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sblivensbliven
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Manually fix cases of space indentation identation found by
``` find . -iname '*.java' | xargs python development/spacestotabs.py ``` Initial spaces were deleted with ``` for f in $(find . -iname '*.java' | xargs python development/spacestotabs.py|awk '{print $2}'); do gsed -ri 's/^ \t/\t/' $f; done ```
1 parent 9ae2c4f commit 5baab5e

9 files changed

Lines changed: 112 additions & 118 deletions

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‎biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -471,7 +471,7 @@ public boolean markSupported() {
471471
* Read a named file and uncompress it.
472472
* @param fileInName Name of compressed file.
473473
* @param out A destination for the result. It is closed after data is sent.
474-
* @return number of bytes sent to the output stream,
474+
* @return number of bytes sent to the output stream,
475475
* @throws IOException for any error
476476
*/
477477
public static long uncompress(String fileInName, FileOutputStream out)
@@ -488,7 +488,7 @@ public static long uncompress(String fileInName, FileOutputStream out)
488488
logger.info("Decompressed {} bytes", total);
489489
UncompressInputStream.logger.info("Time: {} seconds", (end - start) / 1000);
490490
}
491-
return total;
491+
return total;
492492
}
493493

494494
/**
@@ -518,7 +518,7 @@ public static long uncompress(InputStream in, OutputStream out)
518518
* Reads a file, uncompresses it, and sends the result to stdout.
519519
* Also writes trivial statistics to stderr.
520520
* @param args An array with one String element, the name of the file to read.
521-
* @throws IOException for any failure
521+
* @throws IOException for any failure
522522
*/
523523
public static void main(String[] args) throws Exception {
524524
if (args.length != 1) {

‎biojava-genome/src/main/java/org/biojava/nbio/genome/util/ProteinMappingTools.java‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -27,12 +27,12 @@
2727

2828
public class ProteinMappingTools {
2929

30-
/** Converts the DNA sequence to protein sequence.
31-
*
32-
* @param dnaSequence the DNA sequence
33-
*
34-
* @return the protein sequence
35-
*/
30+
/** Converts the DNA sequence to protein sequence.
31+
*
32+
* @param dnaSequence the DNA sequence
33+
*
34+
* @return the protein sequence
35+
*/
3636
public static ProteinSequence convertDNAtoProteinSequence(String dnaSequence) throws CompoundNotFoundException {
3737
DNASequence dna = new DNASequence(dnaSequence);
3838
return convertDNAtoProteinSequence(dna);

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestStructWithMultiparentChemComp.java‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -38,15 +38,15 @@ public void test4Q7U() throws Exception {
3838
cache.setUseMmCif(true);
3939
StructureIO.setAtomCache(cache);
4040

41-
Structure s = StructureIO.getStructure("4q7u");
42-
assertNotNull(s);
43-
Chain c = s.getPolyChain("A");
44-
45-
String seq = c.getSeqResSequence();
46-
assertNotNull(seq);
47-
assertEquals(245, seq.length());
48-
assertFalse(seq.contains("?"));
49-
assertTrue(seq.contains("X"));
41+
Structure s = StructureIO.getStructure("4q7u");
42+
assertNotNull(s);
43+
Chain c = s.getPolyChain("A");
44+
45+
String seq = c.getSeqResSequence();
46+
assertNotNull(seq);
47+
assertEquals(245, seq.length());
48+
assertFalse(seq.contains("?"));
49+
assertTrue(seq.contains("X"));
5050

5151
}
5252

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

Lines changed: 4 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,12 @@
11
/*
2-
* BioJava development code
2+
* BioJava development code
33
*
44
* This code may be freely distributed and modified under the
55
* terms of the GNU Lesser General Public Licence. This should
66
* be distributed with the code. If you do not have a copy,
77
* see:
88
*
9-
* http://www.gnu.org/copyleft/lesser.html
9+
* http://www.gnu.org/copyleft/lesser.html
1010
*
1111
* Copyright for this code is held jointly by the individual
1212
* authors. These should be listed in @author doc comments.
