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Merge branch 'master' of github.com:biojava/biojava
* 'master' of github.com:biojava/biojava: Update readme.md Update readme.md Update readme.md Update readme.md Update readme.md Update readme.md updating project dependencies to latest version based on versioneye. updating to new versioneye location Cleanup - squid:S1858 - "toString()" should never be called on a String object Change stoichiometry check in QuatSymmetryDetector Test Lower to 0.75 (a quarter) the coverage threshold Do not include number 1 in stoichiometries Fix again the stoichiometry order reverse List Fix stoichiometries not sorted descending in Subunits Handle error with structures without protein subunits Set the default subunit clustering to STRUCTURE Normalize percentage of identity by the length without gaps biojava#521 Remove deprecated classes, follow up of biojava#520 Make use of the new methods in sequence alignments
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Lines changed: 142 additions & 1927 deletions

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‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -301,7 +301,7 @@ public List<AbstractSequence<? extends AbstractCompound>> getBioSequences(boolea
301301
private String[] splitSeqName(String sequenceName) {
302302
String[] result = new String[3];
303303

304-
String[] barSplit = sequenceName.toString().split("/");
304+
String[] barSplit = sequenceName.split("/");
305305
if (barSplit.length == 2) {
306306
result[0] = barSplit[0];
307307
String[] positions = barSplit[1].split("-");

‎biojava-core/readme.md‎

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@@ -1 +1 @@
1-
[![Dependency Status](https://www.versioneye.com/user/projects/54ce5357de7924b7ed000542/badge.svg?style=flat)](https://www.versioneye.com/user/projects/54ce5357de7924b7ed000542)
1+
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‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleSequencePair.java‎

Lines changed: 71 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -38,12 +38,14 @@
3838
*
3939
* @author Mark Chapman
4040
* @author Paolo Pavan
41-
* @param <S> each element of the alignment {@link Profile} is of type S
42-
* @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
41+
* @param <S>
42+
* each element of the alignment {@link Profile} is of type S
43+
* @param <C>
44+
* each element of an {@link AlignedSequence} is a {@link Compound}
45+
* of type C
4346
*/
44-
public class SimpleSequencePair<S extends Sequence<C>, C extends Compound> extends SimpleProfile<S, C>
45-
implements SequencePair<S, C> {
46-
47+
public class SimpleSequencePair<S extends Sequence<C>, C extends Compound>
48+
extends SimpleProfile<S, C> implements SequencePair<S, C> {
4749

4850
private static final long serialVersionUID = 1L;
4951

@@ -52,22 +54,34 @@ public class SimpleSequencePair<S extends Sequence<C>, C extends Compound> exten
5254
/**
5355
* Creates a pair profile for the given already aligned sequences.
5456
*
55-
* @param query the first sequence of the pair
56-
* @param target the second sequence of the pair
57-
* @throws IllegalArgumentException if sequences differ in size
57+
* @param query
58+
* the first sequence of the pair
59+
* @param target
60+
* the second sequence of the pair
61+
* @throws IllegalArgumentException
62+
* if sequences differ in size
5863
*/
59-
public SimpleSequencePair(AlignedSequence<S, C> query, AlignedSequence<S, C> target) {
64+
public SimpleSequencePair(AlignedSequence<S, C> query,
65+
AlignedSequence<S, C> target) {
6066
super(query, target);
6167
}
6268

