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Merge branch 'master' into removeLoadChemCompInfo
# Conflicts: # biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java # biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1a4w.java # biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/MyTestHelper.java # biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java # biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/TmpAtomCache.java # biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java # biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java # biojava-structure/src/main/java/demo/DemoSCOP.java # biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java # biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java # biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileParsingParameters.java # biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java # biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java # biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/analysis/ScanSymmetry.java # biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java # biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java # biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestChemCompProvider.java # biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java # biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java # biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/test1DARSeqAlign.java
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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/CommandPrompt.java‎

Lines changed: 41 additions & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,7 @@
4141

4242

4343
public class CommandPrompt {
44-
44+
4545
/**
4646
* The main method
4747
* @param args
@@ -52,7 +52,7 @@ public class CommandPrompt {
5252
public static void main(String[] args) throws Exception{
5353
run(args);
5454
}
55-
55+
5656
private static AminoAcidCompositionTable checkForValidityAndObtainAATable(String inputLocation, int propertyListSize, String aminoAcidCompositionLocation,
5757
String elementMassLocation) throws Exception{
5858
if(inputLocation == null) {
@@ -73,7 +73,7 @@ private static AminoAcidCompositionTable checkForValidityAndObtainAATable(String
7373
}
7474
return aaTable;
7575
}
76-
76+
7777
private static void readInputAndGenerateOutput(String outputLocation, List<Character> propertyList, List<Character> specificList,
7878
String delimiter, String inputLocation, AminoAcidCompositionTable aaTable, int decimalPlace) throws Exception{
7979
PrintStream output;
@@ -90,7 +90,7 @@ private static void readInputAndGenerateOutput(String outputLocation, List<Chara
9090
}
9191
output.close();
9292
}
93-
93+
9494
public static void run(String[] args) throws Exception{
9595
/*
9696
* Parse input arguments
@@ -103,7 +103,7 @@ public static void run(String[] args) throws Exception{
103103
String elementMassLocation = null;
104104
String delimiter = ",";
105105
int decimalPlace = 4;
106-
106+
107107
for(int i = 0; i < args.length; i++){
108108
if(args[i].charAt(0) != '-' || args[i].length() != 2){
109109
showHelp();
@@ -144,13 +144,13 @@ public static void run(String[] args) throws Exception{
144144
case '7': propertyList.add('7'); break;
145145
case '8': propertyList.add('8'); break;
146146
case '9': propertyList.add('9'); break;
147-
case '0':
148-
propertyList.add('0');
147+
case '0':
148+
propertyList.add('0');
149149
i++;
150150
if(args[i].length() != 1) throw new Error("Invalid value: " + args[i] + ". Amino Acid Symbol should be of single character");
151-
specificList.add(args[i].toUpperCase().charAt(0));
151+
specificList.add(args[i].toUpperCase().charAt(0));
152152
break;
153-
default:
153+
default:
154154
showHelp();
155155
throw new Error("Unknown option: " + args[i]);
156156
}
@@ -160,15 +160,15 @@ public static void run(String[] args) throws Exception{
160160
/*
161161
* Check for validity of input arguments
162162
*/
163-
AminoAcidCompositionTable aaTable = checkForValidityAndObtainAATable(inputLocation, propertyList.size(), aminoAcidCompositionLocation,
163+
AminoAcidCompositionTable aaTable = checkForValidityAndObtainAATable(inputLocation, propertyList.size(), aminoAcidCompositionLocation,
164164
elementMassLocation);
165-
165+
166166
/*
167167
* Read input file and generate output
168168
*/
169169
readInputAndGenerateOutput(outputLocation, propertyList, specificList, delimiter, inputLocation, aaTable, decimalPlace);
170170
}
171-
171+
172172
private static LinkedHashMap<String, ProteinSequence> readInputFile(String inputLocation, AminoAcidCompositionTable aaTable) throws Exception{
173173
FileInputStream inStream = new FileInputStream(inputLocation);
174174
CompoundSet<AminoAcidCompound> set;
@@ -180,29 +180,29 @@ private static LinkedHashMap<String, ProteinSequence> readInputFile(String input
180180
LinkedHashMap<String, ProteinSequence> ret;
181181
if ( inputLocation.toLowerCase().contains(".gb")) {
182182
GenbankReader<ProteinSequence, AminoAcidCompound> genbankReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
183-
inStream, new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
183+
inStream, new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
184184
new ProteinSequenceCreator(set));
185185
ret = genbankReader.process();
186-
187-
186+
187+
188188
} else {
189189
FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
190-
inStream, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
190+
inStream, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
191191
new ProteinSequenceCreator(set));
192192
ret = fastaReader.process();
193-
193+
194194
}
195195
return ret;
196196
}
197-
198-
public enum PropertyName{MolecularWeight, Absorbance_True, Absorbance_False, ExtinctionCoefficient_True, ExtinctionCoefficient_False,
199-
InstabilityIndex, ApliphaticIndex, AverageHydropathyValue, IsoelectricPoint, NetCharge_pH_7, A, R,
197+
198+
public enum PropertyName{MolecularWeight, Absorbance_True, Absorbance_False, ExtinctionCoefficient_True, ExtinctionCoefficient_False,
199+
InstabilityIndex, ApliphaticIndex, AverageHydropathyValue, IsoelectricPoint, NetCharge_pH_7, A, R,
200200
N, D, C, E, Q, G, H, I, L,
201201
K, M, F, P, S, T, W, Y, V};
202-
202+
203203
private static void printHeader(PrintStream output, List<Character> propertyList, List<Character> specificList, String delimiter) throws IOException{
204204
int specificCount = 0;
205-
/*
205+
/*
206206
* 1 Molecular weight
207207
* 2 Absorbance (assumed Cys reduced and assume Cys to form cystines)
208208
* 3 Extinction coefficient (assumed Cys reduced and assume Cys to form cystines)
@@ -226,9 +226,9 @@ private static void printHeader(PrintStream output, List<Character> propertyList
226226
case '6': sList.add(PropertyName.AverageHydropathyValue.toString()); break;
227227
case '7': sList.add(PropertyName.IsoelectricPoint.toString()); break;
228228
case '8': sList.add(PropertyName.NetCharge_pH_7.toString()); break;
229-
case '9':
230-
sList.add(PropertyName.A.toString()); sList.add(PropertyName.R.toString());
231-
sList.add(PropertyName.N.toString()); sList.add(PropertyName.D.toString());
229+
case '9':
230+
sList.add(PropertyName.A.toString()); sList.add(PropertyName.R.toString());
231+
sList.add(PropertyName.N.toString()); sList.add(PropertyName.D.toString());
232232
sList.add(PropertyName.C.toString()); sList.add(PropertyName.E.toString());
233233
sList.add(PropertyName.Q.toString()); sList.add(PropertyName.G.toString());
234234
sList.add(PropertyName.H.toString()); sList.add(PropertyName.I.toString());
@@ -249,9 +249,9 @@ private static void printHeader(PrintStream output, List<Character> propertyList
249249
output.flush();
250250
}
251251