@@ -15,14 +15,9 @@
1515
* or to join the biojava-l mailing list, visit the home page
1616
* at:
1717
*
18-
* http://www.biojava.org/
19-
*
20-
* Created on Jun 8, 2010
21-
* Author: Jianjiong Gao
22-
* Author: Peter W. Rose
18+
* http://www.biojava.org/
2319
*
2420
*/
25-
2621
package org.biojava.nbio.protmod.structure;
2722

2823
import org.biojava.nbio.protmod.ProteinModification;
@@ -360,7 +355,7 @@ private void parserTest(String pdbId, String residId) throws IOException, Struct
360355
private void parserTest(String pdbId, Set<ProteinModification> mods) throws IOException, StructureException {
361356
Structure struc = TmpAtomCache.cache.getStructure(pdbId);
362357
/*
363-
//needed for testing 1G20
358+
//needed for testing 1G20
364359
if ( pdbId.equalsIgnoreCase("1G20")) {
365360
Structure n = new StructureImpl();
366361

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

Lines changed: 6 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -76,7 +76,7 @@ public interface Chain extends Serializable {
7676
* Set the 'private' asymId (internal chain IDs in mmCif) for this chain.
7777
*
7878
* @param asymId the internal chain Id
79-
*/
79+
*/
8080
void setId(String asymId) ;
8181

8282

@@ -93,7 +93,7 @@ public interface Chain extends Serializable {
9393
*
9494
* @return the authId for this chain.
9595
* @see #getId()
96-
*/
96+
*/
9797
String getName();
9898

9999

@@ -422,13 +422,13 @@ public interface Chain extends Serializable {
422422
/** Tests if a chain is consisting of water molecules only
423423
*
424424
* @return true if there are only solvent molecules in this chain.
425-
*/
426-
public boolean isWaterOnly();
425+
*/
426+
public boolean isWaterOnly();
427427

428428
/** Returns true if the given chain is composed of non-polymeric (including water) groups only.
429429
*
430-
* @return true if only non-polymeric groups in this chain.
431-
*/
430+
* @return true if only non-polymeric groups in this chain.
431+
*/
432432
public boolean isPureNonPolymer();
433433

434434
/**
@@ -453,7 +453,6 @@ public interface Chain extends Serializable {
453453
/**
454454
* Tell whether given chain is a protein chain
455455
*
456-
457456
* @return true if protein, false if nucleotide or ligand
458457
* @see #getPredominantGroupType()
459458
*/

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1826,7 +1826,7 @@ public static boolean isProtein(Chain c) {
18261826

18271827
/**
18281828
* @deprecated use {@link Chain#isNucleicAcid()} instead.
1829-
*/
1829+
*/
18301830
@Deprecated
18311831
public static boolean isNucleicAcid(Chain c) {
18321832
return c.isNucleicAcid();
@@ -1849,7 +1849,7 @@ public static boolean isChainWaterOnly(Chain c) {
18491849
}
18501850

18511851
/**
1852-
* @deprecated use {@link Chain#isPureNonPolymer()} instead.
1852+
* @deprecated use {@link Chain#isPureNonPolymer()} instead.
18531853
*/
18541854
@Deprecated
18551855
public static boolean isChainPureNonPolymer(Chain c) {

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -389,7 +389,7 @@ private static TreeMap<String,EntityInfo> findEntitiesFromAlignment(List<List<Ch
389389
EntityInfo e = chainIds2entities.get(chain.getId());
390390
chain.setEntityInfo(e);
391391
e.addChain(chain);
392-
}
392+
}
393393
}
394394

395395

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -244,7 +244,7 @@ public String toPDB() {
244244

245245
toPDB(g,str);
246246

247-
waterGroupsExist = true;
247+
waterGroupsExist = true;
248248
}
249249

250250
}

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