6369
/**
6470
* Creates a pair profile for the given sequences with a global alignment.
6571
*
66-
* @param query the first sequence of the pair
67-
* @param target the second sequence of the pair
68-
* @param sx lists whether the query sequence aligns a {@link Compound} or gap at each index of the alignment
69-
* @param sy lists whether the target sequence aligns a {@link Compound} or gap at each index of the alignment
70-
* @throws IllegalArgumentException if alignments differ in size or given sequences do not fit in alignments
72+
* @param query
73+
* the first sequence of the pair
74+
* @param target
75+
* the second sequence of the pair
76+
* @param sx
77+
* lists whether the query sequence aligns a {@link Compound} or
78+
* gap at each index of the alignment
79+
* @param sy
80+
* lists whether the target sequence aligns a {@link Compound} or
81+
* gap at each index of the alignment
82+
* @throws IllegalArgumentException
83+
* if alignments differ in size or given sequences do not fit in
84+
* alignments
7185
*/
7286
public SimpleSequencePair(S query, S target, List<Step> sx, List<Step> sy) {
7387
this(query, target, sx, 0, 0, sy, 0, 0);
@@ -76,17 +90,34 @@ public SimpleSequencePair(S query, S target, List<Step> sx, List<Step> sy) {
7690
/**
7791
* Creates a pair profile for the given sequences with a local alignment.
7892
*
79-
* @param query the first sequence of the pair
80-
* @param target the second sequence of the pair
81-
* @param sx lists whether the query sequence aligns a {@link Compound} or gap at each index of the alignment
82-
* @param xb number of {@link Compound}s skipped in the query sequence before the aligned region
83-
* @param xa number of {@link Compound}s skipped in the query sequence after the aligned region
84-
* @param sy lists whether the target sequence aligns a {@link Compound} or gap at each index of the alignment
85-
* @param yb number of {@link Compound}s skipped in the target sequence before the aligned region
86-
* @param ya number of {@link Compound}s skipped in the target sequence after the aligned region
87-
* @throws IllegalArgumentException if alignments differ in size or given sequences do not fit in alignments
93+
* @param query
94+
* the first sequence of the pair
95+
* @param target
96+
* the second sequence of the pair
97+
* @param sx
98+
* lists whether the query sequence aligns a {@link Compound} or
99+
* gap at each index of the alignment
100+
* @param xb
101+
* number of {@link Compound}s skipped in the query sequence
102+
* before the aligned region
103+
* @param xa
104+
* number of {@link Compound}s skipped in the query sequence
105+
* after the aligned region
106+
* @param sy
107+
* lists whether the target sequence aligns a {@link Compound} or
108+
* gap at each index of the alignment
109+
* @param yb
110+
* number of {@link Compound}s skipped in the target sequence
111+
* before the aligned region
112+
* @param ya
113+
* number of {@link Compound}s skipped in the target sequence
114+
* after the aligned region
115+
* @throws IllegalArgumentException
116+
* if alignments differ in size or given sequences do not fit in
117+
* alignments
88118
*/
89-
public SimpleSequencePair(S query, S target, List<Step> sx, int xb, int xa, List<Step> sy, int yb, int ya) {
119+
public SimpleSequencePair(S query, S target, List<Step> sx, int xb, int xa,
120+
List<Step> sy, int yb, int ya) {
90121
super(query, target, sx, xb, xa, sy, yb, ya);
91122
}
92123

@@ -107,7 +138,8 @@ public int getIndexInQueryAt(int alignmentIndex) {
107138

108139
@Override
109140
public int getIndexInQueryForTargetAt(int targetIndex) {
110-
return getAlignedSequence(1).getSequenceIndexAt(getAlignedSequence(2).getAlignmentIndexAt(targetIndex));
141+
return getAlignedSequence(1).getSequenceIndexAt(
142+
getAlignedSequence(2).getAlignmentIndexAt(targetIndex));
111143
}
112144

113145
@Override
@@ -117,15 +149,17 @@ public int getIndexInTargetAt(int alignmentIndex) {
117149

118150
@Override
119151
public int getIndexInTargetForQueryAt(int queryIndex) {
120-
return getAlignedSequence(2).getSequenceIndexAt(getAlignedSequence(1).getAlignmentIndexAt(queryIndex));
152+
return getAlignedSequence(2).getSequenceIndexAt(
153+
getAlignedSequence(1).getAlignmentIndexAt(queryIndex));
121154
}
122155

