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lafitalafita
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Fix bug in MultipleAlignmentEnsemble, now Atoms are not cloned
1 parent 1abd6cf commit 83a9f87

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+38
-43
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1 file changed

+38
-43
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‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java‎

Lines changed: 38 additions & 43 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,6 @@
1111
import org.biojava.nbio.structure.Atom;
1212
import org.biojava.nbio.structure.Calc;
1313
import org.biojava.nbio.structure.StructureException;
14-
import org.biojava.nbio.structure.StructureTools;
1514
import org.biojava.nbio.structure.align.helper.AlignTools;
1615
import org.biojava.nbio.structure.align.model.AFPChain;
1716
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
@@ -26,41 +25,41 @@
2625
*
2726
*/
2827
public class MultipleAlignmentEnsembleImpl extends AbstractScoresCache
29-
implements MultipleAlignmentEnsemble, Serializable, Cloneable {
28+
implements MultipleAlignmentEnsemble, Serializable, Cloneable {
3029

3130
private static final long serialVersionUID = -5732485866623431898L;
32-
31+
3332
//Creation Properties
3433
private String algorithmName;
3534
private String version;
3635
private Long ioTime;
3736
private Long calculationTime;
38-
37+
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//Structure Identifiers
4039
private List<String> structureNames;
4140
private List<Atom[]> atomArrays;
4241
private List<Matrix> distanceMatrix;
43-
42+
4443
private List<MultipleAlignment> multipleAlignments;
45-
44+
4645
/**
4746
* Default Constructor. Empty ensemble, no structures assigned.
4847
*
4948
* @return MultipleAlignmentEnsemble an empty ensemble instance.
5049
*/
5150
public MultipleAlignmentEnsembleImpl(){
52-
51+
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algorithmName = null;
5453
version = null;
5554
ioTime = null;
5655
calculationTime = null;
57-
56+
5857
structureNames = null;
5958
atomArrays = null;
6059
distanceMatrix = null;
6160
multipleAlignments = null;
6261
}
63-
62+
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/**
6564
* Constructor using structure identifiers.
6665
*
@@ -72,7 +71,7 @@ public MultipleAlignmentEnsembleImpl(List<String> structureNames){
7271
this();
7372
setStructureNames(structureNames);
7473
}
75-
74+
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/**
7776
* Copy constructor. This copies recursively all member variables,
7877
* including MultipleAlignments, Atom arrays and cached variables.
@@ -81,23 +80,13 @@ public MultipleAlignmentEnsembleImpl(List<String> structureNames){
8180
* @return MultipleAlignmentEnsemble identical copy of the input ensemble.
8281
*/
8382
public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e){
84-
83+
8584
super(e); //Copy the scores
8685
algorithmName = e.algorithmName;
8786
version = e.version;
8887
ioTime = e.ioTime;
8988
calculationTime = e.calculationTime;
90-
91-
atomArrays = null;
92-
if (e.atomArrays != null){
93-
//Make a deep copy of everything
94-
atomArrays = new ArrayList<Atom[]>();
95-
for (Atom[] array:e.atomArrays){
96-
Atom[] newArray = StructureTools.cloneAtomArray(array);
97-
atomArrays.add(newArray);
98-
}
99-
}
100-
89+
10190
distanceMatrix = null;
10291
if (e.distanceMatrix!=null){
10392
//Make a deep copy of everything
@@ -106,7 +95,7 @@ public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e){
10695
distanceMatrix.add((Matrix) mat.clone());
10796
}
10897
}
109-
98+
11099
multipleAlignments = null;
111100
if (e.multipleAlignments!=null){
112101
//Make a deep copy of everything
@@ -117,9 +106,15 @@ public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e){
117106
multipleAlignments.add(newMSA);
118107
}
119108
}
120-
structureNames = new ArrayList<String>(e.structureNames);
109+
110+
if (e.atomArrays != null){
111+
atomArrays = new ArrayList<Atom[]>(e.atomArrays);
112+
}
113+
if (e.structureNames != null){
114+
structureNames = new ArrayList<String>(e.structureNames);
115+
}
121116
}
122-
117+
123118
/**
124119
* Constructor from an AFPChain instance. Creates an equivalent pairwise
125120
* alignment, but in the MultipleAlignment format.
@@ -132,26 +127,26 @@ public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e){
132127
*/
133128
public MultipleAlignmentEnsembleImpl(
134129
AFPChain afp, Atom[] ca1, Atom[] ca2, boolean flexible){
135-
130+
136131
this();
137132
//Copy all the creation and algorithm information
138133
atomArrays = Arrays.asList(ca1,ca2);
139134
