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sblivensbliven
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Converting initial spaces to tabs.
This was done in several steps: 1. Fix unambiguous cases automatically (468 files) - python development/spacestotabs.py -t .8 -x $(find . -iname '*.java'|tr \\n ' ') 2. Lower the threshold (.4) and check the results manually. Where needed, do additional reformatting in eclipse or by hand. (128 files) 3. Manually look through the remaining cases (45 files) Some files (e.g. PDBFileParser.java) had legitimate uses for spaces in comment blocks and were reverted.
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‎biojava-aa-prop/src/main/java/demo/BioJavaAADemo.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -32,11 +32,11 @@
3232
public class BioJavaAADemo {
3333

3434

35-
public static void main(String[] args) throws CompoundNotFoundException {
36-
ProteinSequence pSequence = new ProteinSequence("VLSPADKTNVKAAWGKVGAHAG");
35+
public static void main(String[] args) throws CompoundNotFoundException {
36+
ProteinSequence pSequence = new ProteinSequence("VLSPADKTNVKAAWGKVGAHAG");
3737

38-
IPeptideProperties pp = new PeptidePropertiesImpl();
38+
IPeptideProperties pp = new PeptidePropertiesImpl();
3939

40-
System.out.println("Peptide Properties: " + pp.getIsoelectricPoint(pSequence));
41-
}
40+
System.out.println("Peptide Properties: " + pp.getIsoelectricPoint(pSequence));
41+
}
4242
}

‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -315,7 +315,7 @@ public static final double getApliphaticIndex(String sequence) {
315315
ProteinSequence pSequence = null;
316316
try {
317317
pSequence = new ProteinSequence(sequence);
318-
} catch (CompoundNotFoundException e) {
318+
} catch (CompoundNotFoundException e) {
319319
// the sequence was checked with Utils.checkSequence, this shouldn't happen
320320
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
321321
}

‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -43,16 +43,16 @@ public abstract class Convertor {
4343
public final static char group3 = '3';
4444
public final static char unknownGroup = '0';
4545

46-
/**
47-
* Returns the grouping of the amino acid character.
46+
/**
47+
* Returns the grouping of the amino acid character.
4848
* The aminoAcid argument is preferably of non-ambiguous characters.
4949
* Standard amino acids will be converted to '1', '2' or '3' depending on its grouping
5050
* Non-standard amino acids are simply converted to '0'.
5151
*
5252
* @param aminoAcid
5353
* an amino acid character preferably of non-ambiguous characters
5454
* @return its grouping
55-
*/
55+
*/
5656
public abstract char convert(char aminoAcid);
5757

5858
/**

‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java‎

Lines changed: 146 additions & 146 deletions
Original file line numberDiff line numberDiff line change
@@ -39,169 +39,169 @@
3939
*/
4040
public class CaseFreeAminoAcidCompoundSet implements CompoundSet<AminoAcidCompound> {
4141