123156
@Override
124157
public int getNumIdenticals() {
125158
if (identicals == -1) {
126159
identicals = 0;
127160
for (int i = 1; i <= getLength(); i++) {
128-
if (getCompoundInQueryAt(i).equalsIgnoreCase(getCompoundInTargetAt(i))) {
161+
if (getCompoundInQueryAt(i).equalsIgnoreCase(
162+
getCompoundInTargetAt(i))) {
129163
identicals++;
130164
}
131165
}
@@ -144,13 +178,15 @@ public int getNumSimilars() {
144178
C c1 = getCompoundInQueryAt(i);
145179
C c2 = getCompoundInTargetAt(i);
146180

147-
if ( c1 instanceof AminoAcidCompound && c2 instanceof AminoAcidCompound) {
148-
short value = matrix.getValue((AminoAcidCompound)c1, (AminoAcidCompound)c2);
149-
if ( value > 0)
181+
if (c1 instanceof AminoAcidCompound
182+
&& c2 instanceof AminoAcidCompound) {
183+
short value = matrix.getValue((AminoAcidCompound) c1,
184+
(AminoAcidCompound) c2);
185+
if (value > 0)
150186
similars++;
151187
} else {
152188

153-
if (getCompoundSet().compoundsEquivalent(c1,c2)) {
189+
if (getCompoundSet().compoundsEquivalent(c1, c2)) {
154190
similars++;
155191
}
156192
}
@@ -174,7 +210,10 @@ public AlignedSequence<S, C> getTarget() {
174210
@Override
175211
public double getPercentageOfIdentity() {
176212
double seqid = getNumIdenticals();
177-
return seqid / getLength();
213+
double length = getLength()
214+
- getAlignedSequence(1).getNumGapPositions()
215+
- getAlignedSequence(2).getNumGapPositions();
216+
return seqid / length;
178217
}
179218

180219
}

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

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -99,7 +99,8 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
9999

100100
/**
101101
* Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
102-
* This is equivalent to {@link #getNumIdenticals()} / {@link #getLength()}.
102+
* This is equivalent to {@link #getNumIdenticals()} / {@link #getLength()}. Gap positions are exluded
103+
* from the calculation.
103104
*
104105
* @return the percentage of sequence identity as a fraction in [0,1]
105106
*/

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -181,7 +181,7 @@ public ArrayList<ProteinSequence> getProteinCDSSequences() {
181181

182182
DNASequence dnaCodingSequence = null;
183183
try {
184-
dnaCodingSequence = new DNASequence(codingSequence.toString().toUpperCase());
184+
dnaCodingSequence = new DNASequence(codingSequence.toUpperCase());
185185
} catch (CompoundNotFoundException e) {
186186
// if I understand this should not happen, please correct if I'm wrong - JD 2014-10-24
187187
logger.error("Could not create DNA coding sequence, {}. This is most likely a bug.", e.getMessage());

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -126,6 +126,6 @@ public boolean equalsIgnoreCase(Compound compound) {
126126
return false;
127127
}
128128
AbstractCompound them = (AbstractCompound) compound;
129-
return this.base.toString().equalsIgnoreCase(them.base.toString());
129+
return this.base.equalsIgnoreCase(them.base);
130130
}
131131
}

‎biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleSequencePairTest.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -250,8 +250,8 @@ public void testGetNumIdenticals() {
250250

251251
@Test
252252
public void testGetPercentageOfIdentity() {
253-
assertEquals(global.getPercentageOfIdentity(), 0.4, 0.01);
254-
assertEquals(local.getPercentageOfIdentity(), 0.66, 0.01);
253+
assertEquals(global.getPercentageOfIdentity(), 1.0, 0.01);
254+
assertEquals(local.getPercentageOfIdentity(), 1.0, 0.01);
255255
}
256256

257257
@Test

‎biojava-genome/readme.md‎

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‎biojava-phylo/readme.md‎

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‎biojava-protein-disorder/readme.md‎

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