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Javadoc fix: html escaping
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10 files changed

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‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java‎

Lines changed: 16 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -78,127 +78,127 @@ public static SubstitutionMatrix<AminoAcidCompound> getIdentity() {
7878
}
7979

8080
/**
81-
* Returns Blosum 100 matrix by Henikoff & Henikoff
81+
* Returns Blosum 100 matrix by Henikoff &amp; Henikoff
8282
* @return Blosum 100 matrix
8383
*/
8484
public static SubstitutionMatrix<AminoAcidCompound> getBlosum100() {
8585
return getAminoAcidMatrix("blosum100");
8686
}
8787

8888
/**
89-
* Returns Blosum 30 matrix by Henikoff & Henikoff
89+
* Returns Blosum 30 matrix by Henikoff &amp; Henikoff
9090
* @return Blosum 30 matrix
9191
*/
9292
public static SubstitutionMatrix<AminoAcidCompound> getBlosum30() {
9393
return getAminoAcidMatrix("blosum30");
9494
}
9595

9696
/**
97-
* Returns Blosum 35 matrix by Henikoff & Henikoff
97+
* Returns Blosum 35 matrix by Henikoff &amp; Henikoff
9898
* @return Blosum 35 matrix
9999
*/
100100
public static SubstitutionMatrix<AminoAcidCompound> getBlosum35() {
101101
return getAminoAcidMatrix("blosum35");
102102
}
103103

104104
/**
105-
* Returns Blosum 40 matrix by Henikoff & Henikoff
105+
* Returns Blosum 40 matrix by Henikoff &amp; Henikoff
106106
* @return Blosum 40 matrix
107107
*/
108108
public static SubstitutionMatrix<AminoAcidCompound> getBlosum40() {
109109
return getAminoAcidMatrix("blosum40");
110110
}
111111

112112
/**
113-
* Returns Blosum 45 matrix by Henikoff & Henikoff
113+
* Returns Blosum 45 matrix by Henikoff &amp; Henikoff
114114
* @return Blosum 45 matrix
115115
*/
116116
public static SubstitutionMatrix<AminoAcidCompound> getBlosum45() {
117117
return getAminoAcidMatrix("blosum45");
118118
}
119119

120120
/**
121-
* Returns Blosum 50 matrix by Henikoff & Henikoff
121+
* Returns Blosum 50 matrix by Henikoff &amp; Henikoff
122122
* @return Blosum 50 matrix
123123
*/
124124
public static SubstitutionMatrix<AminoAcidCompound> getBlosum50() {
125125
return getAminoAcidMatrix("blosum50");
126126
}
127127

128128
/**
129-
* Returns Blosum 55 matrix by Henikoff & Henikoff
129+
* Returns Blosum 55 matrix by Henikoff &amp; Henikoff
130130
* @return Blosum 55 matrix
131131
*/
132132
public static SubstitutionMatrix<AminoAcidCompound> getBlosum55() {
133133
return getAminoAcidMatrix("blosum55");
134134
}
135135

136136
/**
137-
* Returns Blosum 60 matrix by Henikoff & Henikoff
137+
* Returns Blosum 60 matrix by Henikoff &amp; Henikoff
138138
* @return Blosum 60 matrix
139139
*/
140140
public static SubstitutionMatrix<AminoAcidCompound> getBlosum60() {
141141
return getAminoAcidMatrix("blosum60");
142142
}
143143

144144
/**
145-
* Returns Blosum 62 matrix by Henikoff & Henikoff
145+
* Returns Blosum 62 matrix by Henikoff &amp; Henikoff
146146
* @return Blosum 62 matrix
147147
*/
148148
public static SubstitutionMatrix<AminoAcidCompound> getBlosum62() {
149149
return getAminoAcidMatrix("blosum62");
150150
}
151151

152152
/**
153-
* Returns Blosum 65 matrix by Henikoff & Henikoff
153+
* Returns Blosum 65 matrix by Henikoff &amp; Henikoff
154154
* @return Blosum 65 matrix
155155
*/
156156
public static SubstitutionMatrix<AminoAcidCompound> getBlosum65() {
157157
return getAminoAcidMatrix("blosum65");
158158
}
159159

