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andreasprlicandreasprlic
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trying to fix formatting issues
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‎_wikis/BioJava:CookBook3:PSA.md‎

Lines changed: 84 additions & 84 deletions
Original file line numberDiff line numberDiff line change
@@ -24,28 +24,28 @@ org.biojava.nbio.core.sequence.io.FastaReaderHelper;
2424

2525
public class CookbookAlignPairGlobal {
2626

27-
`   public static void main(String[] args) {`
28-
`       String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
29-
`       try {`
30-
`           alignPairGlobal(ids[0], ids[1]);`
31-
`       } catch (Exception e){`
32-
`           e.printStackTrace();`
33-
`       }`
27+
`   public static void main(String[] args) {`
28+
`       String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
29+
`       try {`
30+
`           alignPairGlobal(ids[0], ids[1]);`
31+
`       } catch (Exception e){`
32+
`           e.printStackTrace();`
33+
`       }`
3434
`   }`
3535

36-
`   private static void alignPairGlobal(String id1, String id2) throws Exception {`
37-
`       ProteinSequence s1 = getSequenceForId(id1), s2 = getSequenceForId(id2);`
38-
`       SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
39-
`       SequencePair`<ProteinSequence, AminoAcidCompound>` pair = Alignments.getPairwiseAlignment(s1, s2,`
40-
`               PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), matrix);`
41-
`       System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
36+
`   private static void alignPairGlobal(String id1, String id2) throws Exception {`
37+
`       ProteinSequence s1 = getSequenceForId(id1), s2 = getSequenceForId(id2);`
38+
`       SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
39+
`       SequencePair`<ProteinSequence, AminoAcidCompound>` pair = Alignments.getPairwiseAlignment(s1, s2,`
40+
`               PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), matrix);`
41+
`       System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
4242
`   }`
4343

44-
`   private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
45-
`       URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
46-
`       ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
47-
`       System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
48-
`       return seq;`
44+
`   private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
45+
`       URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
46+
`       ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
47+
`       System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
48+
`       return seq;`
4949
`   }`
5050

5151
}
@@ -71,28 +71,28 @@ org.biojava.nbio.core.sequence.io.FastaReaderHelper;
7171

7272
public class CookbookAlignPairLocal {
7373

74-
`   public static void main(String[] args) {`
75-
`       String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
76-
`       try {`
77-
`           alignPairLocal(ids[0], ids[1]);`
78-
`       } catch (Exception e){`
79-
`           e.printStackTrace();`
80-
`       }`
74+
`   public static void main(String[] args) {`
75+
`       String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
76+
`       try {`
77+
`           alignPairLocal(ids[0], ids[1]);`
78+
`       } catch (Exception e){`
79+
`           e.printStackTrace();`
80+
`       }`
8181
`   }`
8282

83-
`   private static void alignPairLocal(String id1, String id2) throws Exception {`
84-
`       ProteinSequence s1 = getSequenceForId(id1), s2 = getSequenceForId(id2);`
85-
`       SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
86-
`       SequencePair`<ProteinSequence, AminoAcidCompound>` pair = Alignments.getPairwiseAlignment(s1, s2,`
87-
`               PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);`
88-
`       System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
83+
`   private static void alignPairLocal(String id1, String id2) throws Exception {`
84+
`       ProteinSequence s1 = getSequenceForId(id1), s2 = getSequenceForId(id2);`
85+
`       SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
86+
`       SequencePair`<ProteinSequence, AminoAcidCompound>` pair = Alignments.getPairwiseAlignment(s1, s2,`
87+
`               PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);`
88+
`       System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
8989
`   }`
9090

91-
`   private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
92-
`       URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
93-
`       ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
94-
`       System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
95-
`       return seq;`
91+
`   private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
92+
`       URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
93+
`       ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
94+
`       System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
95+
`       return seq;`
9696
`   }`
9797

9898
}
@@ -122,34 +122,34 @@ org.biojava.nbio.core.util.ConcurrencyTools;
122122

123123
public class CookbookAlignAllGlobal {
124124

125-
`   public static void main(String[] args) {`
126-
`       String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
127-
`       try {`
128-
`           alignAllGlobal(ids);`
129-
`       } catch (Exception e){`
130-
`           e.printStackTrace();`
131-
`       }`
125+
`   public static void main(String[] args) {`
126+
`       String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
127+
`       try {`
128+
`           alignAllGlobal(ids);`
129+
`       } catch (Exception e){`
130+
`           e.printStackTrace();`
131+
`       }`
132132
`   }`
133133