252-
private static void compute(PrintStream output, String header, String sequence, String delimiter,
252+
private static void compute(PrintStream output, String header, String sequence, String delimiter,
253253
AminoAcidCompositionTable aaTable, List<Character> propertyList, List<Character> specificList, int decimalPlace) throws CompoundNotFoundException{
254-
/*
254+
/*
255255
* 1 Molecular weight
256256
* 2 Absorbance (assumed Cys reduced and assume Cys to form cystines)
257257
* 3 Extinction coefficient
@@ -268,38 +268,38 @@ private static void compute(PrintStream output, String header, String sequence,
268268
if(aaTable != null){
269269
sequence = Utils.checkSequence(sequence, aaTable.getSymbolSet());
270270
pSequence = new ProteinSequence(sequence, aaTable.getAminoAcidCompoundSet());
271-
aaSet = aaTable.getAminoAcidCompoundSet();
271+
aaSet = aaTable.getAminoAcidCompoundSet();
272272
}else{
273273
sequence = Utils.checkSequence(sequence);
274274
pSequence = new ProteinSequence(sequence);
275275
aaSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
276276
}
277277
IPeptideProperties pp = new PeptidePropertiesImpl();
278-
278+
279279
int specificCount = 0;
280280
List<Double> dList = new ArrayList<Double>();
281281
for(Character c:propertyList){
282282
switch(c){
283-
case '1':
284-
if(aaTable == null)
283+
case '1':
284+
if(aaTable == null)
285285
dList.add(pp.getMolecularWeight(pSequence));
286-
else
286+
else
287287
dList.add(pp.getMolecularWeight(pSequence));
288288
break;
289-
case '2':
290-
dList.add(pp.getAbsorbance(pSequence, true));
291-
dList.add(pp.getAbsorbance(pSequence, false));
289+
case '2':
290+
dList.add(pp.getAbsorbance(pSequence, true));
291+
dList.add(pp.getAbsorbance(pSequence, false));
292292
break;
293-
case '3':
293+
case '3':
294294
dList.add(pp.getExtinctionCoefficient(pSequence, true));
295-
dList.add(pp.getExtinctionCoefficient(pSequence, false));
295+
dList.add(pp.getExtinctionCoefficient(pSequence, false));
296296
break;
297297
case '4': dList.add(pp.getInstabilityIndex(pSequence)); break;
298298
case '5': dList.add(pp.getApliphaticIndex(pSequence)); break;
299299
case '6': dList.add(pp.getAvgHydropathy(pSequence)); break;
300300
case '7': dList.add(pp.getIsoelectricPoint(pSequence)); break;
301301
case '8': dList.add(pp.getNetCharge(pSequence)); break;
302-
case '9':
302+
case '9':
303303
Map<AminoAcidCompound, Double> aaCompound2Double = pp.getAAComposition(pSequence);
304304
//(A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V)
305305
dList.add(aaCompound2Double.get(Constraints.A));
@@ -338,7 +338,7 @@ private static void showHelp(){
338338
System.err.println("NAME");
339339
System.err.println("\tAn executable to generate physico-chemical properties of protein sequences.");
340340
System.err.println();
341-
341+
342342
System.err.println("EXAMPLES");
343343
System.err.println("\tjava -jar AAProperties.jar -i test.fasta -a");
344344
System.err.println("\t\tGenerates all possible properties.");
@@ -349,7 +349,7 @@ private static void showHelp(){
349349
System.err.println("\tjava -jar AAProperties.jar -i test.fasta -0 A -0 N -1");
350350
System.err.println("\t\tGenerates composition of two specific amino acid symbol and molecular weight.");
351351
System.err.println();
352-
352+
353353
System.err.println("OPTIONS");
354354
System.err.println("\tRequired");
355355
System.err.println("\t\t-i location of input FASTA file");
@@ -362,7 +362,7 @@ private static void showHelp(){
362362
System.err.println("\t\t-y location of Element Mass XML file for defining mass of elements");
363363
System.err.println("\t\t-d number of decimals (int) [4 (default)]");
364364
System.err.println();
365-
365+
366366
System.err.println("\tProvide at least one of them");
367367
System.err.println("\t\t-a compute properties of option 1-9");
368368
System.err.println("\t\t-1 compute molecular weight");

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