160160
/**
161-
* Returns Blosum 70 matrix by Henikoff & Henikoff
161+
* Returns Blosum 70 matrix by Henikoff &amp; Henikoff
162162
* @return Blosum 70 matrix
163163
*/
164164
public static SubstitutionMatrix<AminoAcidCompound> getBlosum70() {
165165
return getAminoAcidMatrix("blosum70");
166166
}
167167

168168
/**
169-
* Returns Blosum 75 matrix by Henikoff & Henikoff
169+
* Returns Blosum 75 matrix by Henikoff &amp; Henikoff
170170
* @return Blosum 75 matrix
171171
*/
172172
public static SubstitutionMatrix<AminoAcidCompound> getBlosum75() {
173173
return getAminoAcidMatrix("blosum75");
174174
}
175175

176176
/**
177-
* Returns Blosum 80 matrix by Henikoff & Henikoff
177+
* Returns Blosum 80 matrix by Henikoff &amp; Henikoff
178178
* @return Blosum 80 matrix
179179
*/
180180
public static SubstitutionMatrix<AminoAcidCompound> getBlosum80() {
181181
return getAminoAcidMatrix("blosum80");
182182
}
183183

184184
/**
185-
* Returns Blosum 85 matrix by Henikoff & Henikoff
185+
* Returns Blosum 85 matrix by Henikoff &amp; Henikoff
186186
* @return Blosum 85 matrix
187187
*/
188188
public static SubstitutionMatrix<AminoAcidCompound> getBlosum85() {
189189
return getAminoAcidMatrix("blosum85");
190190
}
191191

192192
/**
193-
* Returns Blosum 90 matrix by Henikoff & Henikoff
193+
* Returns Blosum 90 matrix by Henikoff &amp; Henikoff
194194
* @return Blosum 90 matrix
195195
*/
196196
public static SubstitutionMatrix<AminoAcidCompound> getBlosum90() {
197197
return getAminoAcidMatrix("blosum90");
198198
}
199199

200200
/**
201-
* Returns PAM 250 matrix by Gonnet, Cohen & Benner
201+
* Returns PAM 250 matrix by Gonnet, Cohen &amp; Benner
202202
* @return Gonnet 250 matrix
203203
*/
204204
public static SubstitutionMatrix<AminoAcidCompound> getGonnet250() {

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

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -58,7 +58,7 @@ enum StringFormat {
5858
*
5959
* @param listIndex index of sequence in profile
6060
* @return desired sequence
61-
* @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences
61+
* @throws IndexOutOfBoundsException if listIndex &lt; 1 or listIndex &gt; number of sequences
6262
*/
6363
AlignedSequence<S, C> getAlignedSequence(int listIndex);
6464

@@ -101,8 +101,8 @@ enum StringFormat {
101101
* @param listIndex index of sequence in profile
102102
* @param alignmentIndex column index within an alignment
103103
* @return the sequence element
104-
* @throws IndexOutOfBoundsException if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or
105-
* alignmentIndex > {@link #getLength()}
104+
* @throws IndexOutOfBoundsException if listIndex &lt; 1, listIndex &gt; number of sequences, alignmentIndex &lt; 1, or
105+
* alignmentIndex &gt; {@link #getLength()}
106106
*/
107107
C getCompoundAt(int listIndex, int alignmentIndex);
108108

@@ -113,7 +113,7 @@ enum StringFormat {
113113
* @param sequence either an {@link AlignedSequence} or an original {@link Sequence}
114114
* @param alignmentIndex column index within an alignment
115115
* @return the sequence element
116-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
116+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
117117
*/
118118
C getCompoundAt(S sequence, int alignmentIndex);
119119

@@ -122,7 +122,7 @@ enum StringFormat {
122122
*
123123
* @param alignmentIndex column index within an alignment
124124
* @return list of counts
125-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
125+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
126126
*/
127127
int[] getCompoundCountsAt(int alignmentIndex);
128128

@@ -132,7 +132,7 @@ enum StringFormat {
132132
* @param alignmentIndex column index within an alignment
133133
* @param compounds list of compounds to count
134134
* @return corresponding list of counts
135-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
135+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
136136
*/
137137
int[] getCompoundCountsAt(int alignmentIndex, List<C> compounds);
138138