134-
`   private static void alignAllGlobal(String[] ids) throws Exception {`
135-
`       List`<ProteinSequence>` lst = new ArrayList`<ProteinSequence>`();`
136-
`       for (String id : ids) {`
137-
`           lst.add(getSequenceForId(id));`
138-
`       }`
139-
`       SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
140-
`       List`<SequencePair<ProteinSequence, AminoAcidCompound>`> alig = Alignments.getAllPairsAlignments(lst,`
141-
`               PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), matrix);`
142-
`       for (SequencePair`<ProteinSequence, AminoAcidCompound>` pair : alig) {`
143-
`           System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
144-
`       }`
145-
`       ConcurrencyTools.shutdown();`
134+
`   private static void alignAllGlobal(String[] ids) throws Exception {`
135+
`       List`<ProteinSequence>` lst = new ArrayList`<ProteinSequence>`();`
136+
`       for (String id : ids) {`
137+
`           lst.add(getSequenceForId(id));`
138+
`       }`
139+
`       SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
140+
`       List`<SequencePair<ProteinSequence, AminoAcidCompound>`> alig = Alignments.getAllPairsAlignments(lst,`
141+
`               PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), matrix);`
142+
`       for (SequencePair`<ProteinSequence, AminoAcidCompound>` pair : alig) {`
143+
`           System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
144+
`       }`
145+
`       ConcurrencyTools.shutdown();`
146146
`   }`
147147

148-
`   private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
149-
`       URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
150-
`       ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
151-
`       System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
152-
`       return seq;`
148+
`   private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
149+
`       URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
150+
`       ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
151+
`       System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
152+
`       return seq;`
153153
`   }`
154154

155155
}
@@ -176,34 +176,34 @@ org.biojava.nbio.core.util.ConcurrencyTools;
176176

177177
public class CookbookAlignAllLocal {
178178

179-
`   public static void main(String[] args) {`
180-
`       String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
181-
`       try {`
182-
`           alignAllLocal(ids);`
183-
`       } catch (Exception e){`
184-
`           e.printStackTrace();`
185-
`       }`
179+
`   public static void main(String[] args) {`
180+
`       String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
181+
`       try {`
182+
`           alignAllLocal(ids);`
183+
`       } catch (Exception e){`
184+
`           e.printStackTrace();`
185+
`       }`
186186
`   }`
187187

188-
`   private static void alignAllLocal(String[] ids) throws Exception {`
189-
`       List`<ProteinSequence>` lst = new ArrayList`<ProteinSequence>`();`
190-
`       for (String id : ids) {`
191-
`           lst.add(getSequenceForId(id));`
192-
`       }`
193-
`       SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
194-
`       List`<SequencePair<ProteinSequence, AminoAcidCompound>`> alig = Alignments.getAllPairsAlignments(lst,`
195-
`               PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);`
196-
`       for (SequencePair`<ProteinSequence, AminoAcidCompound>` pair : alig) {`
197-
`           System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
198-
`       }`
199-
`       ConcurrencyTools.shutdown();`
188+
`   private static void alignAllLocal(String[] ids) throws Exception {`
189+
`       List`<ProteinSequence>` lst = new ArrayList`<ProteinSequence>`();`
190+
`       for (String id : ids) {`
191+
`           lst.add(getSequenceForId(id));`
192+
`       }`
193+
`       SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
194+
`       List`<SequencePair<ProteinSequence, AminoAcidCompound>`> alig = Alignments.getAllPairsAlignments(lst,`
195+
`               PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);`
196+
`       for (SequencePair`<ProteinSequence, AminoAcidCompound>` pair : alig) {`
197+
`           System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
198+
`       }`
199+
`       ConcurrencyTools.shutdown();`
200200
`   }`
201201

202-
`   private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
203-
`       URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
204-
`       ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
205-
`       System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
206-
`       return seq;`
202+
`   private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
203+
`       URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
204+
`       ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
205+
`       System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
206+
`       return seq;`
207207
`   }`
208208

209209
}

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