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Commit 743a9fd

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josemduartejosemduarte
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More cleanup
1 parent 381fedd commit 743a9fd

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2 files changed

+14
-39
lines changed

2 files changed

+14
-39
lines changed

‎biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -178,10 +178,10 @@ public interface Structure extends Cloneable, Serializable {
178178
/**
179179
* Return number of chains of model.
180180
*
181-
* @param modelnr an int specifying the number of the Model that should be used
181+
* @param modelIdx an int specifying the index of the Model that should be used
182182
* @return an int representing the number of Chains in this Model
183183
*/
184-
int size(int modelnr);
184+
int size(int modelIdx);
185185

186186
/**
187187
* Return the number of models .
@@ -269,9 +269,9 @@ public interface Structure extends Cloneable, Serializable {
269269
/**
270270
* Set the chains for a model
271271
* @param chains the chains for a model
272-
* @param modelnr the number of the model
272+
* @param modelIdx the model index
273273
*/
274-
void setChains(int modelnr, List<Chain> chains);
274+
void setChains(int modelIdx, List<Chain> chains);
275275

276276
/**
277277
* Return all polymeric chains for the first model

‎biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java‎

Lines changed: 10 additions & 35 deletions
Original file line numberDiff line numberDiff line change
@@ -268,24 +268,17 @@ public void addChain(Chain chain, int modelIdx) {
268268
/** {@inheritDoc} */
269269
@Override
270270
public Chain getChainByIndex(int number) {
271-
272-
int modelnr = 0 ;
273-
274-
return getChainByIndex(modelnr,number);
271+
return getChainByIndex(0, number);
275272
}
276273

277274

278275
/** {@inheritDoc} */
279276
@Override
280277
public Chain getChainByIndex(int modelIdx, int number) {
281-
282278
Model model = models.get(modelIdx);
283-
284279
return model.getChains().get(number);
285280
}
286281

287-
288-
289282
/** {@inheritDoc} */
290283
@Override
291284
public void addModel(List<Chain> modelChains){
@@ -297,16 +290,13 @@ public void addModel(List<Chain> modelChains){
297290
models.add(model);
298291
}
299292

300-
301293
/** {@inheritDoc} */
302294
@Override
303295
public void setChains(List<Chain> chains){
304296

305297
setModel(0,chains);
306298
}
307299

308-
309-
310300
/** {@inheritDoc} */
311301
@Override
312302
public void setModel(int position, List<Chain> modelChains){
@@ -327,9 +317,6 @@ public void setModel(int position, List<Chain> modelChains){
327317
}
328318
}
329319

330-
/** String representation.
331-
*
332-
*/
333320
@Override
334321
public String toString(){
335322
String newline = System.lineSeparator();
@@ -418,15 +405,11 @@ public int size() {
418405

419406
}
420407

421-
/** return number of chains of model.
422-
*
423-
*/
424408
@Override
425-
public int size(int modelnr) { return models.get(modelnr).size(); }
409+
public int size(int modelIdx) { return models.get(modelIdx).size(); }
426410

427411
// some NMR stuff :
428412

429-
/** return number of models. */
430413
@Override
431414
public int nrModels() {
432415
return models.size() ;
@@ -496,16 +479,15 @@ public List<Chain> getChains(int modelIdx){
496479
/** {@inheritDoc} */
497480
@Override
498481
public List<Chain> getChains(){
499-
if (models.size()==0) {
482+
if (models.isEmpty()) {
500483
return new ArrayList<>(0);
501484
}
502485
return getChains(0);
503-
504486
}
505487

506488
@Override
507489
public List<Chain> getPolyChains() {
508-
if (models.size()==0) {
490+
if (models.isEmpty()) {
509491
return new ArrayList<>(0);
510492
}
511493
return getPolyChains(0);
@@ -518,7 +500,7 @@ public List<Chain> getPolyChains(int modelIdx) {
518500

519501
@Override
520502
public List<Chain> getNonPolyChains() {
521-
if (models.size()==0) {
503+
if (models.isEmpty()) {
522504
return new ArrayList<>(0);
523505
}
524506
return getNonPolyChains(0);
@@ -531,7 +513,7 @@ public List<Chain> getNonPolyChains(int modelIdx) {
531513

532514
@Override
533515
public List<Chain> getWaterChains() {
534-
if (models.size()==0) {
516+
if (models.isEmpty()) {
535517
return new ArrayList<>(0);
536518
}
537519
return getWaterChains(0);
@@ -544,26 +526,24 @@ public List<Chain> getWaterChains(int modelIdx) {
544526

545527
/** {@inheritDoc} */
546528
@Override
547-
public void setChains(int modelnr, List<Chain> chains){
529+
public void setChains(int modelIdx, List<Chain> chains){
548530
for (Chain c: chains){
549531
c.setStructure(this);
550532
}
551-
if (models.size()>modelnr) {
552-
models.remove(modelnr);
533+
if (models.size()> modelIdx) {
534+
models.remove(modelIdx);
553535
}
554536

555537
Model model = new Model();
556538
model.setChains(chains);
557-
models.add(modelnr, model);
558-
539+
models.add(modelIdx, model);
559540
}
560541

561542
/**
562543
* {@inheritDoc}
563544
*/
564545
@Override
565546
public List<Chain> getModel(int modelIdx) {
566-
567547
return models.get(modelIdx).getChains();
568548
}
569549

@@ -606,7 +586,6 @@ public Chain getPolyChain(String asymId, int modelIdx) {
606586
return null;
607587
}
608588

609-
610589
@Override
611590
public Chain getNonPolyChain(String asymId) {
612591
return getNonPolyChain(asymId, 0);
@@ -624,7 +603,6 @@ public Chain getNonPolyChain(String asymId, int modelIdx) {
624603
if (c.getId().equals(asymId))
625604
return c;
626605
}
627-
628606
return null;
629607
}
630608

@@ -676,7 +654,6 @@ public Chain getWaterChain(String asymId) {
676654
return getWaterChain(asymId, 0);
677655
}
678656

679-
680657
@Override
681658
public Chain getWaterChain(String asymId, int modelIdx) {
682659
Model model = models.get(modelIdx);
@@ -697,7 +674,6 @@ public Chain getWaterChainByPDB(String authId) {
697674
return getWaterChainByPDB(authId, 0);
698675
}
699676

700-
701677
@Override
702678
public Chain getWaterChainByPDB(String authId, int modelIdx) {
703679
Model model = models.get(modelIdx);
@@ -820,7 +796,6 @@ public void setDBRefs(List<DBRef> dbrefs) {
820796
this.dbrefs = dbrefs;
821797
}
822798

823-
824799
/** {@inheritDoc} */
825800
@Override
826801
public PDBHeader getPDBHeader() {

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