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sblivensbliven
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Running spacestotabs on recent changes
No java files currently have initial spaces git diff --name-only 38934ac 5e0e78f | xargs ls 2>/dev/null | xargs python development/spacestotabs.py -t .8 -x Manually fix anything returned by find . -iname '*.java' | xargs python development/spacestotabs.py
1 parent 38e327b commit 5074cb2

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+1637
-1633
lines changed

24 files changed

+1637
-1633
lines changed

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

Lines changed: 596 additions & 596 deletions
Large diffs are not rendered by default.

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

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -112,11 +112,11 @@ public int hashCode() {
112112
r = Hashcoder.hash(r, getIdentifier());
113113
r = Hashcoder.hash(r, getVersion());
114114
return r;
115-
}
115+
}
116116

117-
// public void setDataSource(DataSource dataSource){
118-
// source = dataSource;
119-
// }
117+
// public void setDataSource(DataSource dataSource){
118+
// source = dataSource;
119+
// }
120120

121121

122122
/**

‎biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -894,7 +894,7 @@ public static void main(String args[]) throws Exception {
894894
GeneFeatureHelper.outputFastaSequenceLengthGFF3(new File("Scaffolds.fna"), new File("scaffolds.gff3"));
895895
}
896896
897-
*/
897+
*/
898898

899899
try {
900900

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureI.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -23,11 +23,11 @@
2323
import java.util.HashMap;
2424

2525
/**
26-
* A feature on a sequence (for example, an exon or a gene), defined by a location
27-
* and a set of attributes encoded as key/value pairs.
28-
*
29-
* @author Hanno Hinsch
30-
*/
26+
* A feature on a sequence (for example, an exon or a gene), defined by a location
27+
* and a set of attributes encoded as key/value pairs.
28+
*
29+
* @author Hanno Hinsch
30+
*/
3131
public interface FeatureI
3232
{
3333

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Reader.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -162,7 +162,7 @@ private static Feature parseLine(String s) {
162162
} else {
163163
attributes = new String(s.substring(start, end));
164164
}
165-
*/
165+
*/
166166
return new Feature(seqname, source, type, location, score, frame, attributes.split("#")[0]);
167167

168168
}

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -192,7 +192,7 @@ private static void writeLine(Feature f, BufferedWriter bw) throws IOException {
192192
bw.write(s);
193193
bw.newLine();
194194
}
195-
*/
195+
*/
196196

197197
public static void main(String args[]) throws Exception {
198198

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -266,9 +266,9 @@ else if ( pdbName.equals("H2O"))
266266

267267
}
268268

269-
public void testGetHetGroups() {
269+
public void testGetHetGroups() {
270270
// try {
271-
Structure struct = structure;
271+
Structure struct = structure;
272272

273273
// HET TYS I 363 16
274274
// HET NA H 541 1
@@ -293,15 +293,15 @@ public void testGetHetGroups() {
293293
// FORMUL 7 KTH C4 H3 N O S
294294
// FORMUL 8 HOH *157(H2 O)
295295

296-
List<Group> hets = struct.getHetGroups();
297-
298-
assertEquals(7, hets.size());
296+
List<Group> hets = struct.getHetGroups();
297+
298+
assertEquals(7, hets.size());
299299

300-
300+
301301

302302

303303
// } catch (Exception e) {
304304
// fail(e.getMessage());
305305
// }
306-
}
306+
}
307307
}

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/MyTestHelper.java‎

Lines changed: 84 additions & 84 deletions
Original file line numberDiff line numberDiff line change
@@ -36,118 +36,118 @@
3636
public class MyTestHelper
3737
{
3838

39-
40-
public static final String pdbPath = System.getProperty("java.io.tmpdir");
39+
40+
public static final String pdbPath = System.getProperty("java.io.tmpdir");
4141

42-
public static String compareAlignment(String pdb1, String chain1, String pdb2, String chain2, String originalOutput, boolean doRigid){
42+
public static String compareAlignment(String pdb1, String chain1, String pdb2, String chain2, String originalOutput, boolean doRigid){
4343

44-
AFPChain afpChain = null;
44+
AFPChain afpChain = null;
4545

46-
PDBFileReader pdbpars = new PDBFileReader();
47-
pdbpars.setPath(pdbPath);
48-
pdbpars.setFetchBehavior(FetchBehavior.FETCH_FILES);
49-
50-
FileParsingParameters params = new FileParsingParameters();
51-
params.setAlignSeqRes(true);
52-
params.setParseCAOnly(true);
53-
pdbpars.setFileParsingParameters(params);
54-
55-
Structure structure1;
56-
Structure structure2;
46+
PDBFileReader pdbpars = new PDBFileReader();
47+
pdbpars.setPath(pdbPath);
48+
pdbpars.setFetchBehavior(FetchBehavior.FETCH_FILES);
49+
50+
FileParsingParameters params = new FileParsingParameters();
51+
params.setAlignSeqRes(true);
52+
params.setParseCAOnly(true);
53+
pdbpars.setFileParsingParameters(params);
54+
55+
Structure structure1;
56+
Structure structure2;
5757