42-
private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<String, AminoAcidCompound>();
43-
private final Map<AminoAcidCompound, Set<AminoAcidCompound>> equivalentsCache =
44-
new HashMap<AminoAcidCompound, Set<AminoAcidCompound>>();
45-
46-
public CaseFreeAminoAcidCompoundSet() {
47-
aminoAcidCompoundCache.put("A", new AminoAcidCompound(null, "A", "Ala", "Alanine", 71.0788f));
48-
aminoAcidCompoundCache.put("R", new AminoAcidCompound(null, "R", "Arg", "Arginine", 156.1875f));
49-
aminoAcidCompoundCache.put("N", new AminoAcidCompound(null, "N", "Asn", "Asparagine", 114.1039f));
50-
aminoAcidCompoundCache.put("D", new AminoAcidCompound(null, "D", "Asp", "Aspartic acid", 115.0886f));
51-
aminoAcidCompoundCache.put("C", new AminoAcidCompound(null, "C", "Cys", "Cysteine", 103.1388f));
52-
aminoAcidCompoundCache.put("E", new AminoAcidCompound(null, "E", "Glu", "Glutamic acid", 129.1155f));
53-
aminoAcidCompoundCache.put("Q", new AminoAcidCompound(null, "Q", "Gln", "Glutamine", 128.1307f));
54-
aminoAcidCompoundCache.put("G", new AminoAcidCompound(null, "G", "Gly", "Glycine", 57.0519f));
55-
aminoAcidCompoundCache.put("H", new AminoAcidCompound(null, "H", "His", "Histidine", 137.1411f));
56-
aminoAcidCompoundCache.put("I", new AminoAcidCompound(null, "I", "Ile", "Isoleucine", 113.1594f));
57-
aminoAcidCompoundCache.put("L", new AminoAcidCompound(null, "L", "Leu", "Leucine", 113.1594f));
58-
aminoAcidCompoundCache.put("K", new AminoAcidCompound(null, "K", "Lys", "Lysine", 128.1741f));
59-
aminoAcidCompoundCache.put("M", new AminoAcidCompound(null, "M", "Met", "Methionine", 131.1986f));
60-
aminoAcidCompoundCache.put("F", new AminoAcidCompound(null, "F", "Phe", "Phenylalanine", 147.1766f));
61-
aminoAcidCompoundCache.put("P", new AminoAcidCompound(null, "P", "Pro", "Proline", 97.1167f));
62-
aminoAcidCompoundCache.put("S", new AminoAcidCompound(null, "S", "Ser", "Serine", 87.0782f));
63-
aminoAcidCompoundCache.put("T", new AminoAcidCompound(null, "T", "Thr", "Threonine", 101.1051f));
64-
aminoAcidCompoundCache.put("W", new AminoAcidCompound(null, "W", "Trp", "Tryptophan", 186.2132f));
65-
aminoAcidCompoundCache.put("Y", new AminoAcidCompound(null, "Y", "Tyr", "Tyrosine", 163.1760f));
66-
aminoAcidCompoundCache.put("V", new AminoAcidCompound(null, "V", "Val", "Valine", 99.1326f));
67-
aminoAcidCompoundCache.put("B", new AminoAcidCompound(null, "B", "Asx", "Asparagine or Aspartic acid", null));
68-
aminoAcidCompoundCache.put("Z", new AminoAcidCompound(null, "Z", "Glx", "Glutamine or Glutamic acid", null));
69-
aminoAcidCompoundCache.put("J", new AminoAcidCompound(null, "J", "Xle", "Leucine or Isoleucine", null));
70-
aminoAcidCompoundCache.put("X", new AminoAcidCompound(null, "X", "Xaa", "Unspecified", null));
71-
aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "---", "Unspecified", null));
72-
aminoAcidCompoundCache.put(".", new AminoAcidCompound(null, ".", "...", "Unspecified", null));
73-
aminoAcidCompoundCache.put("_", new AminoAcidCompound(null, "_", "___", "Unspecified", null));
74-
aminoAcidCompoundCache.put("*", new AminoAcidCompound(null, "*", "***", "Stop", null));
75-
76-
//Selenocysteine - this is encoded by UGA with the presence
77-
//of a SECIS element (SElenoCysteine Insertion Sequence) in the mRNA
78-
//and is a post-translation modification
79-
aminoAcidCompoundCache.put("U", new AminoAcidCompound(null, "U", "Sec", "Selenocysteine", 150.0388f));
80-
81-
//Pyrrolysine is encoded by UAG in mRNA (normally Amber stop codon) which is translated to
82-
//this amino acid under the presence of pylT which creates an anti-codon CUA & pylS
83-
//which then does the actual conversion to Pyl.
84-
aminoAcidCompoundCache.put("O", new AminoAcidCompound(null, "O", "Pyl", "Pyrrolysine", 255.3172f));
85-
86-
Map<String, AminoAcidCompound> lowerCaseSet = new HashMap<String, AminoAcidCompound>();
87-
for(String s:this.aminoAcidCompoundCache.keySet()){
88-
lowerCaseSet.put(s.toLowerCase(), this.aminoAcidCompoundCache.get(s));
89-
}
90-
this.aminoAcidCompoundCache.putAll(lowerCaseSet);
91-
}
92-
93-
@Override
42+
private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<String, AminoAcidCompound>();
