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sblivensbliven
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Automatically convert spaces to tabs
find . -iname '*.java' | xargs python development/spacestotabs.py -x
1 parent 405b005 commit 9ae2c4f

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76 files changed

+4218
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lines changed

‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -318,11 +318,11 @@ public boolean hasNext() {
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319319
@Override
320320
public GuideTreeNode<S, C> next() {
321-
if(!hasNext()){
322-
throw new NoSuchElementException();
323-
}
321+
if(!hasNext()){
322+
throw new NoSuchElementException();
323+
}
324324

325-
while (hasNext()) {
325+
while (hasNext()) {
326326
Node next = nodes.peek(), child1 = (Node) next.getChild1(), child2 = (Node) next.getChild2();
327327
if (child1 != null && !child1.isVisited()) {
328328
nodes.push(child1);

‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -209,7 +209,7 @@ public Anchor(int queryIndex, int targetIndex) {
209209
this.targetIndex = targetIndex;
210210
}
211211
public static class QueryIndexComparator implements Comparator<Anchor>, Serializable {
212-
private static final long serialVersionUID = 1;
212+
private static final long serialVersionUID = 1;
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214214
@Override
215215
public int compare(Anchor o1, Anchor o2) {

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -132,10 +132,10 @@ public boolean hasNext() {
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133133
@Override
134134
public Hsp next() {
135-
if(!hasNext()){
136-
throw new NoSuchElementException();
137-
}
138-
return hsps.get(current++);
135+
if(!hasNext()){
136+
throw new NoSuchElementException();
137+
}
138+
return hsps.get(current++);
139139
}
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141141
@Override

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -170,10 +170,10 @@ public boolean hasNext() {
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171171
@Override
172172
public Hit next() {
173-
if(!hasNext()){
174-
throw new NoSuchElementException();
175-
}
176-
return hits.get(currentResult++);
173+
if(!hasNext()){
174+
throw new NoSuchElementException();
175+
}
176+
return hits.get(currentResult++);
177177
}
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179179
@Override

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -173,10 +173,10 @@ public boolean hasNext() {
173173

174174
@Override
175175
public Result next() {
176-
if(!hasNext()){
177-
throw new NoSuchElementException();
178-
}
179-
return results.get(currentResult++);
176+
if(!hasNext()){
177+
throw new NoSuchElementException();
178+
}
179+
return results.get(currentResult++);
180180
}
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182182
@Override

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@
2929

3030

3131
public class CDSComparator implements Comparator<CDSSequence>, Serializable{
32-
private static final long serialVersionUID = 1;
32+
private static final long serialVersionUID = 1;
3333

3434
/**
3535
* Used to sort two CDSSequences where Negative Strand makes it tough

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,7 @@
3333
* @author Scooter Willis <willishf at gmail dot com>
3434
*/
3535
public class ExonComparator implements Comparator<ExonSequence>, Serializable{
36-
private static final long serialVersionUID = 1;
36+
private static final long serialVersionUID = 1;
3737

3838
@Override
3939
public int compare(ExonSequence o1, ExonSequence o2) {

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,7 @@
3232
* @author Scooter Willis <willishf at gmail dot com>
3333
*/
3434
public class SequenceComparator implements Comparator<AbstractSequence<?>>, Serializable{
35-
private static final long serialVersionUID = 1;
35+
private static final long serialVersionUID = 1;
3636

3737
@Override
3838
public int compare(AbstractSequence<?> o1, AbstractSequence<?> o2) {

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/ABITracerCompoundSet.java‎

Lines changed: 30 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -29,37 +29,37 @@
2929
*/
3030
public class ABITracerCompoundSet extends AbstractNucleotideCompoundSet<NucleotideCompound> {
3131

32-
private static class InitaliseOnDemand {
33-
public static final ABITracerCompoundSet INSTANCE = new ABITracerCompoundSet();
34-
}
32+
private static class InitaliseOnDemand {
33+
public static final ABITracerCompoundSet INSTANCE = new ABITracerCompoundSet();
34+
}
3535

36-
public static ABITracerCompoundSet getABITracerCompoundSet() {
37-
return InitaliseOnDemand.INSTANCE;
38-
}
36+
public static ABITracerCompoundSet getABITracerCompoundSet() {
37+
return InitaliseOnDemand.INSTANCE;
38+
}
3939

40-
public ABITracerCompoundSet() {
41-
addNucleotideCompound("A", "T");
42-
addNucleotideCompound("T", "A");
43-
addNucleotideCompound("G", "C");
44-
addNucleotideCompound("C", "G");
45-
addNucleotideCompound("N", "N");
46-
addNucleotideCompound("K", "K");
47-
addNucleotideCompound("Y", "Y");
48-
addNucleotideCompound("R", "R");
49-
addNucleotideCompound("-", "-");
50-
}
40+
public ABITracerCompoundSet() {
41+
addNucleotideCompound("A", "T");
42+
addNucleotideCompound("T", "A");
43+
addNucleotideCompound("G", "C");
44+
addNucleotideCompound("C", "G");
45+
addNucleotideCompound("N", "N");
46+
addNucleotideCompound("K", "K");
47+
addNucleotideCompound("Y", "Y");
48+
addNucleotideCompound("R", "R");
49+
addNucleotideCompound("-", "-");
50+
}
5151

52-
@Override
53-
public NucleotideCompound newNucleotideCompound(String base, String complement, String... equivalents) {
54-
if(equivalents.length == 0) {
55-
return new NucleotideCompound(base, this, complement);
56-
}
57-
else {
58-
NucleotideCompound[] compounds = new NucleotideCompound[equivalents.length];
59-
for(int i=0; i<compounds.length; i++) {
60-
compounds[i] = getCompoundForString(equivalents[i]);
61-
}
62-
return new NucleotideCompound(base, this, complement, compounds);
63-
}
64-
}
52+
@Override
53+
public NucleotideCompound newNucleotideCompound(String base, String complement, String... equivalents) {
54+
if(equivalents.length == 0) {
55+
return new NucleotideCompound(base, this, complement);
56+
}
57+
else {
58+
NucleotideCompound[] compounds = new NucleotideCompound[equivalents.length];
59+
for(int i=0; i<compounds.length; i++) {
60+
compounds[i] = getCompoundForString(equivalents[i]);
61+
}
62+
return new NucleotideCompound(base, this, complement, compounds);
63+
}
64+
}
6565
}

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