58-
// default: new:
59-
// 1buz - 1ali : time: 8.3s eqr 68 rmsd 3.1 score 161 | time 6.4 eqr 58 rmsd 3.0 scre 168 | rigid: identical, flexible: not significant alignment,
60-
// 5pti - 1tap : time: 6.2s eqr 48 rmsd 2.67 score 164 | time 5.2 eqr 49 rmsd 2.9 score 151 | rigid:
61-
// 1cdg - 8tim
62-
// 1jbe - 1ord : identical with fatcat
63-
// 1nbw.A - 1kid : rigid: identical, flexible: not identical, alignment not significant.
64-
// 1t4y - 1rp5
65-
// 1a64.A - 1hng.B
66-
// 1zzw - 1bw6
58+
// default: new:
59+
// 1buz - 1ali : time: 8.3s eqr 68 rmsd 3.1 score 161 | time 6.4 eqr 58 rmsd 3.0 scre 168 | rigid: identical, flexible: not significant alignment,
60+
// 5pti - 1tap : time: 6.2s eqr 48 rmsd 2.67 score 164 | time 5.2 eqr 49 rmsd 2.9 score 151 | rigid:
61+
// 1cdg - 8tim
62+
// 1jbe - 1ord : identical with fatcat
63+
// 1nbw.A - 1kid : rigid: identical, flexible: not identical, alignment not significant.
64+
// 1t4y - 1rp5
65+
// 1a64.A - 1hng.B
66+
// 1zzw - 1bw6
6767

68-
try {
69-
structure1 = pdbpars.getStructureById(pdb1);
70-
structure2 = pdbpars.getStructureById(pdb2);
68+
try {
69+
structure1 = pdbpars.getStructureById(pdb1);
70+
structure2 = pdbpars.getStructureById(pdb2);
7171

72-
//structure1 = pdbpars.getStructureById("1cdg");
73-
Chain c1 = structure1.getChainByPDB(chain1);
72+
//structure1 = pdbpars.getStructureById("1cdg");
73+
Chain c1 = structure1.getChainByPDB(chain1);
7474

75-
//structure2 = pdbpars.getStructureById("2aaa");
76-
Chain c2 = structure2.getChainByPDB(chain2);
75+
//structure2 = pdbpars.getStructureById("2aaa");
76+
Chain c2 = structure2.getChainByPDB(chain2);
7777

78-
Structure s3 = new StructureImpl();
79-
s3.addChain(c1);
78+
Structure s3 = new StructureImpl();
79+
s3.addChain(c1);
8080

81-
Structure s4 = new StructureImpl();
82-
s4.addChain(c2);
81+
Structure s4 = new StructureImpl();
82+
s4.addChain(c2);
8383

84-
Atom[] ca1 = StructureTools.getRepresentativeAtomArray(s3);
85-
Atom[] ca2 = StructureTools.getRepresentativeAtomArray(s4);
84+
Atom[] ca1 = StructureTools.getRepresentativeAtomArray(s3);
85+
Atom[] ca2 = StructureTools.getRepresentativeAtomArray(s4);
8686

87-
// keep an independent copy of them for tests further down..
88-
Atom[] ca3 = new Atom[ca2.length];
89-
for (int i = 0 ; i < ca2.length; i++){
90-
Group g = (Group)ca2[i].getGroup().clone();
91-
g.setChain(ca2[i].getGroup().getChain());
92-
ca3[i] = g.getAtom(ca2[i].getName());
93-
}
87+
// keep an independent copy of them for tests further down..
88+
Atom[] ca3 = new Atom[ca2.length];
89+
for (int i = 0 ; i < ca2.length; i++){
90+
Group g = (Group)ca2[i].getGroup().clone();
91+
g.setChain(ca2[i].getGroup().getChain());
92+
ca3[i] = g.getAtom(ca2[i].getName());
93+
}
9494

95-
StructureAlignment fatCat;
95+
StructureAlignment fatCat;
9696

97-
FatCatParameters fparams = new FatCatParameters();
97+
FatCatParameters fparams = new FatCatParameters();
9898

99-
if ( doRigid)
100-
fatCat = new FatCatRigid();
101-
else
102-
fatCat = new FatCatFlexible();
99+
if ( doRigid)
100+
fatCat = new FatCatRigid();
101+
else
102+
fatCat = new FatCatFlexible();
103103

104-
afpChain = fatCat.align(ca1, ca2, fparams);
104+
afpChain = fatCat.align(ca1, ca2, fparams);
105105

106-
afpChain.setName1(pdb1+chain1);
107-
afpChain.setName2(pdb2+chain2);
106+
afpChain.setName1(pdb1+chain1);
107+
afpChain.setName2(pdb2+chain2);
108108

