Skip to content

Commit 73f9247

Browse files
sblivensbliven
committed
Removing warnings.
Also fixes two cases where a member variable was being used instead of a parameter.
1 parent f66a7fa commit 73f9247

48 files changed

Lines changed: 150 additions & 61 deletions

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

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

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -312,10 +312,11 @@ public interface Chain {
312312
/**
313313
* Sets the back-reference to its parent Structure.
314314
* @param parent the parent Structure object for this Chain
315-
* @see #getParent()
315+
* @see #getStructure()
316316
* @deprecated use setStructure instead
317317
*
318318
*/
319+
@Deprecated
319320
public void setParent(Structure parent) ;
320321

321322
/** Sets the back-reference to its parent Structure.
@@ -329,10 +330,10 @@ public interface Chain {
329330
* Returns the parent Structure of this chain.
330331
*
331332
* @return the parent Structure object
332-
* @see #setParent(Structure)
333+
* @see #setStructure(Structure)
333334
* @deprecated use getStructure(Structure) instead.
334335
*/
335-
336+
@Deprecated
336337
public Structure getParent() ;
337338

338339

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

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -110,6 +110,7 @@ public void setId(Long id) {
110110
*
111111
*/
112112
@Override
113+
@Deprecated
113114
public void setParent(Structure parent) {
114115
setStructure(parent);
115116
}
@@ -139,6 +140,7 @@ public Structure getStructure() {
139140
* @deprecated use getStructure instead.
140141
*/
141142
@Override
143+
@Deprecated
142144
public Structure getParent() {
143145

144146

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

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -132,6 +132,7 @@ public void setSpaceGroup(SpaceGroup spaceGroup) {
132132
* @return 0
133133
* @deprecated As of 4.0, use {@link SpaceGroup#getMultiplicity()} and {@link Structure#size()}
134134
*/
135+
@Deprecated
135136
public int getZ() {
136137
return 0;
137138
}

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

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -34,14 +34,16 @@
3434
*
3535
*/
3636
public interface SSBond extends PDBRecord, Serializable, Cloneable {
37-
public String toPDB();
37+
@Override
38+
public String toPDB();
3839

3940
/**
4041
* append the PDB representation of this SSBOND to the provided StringBUffer
4142
*
4243
* @param buf a StringBuffer to print the PDB representation to
4344
*/
44-
public void toPDB(StringBuffer buf);
45+
@Override
46+
public void toPDB(StringBuffer buf);
4547

4648
public String getInsCode1();
4749

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

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -155,7 +155,7 @@ public Structure clone() {
155155
Chain cloned_chain = (Chain) getChain(i,j).clone();
156156

157157
// setting the parent: can only be done from the parent
158-
cloned_chain.setParent(n);
158+
cloned_chain.setStructure(n);
159159

160160
cloned_model.add(cloned_chain);
161161

@@ -302,7 +302,7 @@ public void addChain(Chain chain) {
302302
@Override
303303
public void addChain(Chain chain, int modelnr) {
304304
// if model has not been initialized, init it!
305-
chain.setParent(this);
305+
chain.setStructure(this);
306306
if (models.isEmpty()) {
307307
List<Chain> model = new ArrayList<Chain>() ;
308308
model.add(chain);
@@ -341,7 +341,7 @@ public Chain getChain(int modelnr,int number) {
341341
@Override
342342
public void addModel(List<Chain> model){
343343
for (Chain c: model){
344-
c.setParent(this);
344+
c.setStructure(this);
345345
}
346346
models.add(model);
347347
}
@@ -361,7 +361,7 @@ public void setModel(int position, List<Chain> model){
361361
throw new IllegalArgumentException("trying to set model to null!");
362362

363363
for (Chain c: model)
364-
c.setParent(this);
364+
c.setStructure(this);
365365

366366
//System.out.println("model size:" + models.size());
367367

@@ -556,7 +556,7 @@ public List<Chain> getChains(){
556556
@Override
557557
public void setChains(int modelnr, List<Chain> chains){
558558
for (Chain c: chains){
559-
c.setParent(this);
559+
c.setStructure(this);
560560
}
561561
models.remove(modelnr);
562562
models.add(modelnr, chains);

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -387,7 +387,7 @@ public static List<Group> getUnalignedGroups(Atom[] ca) {
387387
if(g != null) {
388388
Chain c = g.getChain();
389389
if( c != null) {
390-
s = c.getParent();
390+
s = c.getStructure();
391391
}
392392
}
393393
}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -157,7 +157,7 @@ private AFPChain alignRight(Atom[] ca1, Atom[] ca2, CECPParameters cpparams)
157157

158158
// since the process of creating ca2m strips the name info away, set it explicitely
159159
try {
160-
afpChain.setName2(ca2[0].getGroup().getChain().getParent().getName());
160+
afpChain.setName2(ca2[0].getGroup().getChain().getStructure().getName());
161161
} catch( Exception e) {}
162162

163163
if(debug) {

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -114,11 +114,11 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureExce
114114

115115
// Try to guess names
116116

117-
if (ca1.length!=0 && ca1[0].getGroup().getChain()!=null && ca1[0].getGroup().getChain().getParent()!=null)
118-
afpChain.setName1(ca1[0].getGroup().getChain().getParent().getName());
117+
if (ca1.length!=0 && ca1[0].getGroup().getChain()!=null && ca1[0].getGroup().getChain().getStructure()!=null)
118+
afpChain.setName1(ca1[0].getGroup().getChain().getStructure().getName());
119119

120-
if (ca2.length!=0 && ca2[0].getGroup().getChain()!=null && ca2[0].getGroup().getChain().getParent()!=null)
121-
afpChain.setName2(ca2[0].getGroup().getChain().getParent().getName());
120+
if (ca2.length!=0 && ca2[0].getGroup().getChain()!=null && ca2[0].getGroup().getChain().getStructure()!=null)
121+
afpChain.setName2(ca2[0].getGroup().getChain().getStructure().getName());
122122

123123
if ( afpChain.getNrEQR() == 0)
124124
return afpChain;

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -508,8 +508,8 @@ public AFPChain alignOptimal(Atom[] ca1, Atom[] ca2, Object param, AFPChain[] al
508508

509509
// fix up names, since cloning ca2 wipes it
510510

511-
if (ca2.length!=0 && ca2[0].getGroup().getChain()!=null && ca2[0].getGroup().getChain().getParent()!=null) {
512-
currentAlignment.setName2(ca2[0].getGroup().getChain().getParent().getName()+" CP="+cp);
511+
if (ca2.length!=0 && ca2[0].getGroup().getChain()!=null && ca2[0].getGroup().getChain().getStructure()!=null) {
512+
currentAlignment.setName2(ca2[0].getGroup().getChain().getStructure().getName()+" CP="+cp);
513513
}
514514

515515
double currentScore = currentAlignment.getAlignScore();

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -137,7 +137,7 @@ public MultipleAlignmentEnsembleImpl(
137137
calculationTime = afp.getCalculationTime();
138138

139139
MultipleAlignment msa = new MultipleAlignmentImpl(this);
140-
setMultipleAlignments(Arrays.asList((MultipleAlignment) msa));
140+
setMultipleAlignments(Arrays.asList(msa));
141141

142142
//Convert the rotation and translation to a Matrix4D and set it
143143
Matrix4d ident = new Matrix4d();

0 commit comments

Comments
 (0)