43+
private final Map<AminoAcidCompound, Set<AminoAcidCompound>> equivalentsCache =
44+
new HashMap<AminoAcidCompound, Set<AminoAcidCompound>>();
45+
46+
public CaseFreeAminoAcidCompoundSet() {
47+
aminoAcidCompoundCache.put("A", new AminoAcidCompound(null, "A", "Ala", "Alanine", 71.0788f));
48+
aminoAcidCompoundCache.put("R", new AminoAcidCompound(null, "R", "Arg", "Arginine", 156.1875f));
49+
aminoAcidCompoundCache.put("N", new AminoAcidCompound(null, "N", "Asn", "Asparagine", 114.1039f));
50+
aminoAcidCompoundCache.put("D", new AminoAcidCompound(null, "D", "Asp", "Aspartic acid", 115.0886f));
51+
aminoAcidCompoundCache.put("C", new AminoAcidCompound(null, "C", "Cys", "Cysteine", 103.1388f));
52+
aminoAcidCompoundCache.put("E", new AminoAcidCompound(null, "E", "Glu", "Glutamic acid", 129.1155f));
53+
aminoAcidCompoundCache.put("Q", new AminoAcidCompound(null, "Q", "Gln", "Glutamine", 128.1307f));
54+
aminoAcidCompoundCache.put("G", new AminoAcidCompound(null, "G", "Gly", "Glycine", 57.0519f));
55+
aminoAcidCompoundCache.put("H", new AminoAcidCompound(null, "H", "His", "Histidine", 137.1411f));
56+
aminoAcidCompoundCache.put("I", new AminoAcidCompound(null, "I", "Ile", "Isoleucine", 113.1594f));
57+
aminoAcidCompoundCache.put("L", new AminoAcidCompound(null, "L", "Leu", "Leucine", 113.1594f));
58+
aminoAcidCompoundCache.put("K", new AminoAcidCompound(null, "K", "Lys", "Lysine", 128.1741f));
59+
aminoAcidCompoundCache.put("M", new AminoAcidCompound(null, "M", "Met", "Methionine", 131.1986f));
60+
aminoAcidCompoundCache.put("F", new AminoAcidCompound(null, "F", "Phe", "Phenylalanine", 147.1766f));
61+
aminoAcidCompoundCache.put("P", new AminoAcidCompound(null, "P", "Pro", "Proline", 97.1167f));
62+
aminoAcidCompoundCache.put("S", new AminoAcidCompound(null, "S", "Ser", "Serine", 87.0782f));
63+
aminoAcidCompoundCache.put("T", new AminoAcidCompound(null, "T", "Thr", "Threonine", 101.1051f));
64+
aminoAcidCompoundCache.put("W", new AminoAcidCompound(null, "W", "Trp", "Tryptophan", 186.2132f));
65+
aminoAcidCompoundCache.put("Y", new AminoAcidCompound(null, "Y", "Tyr", "Tyrosine", 163.1760f));
66+
aminoAcidCompoundCache.put("V", new AminoAcidCompound(null, "V", "Val", "Valine", 99.1326f));
67+
aminoAcidCompoundCache.put("B", new AminoAcidCompound(null, "B", "Asx", "Asparagine or Aspartic acid", null));
68+
aminoAcidCompoundCache.put("Z", new AminoAcidCompound(null, "Z", "Glx", "Glutamine or Glutamic acid", null));
69+
aminoAcidCompoundCache.put("J", new AminoAcidCompound(null, "J", "Xle", "Leucine or Isoleucine", null));
70+
aminoAcidCompoundCache.put("X", new AminoAcidCompound(null, "X", "Xaa", "Unspecified", null));
71+
aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "---", "Unspecified", null));
72+
aminoAcidCompoundCache.put(".", new AminoAcidCompound(null, ".", "...", "Unspecified", null));
73+
aminoAcidCompoundCache.put("_", new AminoAcidCompound(null, "_", "___", "Unspecified", null));
74+
aminoAcidCompoundCache.put("*", new AminoAcidCompound(null, "*", "***", "Stop", null));
75+
76+
//Selenocysteine - this is encoded by UGA with the presence
77+
//of a SECIS element (SElenoCysteine Insertion Sequence) in the mRNA
78+
//and is a post-translation modification
79+
aminoAcidCompoundCache.put("U", new AminoAcidCompound(null, "U", "Sec", "Selenocysteine", 150.0388f));
80+
81+
//Pyrrolysine is encoded by UAG in mRNA (normally Amber stop codon) which is translated to
82+
//this amino acid under the presence of pylT which creates an anti-codon CUA & pylS
83+
//which then does the actual conversion to Pyl.
84+
aminoAcidCompoundCache.put("O", new AminoAcidCompound(null, "O", "Pyl", "Pyrrolysine", 255.3172f));
85+
86+
Map<String, AminoAcidCompound> lowerCaseSet = new HashMap<String, AminoAcidCompound>();
87+
for(String s:this.aminoAcidCompoundCache.keySet()){
88+
lowerCaseSet.put(s.toLowerCase(), this.aminoAcidCompoundCache.get(s));
89+
}
90+
this.aminoAcidCompoundCache.putAll(lowerCaseSet);
91+
}
92+
93+
@Override
9494
public String getStringForCompound(AminoAcidCompound compound) {
95-
return compound.toString();
96-
}
95+
return compound.toString();
96+
}
9797

