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lafitalafita
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Fix compilation errors and tests for QuatSymmetry 1
1 parent 69cf5eb commit 1768642

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21 files changed

+211
-123
lines changed

21 files changed

+211
-123
lines changed

‎biojava-structure-gui/src/main/java/demo/DemoQuatSymmetryJmol.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -92,10 +92,10 @@ public static void main(String[] args) throws IOException,
9292
private static void showResults(Structure s, String name,
9393
QuatSymmetryResults results) {
9494

95-
String title = name + ": " + results.getSubunits().getStoichiometry()
95+
String title = name + ": " + results.getStoichiometry()
9696
+ ", " + results.getSymmetry();
9797

98-
if (results.getSubunits().isPseudoSymmetric())
98+
if (results.isPseudosymmetric())
9999
title += ", pseudosymmetric";
100100

101101
if (results.isLocal())

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@
2424
package org.biojava.nbio.structure.symmetry.jmolScript;
2525

2626
import org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner;
27-
import org.biojava.nbio.structure.symmetry.core.Subunits;
27+
import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
2828
import org.jcolorbrewer.ColorBrewer;
2929

3030
import javax.vecmath.*;
@@ -401,7 +401,7 @@ public String playOrientations() {
401401
*/
402402
@Override
403403
public String colorBySubunit() {
404-
Subunits subunits = helixAxisAligner.getSubunits();
404+
QuatSymmetrySubunits subunits = helixAxisAligner.getSubunits();
405405
List<Integer> modelNumbers = subunits.getModelNumbers();
406406
List<String> chainIds = subunits.getChainIds();
407407
List<List<Integer>> orbits = helixAxisAligner.getOrbits();
@@ -440,7 +440,7 @@ public String colorBySubunit() {
440440
*/
441441
@Override
442442
public String colorBySequenceCluster() {
443-
Subunits subunits = helixAxisAligner.getSubunits();
443+
QuatSymmetrySubunits subunits = helixAxisAligner.getSubunits();
444444
int n = subunits.getSubunitCount();
445445
List<Integer> modelNumbers = subunits.getModelNumbers();
446446
List<String> chainIds = subunits.getChainIds();
@@ -475,7 +475,7 @@ public String colorBySequenceCluster() {
475475
public String colorBySymmetry() {
476476
List<List<Integer>> units = helixAxisAligner.getHelixLayers().getByLargestContacts().getLayerLines();
477477
units = orientLayerLines(units);
478-
Subunits subunits = helixAxisAligner.getSubunits();
478+
QuatSymmetrySubunits subunits = helixAxisAligner.getSubunits();
479479
List<Integer> modelNumbers = subunits.getModelNumbers();
480480
List<String> chainIds = subunits.getChainIds();
481481
List<Integer> clusterIds = subunits.getSequenceClusterIds();

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@
2626
import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
2727
import org.biojava.nbio.structure.symmetry.core.Rotation;
2828
import org.biojava.nbio.structure.symmetry.core.RotationGroup;
29-
import org.biojava.nbio.structure.symmetry.core.Subunits;
29+
import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
3030
import org.biojava.nbio.structure.symmetry.geometry.Polyhedron;
3131
import org.jcolorbrewer.ColorBrewer;
3232

@@ -292,7 +292,7 @@ public String playOrientations() {
292292
*/
293293
@Override
294294
public String colorBySubunit() {
295-
Subunits subunits = rotationAxisAligner.getSubunits();
295+
QuatSymmetrySubunits subunits = rotationAxisAligner.getSubunits();
296296
List<Integer> modelNumbers = subunits.getModelNumbers();
297297
List<String> chainIds = subunits.getChainIds();
298298
List<List<Integer>> orbits = rotationAxisAligner.getOrbits();
@@ -348,11 +348,11 @@ public String colorBySubunit() {
348348
*/
349349
@Override
350350
public String colorBySequenceCluster() {
351-
Subunits subunits = rotationAxisAligner.getSubunits();
351+
QuatSymmetrySubunits subunits = rotationAxisAligner.getSubunits();
352352
int n = subunits.getSubunitCount();
353353
List<Integer> modelNumbers = subunits.getModelNumbers();
354354
List<String> chainIds = subunits.getChainIds();
355-
List<Integer> seqClusterIds = subunits.getSequenceClusterIds();
355+
List<Integer> seqClusterIds = subunits.getClusterIds();
356356
int clusters = Collections.max(seqClusterIds) + 1;
357357
Color[] col = ColorBrewer.BrBG.getColorPalette(clusters);
358358
Color4f[] colors = ColorConverter.convertColor4f(col);
@@ -380,7 +380,7 @@ public String colorBySequenceCluster() {
380380
public String colorBySymmetry() {
381381
// TODO needs some refactoring
382382
String pointGroup = rotationGroup.getPointGroup();
383-
Subunits subunits = rotationAxisAligner.getSubunits();
383+
QuatSymmetrySubunits subunits = rotationAxisAligner.getSubunits();
384384
List<Integer> modelNumbers = subunits.getModelNumbers();
385385
List<String> chainIds = subunits.getChainIds();
386386
List<List<Integer>> orbits = rotationAxisAligner.getOrbits();
@@ -524,7 +524,7 @@ private String getChainSpecification(List<Integer> modelNumbers, List<String> ch
524524
}
525525