109109

110-
// TEST THE XML SERIALIZATION AND DE_SERIALIZATION!
111-
String result = afpChain.toFatcat(ca1, ca2);
110+
// TEST THE XML SERIALIZATION AND DE_SERIALIZATION!
111+
String result = afpChain.toFatcat(ca1, ca2);
112112

113-
String xml = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
113+
String xml = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
114114

115-
//System.out.println(xml);
115+
//System.out.println(xml);
116116

117-
AFPChain newChain = AFPChainXMLParser.fromXML (xml, ca1, ca3);
117+
AFPChain newChain = AFPChainXMLParser.fromXML (xml, ca1, ca3);
118118

119-
String resultSerialized = newChain.toFatcat(ca1, ca3);
120-
//System.out.println("*** RESULT2 "+result2);
119+
String resultSerialized = newChain.toFatcat(ca1, ca3);
120+
//System.out.println("*** RESULT2 "+result2);
121121

122-
if ( ! result.equals(resultSerialized)) {
123-
System.out.println("not identical toFatCat()!!!");
124-
System.out.println(xml);
125-
System.out.println(result);
126-
System.out.println("***");
127-
System.out.println(resultSerialized);
128-
throw new StructureException("the JFatCat alignment image does not look identical after XML serialization.");
129-
}
122+
if ( ! result.equals(resultSerialized)) {
123+
System.out.println("not identical toFatCat()!!!");
124+
System.out.println(xml);
125+
System.out.println(result);
126+
System.out.println("***");
127+
System.out.println(resultSerialized);
128+
throw new StructureException("the JFatCat alignment image does not look identical after XML serialization.");
129+
}
130130

131-
if ( ! afpChain.toString().equals(newChain.toString())){
132-
System.err.println("not identical toStrings!!!");
133-
System.err.println(afpChain.toString());
134-
System.err.println(newChain.toString());
135-
throw new StructureException("The AFPChain.toString() does not look identical after XML serialization.");
136-
}
131+
if ( ! afpChain.toString().equals(newChain.toString())){
132+
System.err.println("not identical toStrings!!!");
133+
System.err.println(afpChain.toString());
134+
System.err.println(newChain.toString());
135+
throw new StructureException("The AFPChain.toString() does not look identical after XML serialization.");
136+
}
137137

138138

139139

140-
if ( result.equals(originalOutput)){
141-
return "";
142-
} else {
143-
return result;
144-
}
140+
if ( result.equals(originalOutput)){
141+
return "";
142+
} else {
143+
return result;
144+
}
145145

146-
} catch ( Exception e){
147-
e.printStackTrace();
148-
return e.getMessage();
149-
}
146+
} catch ( Exception e){
147+
e.printStackTrace();
148+
return e.getMessage();
149+
}
150150

151-
}
151+
}
152152

153153
}

‎biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/TmpAtomCache.java‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -30,13 +30,13 @@
3030

3131
public class TmpAtomCache
3232
{
33-
static String tmpDir = System.getProperty("java.io.tmpdir");
34-
public static AtomCache cache = new AtomCache(tmpDir, tmpDir);
35-
static {
36-
FileParsingParameters params = new FileParsingParameters();
37-
params.setAlignSeqRes(true);
38-
params.setParseSecStruc(false);
39-
cache.setFetchBehavior(FetchBehavior.FETCH_REMEDIATED);
40-
cache.setFileParsingParams(params);
41-
}
33+
static String tmpDir = System.getProperty("java.io.tmpdir");
34+
public static AtomCache cache = new AtomCache(tmpDir, tmpDir);
35+
static {
36+
FileParsingParameters params = new FileParsingParameters();
37+
params.setAlignSeqRes(true);
38+
params.setParseSecStruc(false);
39+
cache.setFetchBehavior(FetchBehavior.FETCH_REMEDIATED);
40+
cache.setFileParsingParams(params);
41+
}
4242
}

‎biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -35,14 +35,14 @@
3535
/**
3636
* Tests the following UniProt IDs:
3737
*
38-
Methyltransferase mtmB1, UniProt O30642
39-
Sec (U), Selenoprotein V, UniProt P59797
40-
Asx (B), 5-hydroxytryptamine receptor 1F, UniProt Q9N2D9
41-
Xaa (X), DNA-3-methyladenine glycosylase (Fragment), UniProt P23571
42-
Glx (Z), 14-3-3 protein gamma-1, UniProt Q6UFZ3
43-
44-
45-
*/
38+
* Methyltransferase mtmB1, UniProt O30642
39+
* Sec (U), Selenoprotein V, UniProt P59797
40+
* Asx (B), 5-hydroxytryptamine receptor 1F, UniProt Q9N2D9
41+
* Xaa (X), DNA-3-methyladenine glycosylase (Fragment), UniProt P23571
42+
* Glx (Z), 14-3-3 protein gamma-1, UniProt Q6UFZ3
43+
*
44+
*
45+
*/
4646
public class NonstandardProteinCompoundTest {
4747

4848
@Test

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