@@ -141,7 +141,7 @@ enum StringFormat {
141141
*
142142
* @param alignmentIndex column index within an alignment
143143
* @return the sequence elements
144-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
144+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
145145
*/
146146
List<C> getCompoundsAt(int alignmentIndex);
147147

@@ -157,7 +157,7 @@ enum StringFormat {
157157
*
158158
* @param alignmentIndex column index within an alignment
159159
* @return list of fractional weights
160-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
160+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
161161
*/
162162
float[] getCompoundWeightsAt(int alignmentIndex);
163163

@@ -167,7 +167,7 @@ enum StringFormat {
167167
* @param alignmentIndex column index within an alignment
168168
* @param compounds list of compounds to count
169169
* @return corresponding list of fractional weights
170-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
170+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
171171
*/
172172
float[] getCompoundWeightsAt(int alignmentIndex, List<C> compounds);
173173

@@ -177,7 +177,7 @@ enum StringFormat {
177177
*
178178
* @param alignmentIndex column index within an alignment
179179
* @return the sequence indices
180-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
180+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
181181
*/
182182
int[] getIndicesAt(int alignmentIndex);
183183

@@ -236,7 +236,7 @@ enum StringFormat {
236236
*
237237
* @param alignmentIndex column index within an alignment
238238
* @return true if any {@link AlignedSequence} has a gap at the given index
239-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
239+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
240240
*/
241241
boolean hasGap(int alignmentIndex);
242242

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

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
4141
*
4242
* @param alignmentIndex column index in alignment
4343
* @return the query sequence element
44-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
44+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
4545
*/
4646
C getCompoundInQueryAt(int alignmentIndex);
4747

@@ -50,7 +50,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
5050
*
5151
* @param alignmentIndex column index in alignment
5252
* @return the target sequence element
53-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
53+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
5454
*/
5555
C getCompoundInTargetAt(int alignmentIndex);
5656

@@ -59,7 +59,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
5959
*
6060
* @param alignmentIndex column index in alignment
6161
* @return index in query {@link Sequence}
62-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
62+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
6363
*/
6464
int getIndexInQueryAt(int alignmentIndex);
6565

@@ -68,7 +68,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
6868
*
6969
* @param targetIndex index in target {@link Sequence}
7070
* @return index in query {@link Sequence}
71-
* @throws IndexOutOfBoundsException if targetIndex < 1 or targetIndex > {@link #getTarget()}.getLength()
71+
* @throws IndexOutOfBoundsException if targetIndex &lt; 1 or targetIndex &gt; {@link #getTarget()}.getLength()
7272
*/
7373
int getIndexInQueryForTargetAt(int targetIndex);
7474

@@ -77,7 +77,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
7777
*
7878
* @param alignmentIndex column index in alignment
7979
* @return index in target {@link Sequence}
80-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
80+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
8181
*/
8282
int getIndexInTargetAt(int alignmentIndex);
8383

@@ -86,7 +86,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
8686
*
8787
* @param queryIndex index in query {@link Sequence}
8888
* @return index in target {@link Sequence}
89-
* @throws IndexOutOfBoundsException if queryIndex < 1 or queryIndex > {@link #getQuery()}.getLength()
89+
* @throws IndexOutOfBoundsException if queryIndex &lt; 1 or queryIndex &gt; {@link #getQuery()}.getLength()
9090
*/
9191
int getIndexInTargetForQueryAt(int queryIndex);
9292

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -103,7 +103,7 @@ public interface SubstitutionMatrix<C extends Compound> {
103103
* Rescales the matrix so that to {@link #getMaxValue()} - {@link #getMinValue()} = scale.
104104
*
105105
* @param scale new normalization scale of this matrix
106-
* @throws IllegalArgumentException if scale < 1
106+
* @throws IllegalArgumentException if scale &lt; 1
107107
*/
108108
SubstitutionMatrix<C> normalizeMatrix(short scale);
109109

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -307,7 +307,7 @@ public static Strand detectStrand(List<Location> subLocations) {
307307
}
308308