526526
private Map<Color4f, List<String>> getCnColorMap() {
527-
Subunits subunits = rotationAxisAligner.getSubunits();
527+
QuatSymmetrySubunits subunits = rotationAxisAligner.getSubunits();
528528
List<Integer> modelNumbers = subunits.getModelNumbers();
529529
List<String> chainIds = subunits.getChainIds();
530530
List<List<Integer>> orbits = rotationAxisAligner.getOrbits();

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlign.java‎

Lines changed: 9 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -48,8 +48,15 @@ public class QsAlign {
4848
public static QsAlignResult align(Structure s1, Structure s2,
4949
SubunitClustererParameters cParams, QsAlignParameters aParams)
5050
throws StructureException {
51-
return align(SubunitExtractor.extractSubunits(s1, cParams),
52-
SubunitExtractor.extractSubunits(s2, cParams), cParams, aParams);
51+
return align(
52+
SubunitExtractor.extractSubunits(s1,
53+
cParams.getAbsoluteMinimumSequenceLength(),
54+
cParams.getMinimumSequenceLengthFraction(),
55+
cParams.getMinimumSequenceLength()),
56+
SubunitExtractor.extractSubunits(s2,
57+
cParams.getAbsoluteMinimumSequenceLength(),
58+
cParams.getMinimumSequenceLengthFraction(),
59+
cParams.getMinimumSequenceLength()), cParams, aParams);
5360
}
5461

5562
public static QsAlignResult align(List<Subunit> s1, List<Subunit> s2,

‎biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@
4343
import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
4444
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
4545
import org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer;
46-
import org.biojava.nbio.structure.symmetry.core.Subunits;
46+
import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
4747
import org.biojava.nbio.structure.symmetry.internal.CESymmParameters;
4848
import org.biojava.nbio.structure.symmetry.internal.CeSymm;
4949
import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
@@ -54,7 +54,7 @@
5454
import java.util.stream.Collectors;
5555

5656
/**
57-
* A SubunitCluster contains a set of equivalent {@link Subunits}, the set of
57+
* A SubunitCluster contains a set of equivalent {@link QuatSymmetrySubunits}, the set of
5858
* equivalent residues (EQR) between {@link Subunit} and a {@link Subunit}
5959
* representative. It also stores the method used for clustering.
6060
* <p>

‎biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -49,7 +49,9 @@ private SubunitClusterer() {
4949
public static List<SubunitCluster> cluster(Structure structure,
5050
SubunitClustererParameters params) {
5151
List<Subunit> subunits = SubunitExtractor.extractSubunits(structure,
52-
params);
52+
params.getAbsoluteMinimumSequenceLength(),
53+
params.getMinimumSequenceLengthFraction(),
54+
params.getMinimumSequenceLength());
5355
return cluster(subunits, params);
5456
}
5557

@@ -124,7 +126,7 @@ public static List<SubunitCluster> cluster(List<Subunit> subunits,
124126
e.getMessage());
125127
}
126128
}
127-
129+
128130
// After internal symmetry merge again by structural similarity
129131
// Use case: C8 propeller with 3 chains with 3+3+2 repeats each
130132
for (int c1 = 0; c1 < clusters.size(); c1++) {
@@ -140,7 +142,6 @@ public static List<SubunitCluster> cluster(List<Subunit> subunits,
140142
}
141143
}
142144
}
143-
144145