98-
@Override
98+
@Override
9999
public AminoAcidCompound getCompoundForString(String string) {
100-
if (string.length() == 0) {
101-
return null;
102-
}
103-
if (string.length() > this.getMaxSingleCompoundStringLength()) {
104-
throw new IllegalArgumentException("String supplied ("+string+") is too long. Max is "+getMaxSingleCompoundStringLength());
105-
}
106-
return this.aminoAcidCompoundCache.get(string);
107-
}
108-
109-
@Override
100+
if (string.length() == 0) {
101+
return null;
102+
}
103+
if (string.length() > this.getMaxSingleCompoundStringLength()) {
104+
throw new IllegalArgumentException("String supplied ("+string+") is too long. Max is "+getMaxSingleCompoundStringLength());
105+
}
106+
return this.aminoAcidCompoundCache.get(string);
107+
}
108+
109+
@Override
110110
public int getMaxSingleCompoundStringLength() {
111-
return 1;
112-
}
111+
return 1;
112+
}
113113

114114

115-
@Override
115+
@Override
116116
public boolean isCompoundStringLengthEqual() {
117-
return true;
118-
}
117+
return true;
118+
}
119119

120-
private final static CaseFreeAminoAcidCompoundSet aminoAcidCompoundSet = new CaseFreeAminoAcidCompoundSet();
120+
private final static CaseFreeAminoAcidCompoundSet aminoAcidCompoundSet = new CaseFreeAminoAcidCompoundSet();
121121

122-
public static CaseFreeAminoAcidCompoundSet getAminoAcidCompoundSet() {
123-
return aminoAcidCompoundSet;
124-
}
122+
public static CaseFreeAminoAcidCompoundSet getAminoAcidCompoundSet() {
123+
return aminoAcidCompoundSet;
124+
}
125125

126-
@Override
126+
@Override
127127
public boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo) {
128-
Set<AminoAcidCompound> equivalents = getEquivalentCompounds(compoundOne);
129-
return (equivalents != null) && equivalents.contains(compoundTwo);
130-
}
128+
Set<AminoAcidCompound> equivalents = getEquivalentCompounds(compoundOne);
129+
return (equivalents != null) && equivalents.contains(compoundTwo);
130+
}
131131

