Manually fix cases of space indentation identation found by

sbliven · sbliven · commit 5baab5ef23be · 2019-01-03T16:12:49.000+01:00
```
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
```
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java
@@ -471,7 +471,7 @@ public boolean markSupported() {
 	 * Read a named file and uncompress it.
 	 * @param fileInName Name of compressed file.
 	 * @param out A destination for the result. It is closed after data is sent.
-         * @return number of bytes sent to the output stream,
+	 * @return number of bytes sent to the output stream,
 	 * @throws IOException for any error
 	 */
 	public static long uncompress(String fileInName, FileOutputStream out)
@@ -488,7 +488,7 @@ public static long uncompress(String fileInName, FileOutputStream out)
 			logger.info("Decompressed {} bytes", total);
 			UncompressInputStream.logger.info("Time: {} seconds", (end - start) / 1000);
 		}
-                return total;
+		return total;
 	}
 
 	/**
@@ -518,7 +518,7 @@ public static long uncompress(InputStream in, OutputStream out)
 	 * Reads a file, uncompresses it, and sends the result to stdout.
 	 * Also writes trivial statistics to stderr.
 	 * @param args An array with one String element, the name of the file to read.
- 	 * @throws IOException for any failure
+	 * @throws IOException for any failure
 	 */
 	public static void main(String[] args) throws Exception {
 		if (args.length != 1) {
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ProteinMappingTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ProteinMappingTools.java
@@ -27,12 +27,12 @@
 
 public class ProteinMappingTools {
 
-    /** Converts the DNA sequence to protein sequence.
-    *
-    * @param dnaSequence the DNA sequence
-    *
-    * @return the protein sequence
-    */
+	/** Converts the DNA sequence to protein sequence.
+	 *
+	 * @param dnaSequence the DNA sequence
+	 *
+	 * @return the protein sequence
+	 */
 	public static ProteinSequence convertDNAtoProteinSequence(String dnaSequence) throws CompoundNotFoundException {
 		DNASequence dna = new DNASequence(dnaSequence);
 		return convertDNAtoProteinSequence(dna);
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestStructWithMultiparentChemComp.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestStructWithMultiparentChemComp.java
@@ -38,15 +38,15 @@ public void test4Q7U() throws Exception {
 		cache.setUseMmCif(true);
 		StructureIO.setAtomCache(cache);
 
- 		Structure s = StructureIO.getStructure("4q7u");
- 		assertNotNull(s);
- 		Chain c = s.getPolyChain("A");
-
- 		String seq = c.getSeqResSequence();
- 		assertNotNull(seq);
- 		assertEquals(245, seq.length());
- 		assertFalse(seq.contains("?"));
- 		assertTrue(seq.contains("X"));
+		Structure s = StructureIO.getStructure("4q7u");
+		assertNotNull(s);
+		Chain c = s.getPolyChain("A");
+
+		String seq = c.getSeqResSequence();
+		assertNotNull(seq);
+		assertEquals(245, seq.length());
+		assertFalse(seq.contains("?"));
+		assertTrue(seq.contains("X"));
 
 	}
 
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java
@@ -1,12 +1,12 @@
 /*
- *			BioJava development code
+ *                    BioJava development code
  *
  * This code may be freely distributed and modified under the
  * terms of the GNU Lesser General Public Licence.  This should
  * be distributed with the code.  If you do not have a copy,
  * see:
  *
- *	  http://www.gnu.org/copyleft/lesser.html
+ *      http://www.gnu.org/copyleft/lesser.html
  *
  * Copyright for this code is held jointly by the individual
  * authors.  These should be listed in @author doc comments.
@@ -15,14 +15,9 @@
  * or to join the biojava-l mailing list, visit the home page
  * at:
  *
- *	  http://www.biojava.org/
- *
- * Created on Jun 8, 2010
- * Author: Jianjiong Gao
- * Author: Peter W. Rose
+ *      http://www.biojava.org/
  *
  */
-
 package org.biojava.nbio.protmod.structure;
 