structureNames = Arrays.asList(afp.getName1(),afp.getName2());
140135
algorithmName = afp.getAlgorithmName();
141136
version = afp.getVersion();
142137
calculationTime = afp.getCalculationTime();
143-
138+
144139
MultipleAlignment msa = new MultipleAlignmentImpl(this);
145140
setMultipleAlignments(Arrays.asList((MultipleAlignment) msa));
146-
141+
147142
//Convert the rotation and translation to a Matrix4D and set it
148143
Matrix4d ident = new Matrix4d();
149144
ident.setIdentity();
150145
Matrix rot = afp.getBlockRotationMatrix()[0];
151146
Atom shift = afp.getBlockShiftVector()[0];
152147
Matrix4d transform = Calc.getTransformation(rot, shift);
153148
msa.setTransformations(Arrays.asList(ident, transform));
154-
149+
155150
//Create a BlockSet for every block in AFPChain if flexible
156151
if (flexible){
157152
for (int bs=0; bs<afp.getBlockNum(); bs++){
@@ -160,13 +155,13 @@ public MultipleAlignmentEnsembleImpl(
160155
block.setAlignRes(new ArrayList<List<Integer>>());
161156
block.getAlignRes().add(new ArrayList<Integer>());
162157
block.getAlignRes().add(new ArrayList<Integer>());
163-
158+
164159
//Set the transformation of the BlockSet
165160
Matrix rotB = afp.getBlockRotationMatrix()[bs];
166161
Atom shiftB = afp.getBlockShiftVector()[bs];
167162
Matrix4d transformB = Calc.getTransformation(rotB, shiftB);
168163
blockSet.setTransformations(Arrays.asList(ident, transformB));
169-
164+
170165
//Convert the optimal alignment to a Block
171166
for (int i=0; i<afp.getOptAln()[bs][0].length; i++){
172167
block.getAlignRes().get(0).add(afp.getOptAln()[bs][0][i]);
@@ -181,27 +176,27 @@ public MultipleAlignmentEnsembleImpl(
181176
block.setAlignRes(new ArrayList<List<Integer>>());
182177
block.getAlignRes().add(new ArrayList<Integer>());
183178
block.getAlignRes().add(new ArrayList<Integer>());
184-
179+
185180
//Convert the optimal alignment to a Block
186181
for (int i=0; i<afp.getOptAln()[bs][0].length; i++){
187182
block.getAlignRes().get(0).add(afp.getOptAln()[bs][0][i]);
188183
block.getAlignRes().get(1).add(afp.getOptAln()[bs][1][i]);
189184
}
190185
}
191186
}
192-
187+
193188
//Copy the scores stored in the AFPChain
194189
msa.putScore(MultipleAlignmentScorer.PROBABILITY,afp.getProbability());
195190
msa.putScore(MultipleAlignmentScorer.AVGTM_SCORE,afp.getTMScore());
196191
msa.putScore(MultipleAlignmentScorer.CE_SCORE,afp.getAlignScore());
197192
msa.putScore(MultipleAlignmentScorer.RMSD, afp.getTotalRmsdOpt());
198193
}
199-
194+
200195
@Override
201196
public MultipleAlignmentEnsembleImpl clone() {
202197
return new MultipleAlignmentEnsembleImpl(this);
203198
}
204-
199+
205200
@Override
206201
public String getAlgorithmName() {
207202
return algorithmName;
@@ -231,7 +226,7 @@ public Long getIoTime() {
231226
public void setIoTime(Long millis) {
232227
this.ioTime = millis;
233228
}
234-
229+
235230
@Override
236231
public Long getCalculationTime() {
237232
return calculationTime;
@@ -270,7 +265,7 @@ public List<Atom[]> getAtomArrays() {
270265
public void setAtomArrays(List<Atom[]> atomArrays) {
271266
this.atomArrays = atomArrays;
272267
}
273-
268+
274269
/**
275270
* Force the atom arrays to regenerate based on
276271
* {@link #getStructureNames()}.
@@ -297,10 +292,10 @@ public List<Matrix> getDistanceMatrix() {
297292
* Force recalculation of the distance matrices.
298293
*/
299294
public void updateDistanceMatrix() {
300-
295+
301296
//Reset the distance Matrix variable
302297
distanceMatrix = new ArrayList<Matrix>();
303-
298+
304299
for (int s=0; s<size(); s++){
305300
Atom[] ca = atomArrays.get(s);
306301
Matrix distMat =AlignTools.getDistanceMatrix(ca, ca);
@@ -310,7 +305,7 @@ public void updateDistanceMatrix() {
310305

311306
@Override
312307
public List<MultipleAlignment> getMultipleAlignments() {
313-
308+
314309
if (multipleAlignments == null){
315310
multipleAlignments = new ArrayList<MultipleAlignment>();
316311
}
@@ -321,7 +316,7 @@ public List<MultipleAlignment> getMultipleAlignments() {
321316
public void setMultipleAlignments(List<MultipleAlignment> alignments) {
322317
this.multipleAlignments = alignments;
323318
}
324-
319+
325320
@Override
326321
public void addMultipleAlignment(MultipleAlignment alignment) {
327322
if (multipleAlignments == null){
@@ -337,10 +332,10 @@ public int size() {
337332
else if (atomArrays != null) return atomArrays.size();
338333
else {
339334
throw new IndexOutOfBoundsException(
340-
"Empty ensemble: names == null && atoms == null");
335+
"Empty ensemble: names == null && atoms == null");
341336
}
342337
}
343-
338+
344339
@Override
345340
public void clear() {
346341
super.clear();

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