309309
/**
310-
* Assumes that the first element is the start & clones it
310+
* Assumes that the first element is the start &amp; clones it
311311
*/
312312
public static Point detectStart(List<Location> subLocations) {
313313
return subLocations.get(0).getStart().clonePoint();

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -56,7 +56,7 @@ public class JoiningSequenceReader<C extends Compound> implements ProxySequenceR
5656
private int[] minSequenceIndex;
5757

5858
/**
59-
* Allows creation of the store from Vargs Sequence<C> objects. CompoundSet
59+
* Allows creation of the store from Vargs {@link Sequence<C>} objects. CompoundSet
6060
* defaults to the first element of the array (assuming there are elements
6161
* available during construction otherwise we will throw an illegal
6262
* state exception).
@@ -66,7 +66,7 @@ public JoiningSequenceReader(Sequence<C>... sequences) {
6666
}
6767

6868
/**
69-
* Allows creation of the store from List<Sequence<C>>. CompoundSet
69+
* Allows creation of the store from {@link List<Sequence<C>>}. CompoundSet
7070
* defaults to the first element of the List (assuming there are elements
7171
* available during construction otherwise we will throw an illegal
7272
* state exception).
@@ -217,7 +217,7 @@ else if (midMinPosition > position && midMaxPosition > position) {
217217

218218
/**
219219
* Iterator implementation which attempts to move through the 2D structure
220-
* attempting to skip onto the next sequence as & when it is asked to
220+
* attempting to skip onto the next sequence as &amp; when it is asked to
221221
*/
222222

223223
@Override

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -52,7 +52,7 @@ enum StringFormat {
5252
*
5353
* @param listIndex index of sequence in profile
5454
* @return desired sequence
55-
* @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences
55+
* @throws IndexOutOfBoundsException if listIndex &lt; 1 or listIndex &gt; number of sequences
5656
*/
5757
S getAlignedSequence(int listIndex);
5858

@@ -68,7 +68,7 @@ enum StringFormat {
6868
*
6969
* @param alignmentIndex column index within an alignment
7070
* @return the sequence elements
71-
* @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
71+
* @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
7272
*/
7373
List<C> getCompoundsAt(int alignmentIndex);
7474

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -285,7 +285,7 @@ public static <C extends Compound> List<SequenceView<C>> nonOverlappingKmers(Seq
285285

286286
/**
287287
* Used to generate overlapping k-mers such i.e. ATGTA will give rise to
288-
* ATG, TGT & GTA
288+
* ATG, TGT &amp; GTA
289289
*
290290
* @param <C> Compound to use
291291
* @param sequence Sequence to build from
@@ -343,7 +343,7 @@ public static <C extends Compound> SequenceView<C> inverse(Sequence<C> sequence)
343343
/**
344344
* A case-insensitive manner of comparing two sequence objects together.
345345
* We will throw out any compounds which fail to match on their sequence
346-
* length & compound sets used. The code will also bail out the moment
346+
* length &amp; compound sets used. The code will also bail out the moment
347347
* we find something is wrong with a Sequence. Cost to run is linear to
348348
* the length of the Sequence.
349349
*
@@ -359,7 +359,7 @@ public static <C extends Compound> boolean sequenceEqualityIgnoreCase(Sequence<C
359359
/**
360360
* A case-sensitive manner of comparing two sequence objects together.
361361
* We will throw out any compounds which fail to match on their sequence
362-
* length & compound sets used. The code will also bail out the moment
362+
* length &amp; compound sets used. The code will also bail out the moment
363363
* we find something is wrong with a Sequence. Cost to run is linear to
364364
* the length of the Sequence.
365365
*

‎biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -350,7 +350,7 @@ public static URLConnection prepareURLConnection(String url, int timeout) throws
350350
}
351351

352352
/**
353-
* Recursively delete a folder & contents
353+
* Recursively delete a folder &amp; contents
354354
*
355355
* @param dir directory to delete
356356
*/
@@ -375,7 +375,7 @@ public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOExce
375375
});
376376
}
377377
/**
378-
* Recursively delete a folder & contents
378+
* Recursively delete a folder &amp; contents
379379
*
380380
* @param dir directory to delete
381381
*/

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