 import org.biojava.nbio.protmod.ProteinModification;
@@ -360,7 +355,7 @@ private void parserTest(String pdbId, String residId) throws IOException, Struct
 	private void parserTest(String pdbId, Set<ProteinModification> mods) throws IOException, StructureException {
 		Structure struc = TmpAtomCache.cache.getStructure(pdbId);
 /*
- //needed for testing 1G20
+		//needed for testing 1G20
 		if ( pdbId.equalsIgnoreCase("1G20")) {
 			Structure n = new StructureImpl();
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
@@ -76,7 +76,7 @@ public interface Chain extends Serializable {
 	 * Set the 'private' asymId (internal chain IDs in mmCif) for this chain.
 	 *
 	 * @param asymId the internal chain Id
-     */
+	 */
 	void setId(String asymId) ;
 
 
@@ -93,7 +93,7 @@ public interface Chain extends Serializable {
 	 *
 	 * @return the authId for this chain.
 	 * @see #getId()
-     */
+	 */
 	String getName();
 
 
@@ -422,13 +422,13 @@ public interface Chain extends Serializable {
 	/** Tests if a chain is consisting of water molecules only
 	 *
 	 * @return true if there are only solvent molecules in this chain.
-     */
-	 public boolean isWaterOnly();
+	 */
+	public boolean isWaterOnly();
 
 	/**  Returns true if the given chain is composed of non-polymeric (including water) groups only.
 	 *
- 	 * @return true if only non-polymeric groups in this chain.
-     */
+	 * @return true if only non-polymeric groups in this chain.
+	 */
 	public boolean isPureNonPolymer();
 
 	/**
@@ -453,7 +453,6 @@ public interface Chain extends Serializable {
 	/**
 	 * Tell whether given chain is a protein chain
 	 *
-
 	 * @return true if protein, false if nucleotide or ligand
 	 * @see #getPredominantGroupType()
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -1826,7 +1826,7 @@ public static boolean isProtein(Chain c) {
 
 	/**
 	 * @deprecated use {@link Chain#isNucleicAcid()} instead.
- 	 */
+	 */
 	@Deprecated
 	public static boolean isNucleicAcid(Chain c) {
 		return c.isNucleicAcid();
@@ -1849,7 +1849,7 @@ public static boolean isChainWaterOnly(Chain c) {
 	}
 
 	/**
-     * @deprecated  use {@link Chain#isPureNonPolymer()} instead.
+	 * @deprecated  use {@link Chain#isPureNonPolymer()} instead.
 	 */
 	@Deprecated
 	public static boolean isChainPureNonPolymer(Chain c) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/EntityFinder.java
@@ -389,7 +389,7 @@ private static TreeMap<String,EntityInfo> findEntitiesFromAlignment(List<List<Ch
 				EntityInfo e = chainIds2entities.get(chain.getId());
 				chain.setEntityInfo(e);
 				e.addChain(chain);
- 			}
+			}
 		}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java
@@ -244,7 +244,7 @@ public String toPDB() {
 
 					toPDB(g,str);
 
- 					waterGroupsExist = true;
+					waterGroupsExist = true;
 				}
 
 			}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java

Original file line number	Diff line number	Diff line change
`@@ -389,7 +389,7 @@ private static TreeMap<String,EntityInfo> findEntitiesFromAlignment(List<List<Ch`
`389`	`389`	`EntityInfo e = chainIds2entities.get(chain.getId());`
`390`	`390`	`chain.setEntityInfo(e);`
`391`	`391`	`e.addChain(chain);`
`392`		`- }`
	`392`	`+ }`
`393`	`393`	`}`
`394`	`394`
`395`	`395`
Original file line number	Diff line number	Diff line change
`@@ -244,7 +244,7 @@ public String toPDB() {`
`244`	`244`
`245`	`245`	`toPDB(g,str);`
`246`	`246`
`247`		`- waterGroupsExist = true;`
	`247`	`+ waterGroupsExist = true;`
`248`	`248`	`}`
`249`	`249`
`250`	`250`	`}`