145146
return clusters;
146147
}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/AxisAligner.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@
2626
import javax.vecmath.Vector3d;
2727

2828
import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
29-
import org.biojava.nbio.structure.symmetry.core.Subunits;
29+
import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
3030

3131
import java.util.List;
3232

@@ -87,7 +87,7 @@ public static AxisAligner getInstance(QuatSymmetryResults results) {
8787

8888
public abstract Point3d getCentroid();
8989

90-
public abstract Subunits getSubunits();
90+
public abstract QuatSymmetrySubunits getSubunits();
9191

9292
public abstract List<List<Integer>> getOrbits();
9393

‎biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,7 @@
2323
import org.biojava.nbio.structure.symmetry.core.Helix;
2424
import org.biojava.nbio.structure.symmetry.core.HelixLayers;
2525
import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
26-
import org.biojava.nbio.structure.symmetry.core.Subunits;
26+
import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
2727
import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
2828
import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
2929

@@ -35,7 +35,7 @@ public class HelixAxisAligner extends AxisAligner {
3535
private static final Vector3d Y_AXIS = new Vector3d(0,1,0);
3636
private static final Vector3d Z_AXIS = new Vector3d(0,0,1);
3737

38-
private Subunits subunits = null;
38+
private QuatSymmetrySubunits subunits = null;
3939
private HelixLayers helixLayers = null;
4040

4141
private Matrix4d transformationMatrix = new Matrix4d();
@@ -201,7 +201,7 @@ public Point3d getCentroid() {
201201
* @see org.biojava.nbio.structure.quaternary.core.AxisAligner#getSubunits()
202202
*/
203203
@Override
204-
public Subunits getSubunits() {
204+
public QuatSymmetrySubunits getSubunits() {
205205
return subunits;
206206
}
207207

‎biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,7 @@
2323
import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
2424
import org.biojava.nbio.structure.symmetry.core.Rotation;
2525
import org.biojava.nbio.structure.symmetry.core.RotationGroup;
26-
import org.biojava.nbio.structure.symmetry.core.Subunits;
26+
import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;
2727
import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
2828
import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
2929

@@ -36,7 +36,7 @@ public class RotationAxisAligner extends AxisAligner{
3636
private static final Vector3d Y_AXIS = new Vector3d(0,1,0);
3737
private static final Vector3d Z_AXIS = new Vector3d(0,0,1);
3838

39-
private Subunits subunits = null;
39+
private QuatSymmetrySubunits subunits = null;
4040
private RotationGroup rotationGroup = null;
4141

4242
private Matrix4d transformationMatrix = new Matrix4d();
@@ -53,7 +53,7 @@ public class RotationAxisAligner extends AxisAligner{
5353
boolean modified = true;
5454

5555
public RotationAxisAligner(QuatSymmetryResults results) {
56-
this.subunits = results.getSubunits();
56+
this.subunits = new QuatSymmetrySubunits(results.getSubunitClusters());
5757
this.rotationGroup = results.getRotationGroup();
5858

5959
if (subunits == null) {
@@ -181,7 +181,7 @@ public Point3d getCentroid() {
181181
}
182182

183183
@Override
184-
public Subunits getSubunits() {
184+
public QuatSymmetrySubunits getSubunits() {
185185
return subunits;
186186
}
187187

‎biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -37,15 +37,15 @@
3737
* @author Peter
3838
*/
3939
public class C2RotationSolver implements QuatSymmetrySolver {
40-
private Subunits subunits = null;
40+
private QuatSymmetrySubunits subunits = null;
4141
private QuatSymmetryParameters parameters = null;
4242
private Vector3d centroid = new Vector3d();
4343
private Matrix4d centroidInverse = new Matrix4d();
4444

4545
private RotationGroup rotations = new RotationGroup();
4646

4747

48-
public C2RotationSolver(Subunits subunits, QuatSymmetryParameters parameters) {
48+
public C2RotationSolver(QuatSymmetrySubunits subunits, QuatSymmetryParameters parameters) {
4949
if (subunits.getSubunitCount() != 2) {
5050
throw new IllegalArgumentException("C2RotationSolver can only be applied to cases with 2 centers");
5151
}

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