132-
@Override
132+
@Override
133133
public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound) {
134-
if (equivalentsCache.isEmpty()) {
135-
// most compounds are equivalent to themselves alone
136-
for (AminoAcidCompound c : aminoAcidCompoundCache.values()) {
137-
equivalentsCache.put(c, Collections.singleton(c));
138-
}
139-
// ambiguous Asparagine or Aspartic acid
140-
addAmbiguousEquivalents("N", "D", "B");
141-
// ambiguous Glutamine or Glutamic acid
142-
addAmbiguousEquivalents("E", "Q", "Z");
143-
// ambiguous Leucine or Isoleucine
144-
addAmbiguousEquivalents("I", "L", "J");
145-
// ambiguous gaps
146-
AminoAcidCompound gap1, gap2, gap3;
147-
Set<AminoAcidCompound> gaps = new HashSet<AminoAcidCompound>();
148-
gaps.add(gap1 = aminoAcidCompoundCache.get("-"));
149-
gaps.add(gap2 = aminoAcidCompoundCache.get("."));
150-
gaps.add(gap3 = aminoAcidCompoundCache.get("_"));
151-
equivalentsCache.put(gap1, gaps);
152-
equivalentsCache.put(gap2, gaps);
153-
equivalentsCache.put(gap3, gaps);
154-
// X is never equivalent, even to itself
155-
equivalentsCache.put(aminoAcidCompoundCache.get("X"), new HashSet<AminoAcidCompound>());
156-
}
157-
return equivalentsCache.get(compound);
158-
}
159-
160-
// helper method to initialize the equivalent sets for 2 amino acid compounds and their ambiguity compound
161-
private void addAmbiguousEquivalents(String one, String two, String either) {
162-
Set<AminoAcidCompound> equivalents;
163-
AminoAcidCompound cOne, cTwo, cEither;
164-
165-
equivalents = new HashSet<AminoAcidCompound>();
166-
equivalents.add(cOne = aminoAcidCompoundCache.get(one));
167-
equivalents.add(cTwo = aminoAcidCompoundCache.get(two));
168-
equivalents.add(cEither = aminoAcidCompoundCache.get(either));
169-
equivalentsCache.put(cEither, equivalents);
170-
171-
equivalents = new HashSet<AminoAcidCompound>();
172-
equivalents.add(cOne);
173-
equivalents.add(cEither);
174-
equivalentsCache.put(cOne, equivalents);
175-
176-
equivalents = new HashSet<AminoAcidCompound>();
177-
equivalents.add(cTwo);
178-
equivalents.add(cEither);
179-
equivalentsCache.put(cTwo, equivalents);
180-
}
181-
182-
@Override
134+
if (equivalentsCache.isEmpty()) {
135+
// most compounds are equivalent to themselves alone
136+
for (AminoAcidCompound c : aminoAcidCompoundCache.values()) {
137+
equivalentsCache.put(c, Collections.singleton(c));
138+
}
139+
// ambiguous Asparagine or Aspartic acid
140+
addAmbiguousEquivalents("N", "D", "B");
141+
// ambiguous Glutamine or Glutamic acid
142+
addAmbiguousEquivalents("E", "Q", "Z");
143+
// ambiguous Leucine or Isoleucine
144+
addAmbiguousEquivalents("I", "L", "J");
145+
// ambiguous gaps
146+
AminoAcidCompound gap1, gap2, gap3;
147+
Set<AminoAcidCompound> gaps = new HashSet<AminoAcidCompound>();
148+
gaps.add(gap1 = aminoAcidCompoundCache.get("-"));
149+
gaps.add(gap2 = aminoAcidCompoundCache.get("."));
150+
gaps.add(gap3 = aminoAcidCompoundCache.get("_"));
151+
equivalentsCache.put(gap1, gaps);
152+
equivalentsCache.put(gap2, gaps);
153+
equivalentsCache.put(gap3, gaps);
154+
// X is never equivalent, even to itself
155+
equivalentsCache.put(aminoAcidCompoundCache.get("X"), new HashSet<AminoAcidCompound>());
156+
}
157+
return equivalentsCache.get(compound);
158+
}
159+
160+
// helper method to initialize the equivalent sets for 2 amino acid compounds and their ambiguity compound
161+
private void addAmbiguousEquivalents(String one, String two, String either) {
162+
Set<AminoAcidCompound> equivalents;
163+
AminoAcidCompound cOne, cTwo, cEither;
164+
165+
equivalents = new HashSet<AminoAcidCompound>();
166+
equivalents.add(cOne = aminoAcidCompoundCache.get(one));
167+
equivalents.add(cTwo = aminoAcidCompoundCache.get(two));
168+
equivalents.add(cEither = aminoAcidCompoundCache.get(either));
169+
equivalentsCache.put(cEither, equivalents);
170+
171+
equivalents = new HashSet<AminoAcidCompound>();
172+
equivalents.add(cOne);
173+
equivalents.add(cEither);
174+
equivalentsCache.put(cOne, equivalents);
175+
176+
equivalents = new HashSet<AminoAcidCompound>();
177+
equivalents.add(cTwo);
178+
equivalents.add(cEither);
179+
equivalentsCache.put(cTwo, equivalents);
180+
}
181+
182+
@Override
183183
public boolean hasCompound(AminoAcidCompound compound) {
184-
return aminoAcidCompoundCache.containsValue(compound);
185-
}
184+
return aminoAcidCompoundCache.containsValue(compound);
185+
}
186186

187-
@Override
187+
@Override
188188
public List<AminoAcidCompound> getAllCompounds() {
189-
return new ArrayList<AminoAcidCompound>(aminoAcidCompoundCache.values());
190-
}
189+
return new ArrayList<AminoAcidCompound>(aminoAcidCompoundCache.values());
190+
}
191191

192192

193-
@Override
193+
@Override
194194
public boolean isComplementable() {
195-
return false;
196-
}
197-
198-
@Override
199-
public boolean isValidSequence(Sequence<AminoAcidCompound> sequence) {
200-
for (AminoAcidCompound c: sequence) {
201-
if (!hasCompound(c)) {
202-
return false;
203-
}
204-
}
205-
return true;
206-
}
195+
return false;
196+
}
197+
198+
@Override
199+
public boolean isValidSequence(Sequence<AminoAcidCompound> sequence) {
200+
for (AminoAcidCompound c: sequence) {
201+
if (!hasCompound(c)) {
202+
return false;
203+
}
204+
}
205+
return true;
206+
}
207207
}

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