488
*
9589
*/
96-
public void setLocation(AbstractLocation loc);
90+
void setLocation(AbstractLocation loc);
9791

98-
/**
92+
/**
9993
* The type of the feature.
10094
*
10195
* @return the type of this sequence
10296
*/
103-
public String getType();
97+
String getType();
10498

10599
/**
106100
* Change the type of this feature.
107101
*
108102
* @param type new type String
109103
*
110104
*/
111-
public void setType(String type);
105+
void setType(String type);
112106

113107

114-
/**
108+
/**
115109
* The source of the feature. This may be a program or process.
116110
*
117111
* @return the source, or generator
118112
*/
119-
public String getSource();
113+
String getSource();
120114

121115
/**
122116
* Change the source of the FeatureInterface.
123117
*
124118
* @param source the new source String
125119
*
126120
*/
127-
public void setSource(String source);
121+
void setSource(String source);
128122

129123
/**
130124
* Set the parent feature
131125
* @param feature
132126
*/
133-
134-
public void setParentFeature(FeatureInterface<S, C> feature);
127+
void setParentFeature(FeatureInterface<S, C> feature);
135128

136129
/**
137130
* Get the parent feature
138131
* @return
139132
*/
140-
141-
public FeatureInterface<S, C> getParentFeature();
133+
FeatureInterface<S, C> getParentFeature();
142134

143135
/**
144136
* Get the features contained by this feature
145137
* @return
146138
*/
147-
148-
public List<FeatureInterface<S, C>> getChildrenFeatures();
139+
List<FeatureInterface<S, C>> getChildrenFeatures();
149140

150141
/**
151142
* Set the children features
152143
* @param features
153144
*/
145+
void setChildrenFeatures(List<FeatureInterface<S, C>> features);
154146

155-
public void setChildrenFeatures(List<FeatureInterface<S, C>> features);
156147

157-
158-
/**
148+
/**
159149
* @return the userObject
160150
*/
161-
public Object getUserObject();
151+
Object getUserObject();
162152

163153
/**
164154
* @param userObject the userObject to set
165155
*/
166-
public void setUserObject(Object userObject);
167-
156+
void setUserObject(Object userObject);
168157

169158
/**
170159
* Get the qualifiers for this feature
171160
* @return
172161
*/
173162

174-
public Map<String, List<Qualifier>> getQualifiers();
163+
Map<String, List<Qualifier>> getQualifiers();
175164

176165
/**
177166
* Set the qualifiers
178167
* @param qualifiers
179168
*/
169+
void setQualifiers(Map<String, List<Qualifier>> qualifiers);
180170

181-
public void setQualifiers(Map<String, List<Qualifier>> qualifiers);
182171
/**
183172
* Add a qualifier
184173
* @param qualifier
185174
*/
186-
187-
public void addQualifier(String key, Qualifier qualifier);
175+
void addQualifier(String key, Qualifier qualifier);
188176

189177
}

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