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‎_wikis/BioJava:CookBook3:PSA.md‎

Lines changed: 144 additions & 144 deletions
Original file line numberDiff line numberDiff line change
@@ -8,204 +8,204 @@ How to create a Pairwise Sequence Alignment in BioJava
88
Global alignment
99
----------------
1010

11-
<java>
11+
```java
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1313
package org.biojava.nbio.alignment;
1414

1515
import java.net.URL;
1616

17-
import
18-
org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
19-
import org.biojava.nbio.alignment.template.SequencePair; import
20-
org.biojava.nbio.alignment.template.SubstitutionMatrix; import
21-
org.biojava.nbio.core.sequence.ProteinSequence; import
22-
org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
23-
org.biojava.nbio.core.sequence.io.FastaReaderHelper;
17+
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
18+
import org.biojava.nbio.alignment.template.SequencePair;
19+
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
20+
import org.biojava.nbio.core.sequence.ProteinSequence;
21+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
22+
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
2423

2524
public class CookbookAlignPairGlobal {
2625

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-
`       }`
34-
`   }`
35-
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);`
42-
`   }`
43-
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;`
49-
`   }`
26+
` public static void main(String[] args) {`
27+
` String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
28+
` try {`
29+
` alignPairGlobal(ids[0], ids[1]);`
30+
` } catch (Exception e){`
31+
` e.printStackTrace();`
32+
` }`
33+
` }`
34+
35+
` private static void alignPairGlobal(String id1, String id2) throws Exception {`
36+
` ProteinSequence s1 = getSequenceForId(id1), s2 = getSequenceForId(id2);`
37+
` SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
38+
` SequencePair`<ProteinSequence, AminoAcidCompound>` pair = Alignments.getPairwiseAlignment(s1, s2,`
39+
` PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), matrix);`
40+
` System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
41+
` }`
42+
43+
` private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
44+
` URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
45+
` ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
46+
` System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
47+
` return seq;`
48+
` }`
5049

5150
}
5251

53-
</java>
52+
```
5453

5554
Local alignment
5655
---------------
5756

58-
<java>
57+
```java
5958

6059
package org.biojava.nbio.alignment;
6160

6261
import java.net.URL;
6362

64-
import
65-
org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
66-
import org.biojava.nbio.alignment.template.SequencePair; import
67-
org.biojava.nbio.alignment.template.SubstitutionMatrix; import
68-
org.biojava.nbio.core.sequence.ProteinSequence; import
69-
org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
70-
org.biojava.nbio.core.sequence.io.FastaReaderHelper;
63+
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
64+
import org.biojava.nbio.alignment.template.SequencePair;
65+
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
66+
import org.biojava.nbio.core.sequence.ProteinSequence;
67+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
68+
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
7169

7270
public class CookbookAlignPairLocal {
7371

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-
`       }`
81-
`   }`
82-
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);`
89-
`   }`
90-
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;`
96-
`   }`
72+
` public static void main(String[] args) {`
73+
` String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
74+
` try {`
75+
` alignPairLocal(ids[0], ids[1]);`
76+
` } catch (Exception e){`
77+
` e.printStackTrace();`
78+
` }`
79+
` }`
80+
81+
` private static void alignPairLocal(String id1, String id2) throws Exception {`
82+
` ProteinSequence s1 = getSequenceForId(id1), s2 = getSequenceForId(id2);`
83+
` SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
84+
` SequencePair`<ProteinSequence, AminoAcidCompound>` pair = Alignments.getPairwiseAlignment(s1, s2,`
85+
` PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);`
86+
` System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
87+
` }`
88+
89+
` private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
90+
` URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
91+
` ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
92+
` System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
93+
` return seq;`
94+
` }`
9795

9896
}
9997

100-
</java>
98+
```
10199

102100
How to concurrently create a PSA for each pair in a sequence list in BioJava
103101
============================================================================
104102

105103
Global alignments
106104
-----------------
107105

108-
<java>
106+
```java
109107

110108
package org.biojava3.alignment;
111109

112-
import java.net.URL; import java.util.ArrayList; import java.util.List;
110+
import java.net.URL;
111+
import java.util.ArrayList;
112+
import java.util.List;
113113

114-
import
115-
org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
116-
import org.biojava.nbio.alignment.template.SequencePair; import
117-
org.biojava.nbio.alignment.template.SubstitutionMatrix; import
118-
org.biojava.nbio.core.sequence.ProteinSequence; import
119-
org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
120-
org.biojava.nbio.core.sequence.io.FastaReaderHelper; import
121-
org.biojava.nbio.core.util.ConcurrencyTools;
114+
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
115+
import org.biojava.nbio.alignment.template.SequencePair;
116+
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
117+
import org.biojava.nbio.core.sequence.ProteinSequence;
118+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
119+
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
120+
import org.biojava.nbio.core.util.ConcurrencyTools;
122121

123122
public class CookbookAlignAllGlobal {
124123

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-
`       }`
132-
`   }`
133-
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();`
146-
`   }`
147-
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;`
153-
`   }`
124+
` public static void main(String[] args) {`
125+
` String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
126+
` try {`
127+
` alignAllGlobal(ids);`
128+
` } catch (Exception e){`
129+
` e.printStackTrace();`
130+
` }`
131+
` }`
132+
133+
` private static void alignAllGlobal(String[] ids) throws Exception {`
134+
` List`<ProteinSequence>` lst = new ArrayList`<ProteinSequence>`();`
135+
` for (String id : ids) {`
136+
` lst.add(getSequenceForId(id));`
137+
` }`
138+
` SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
139+
` List`<SequencePair<ProteinSequence, AminoAcidCompound>`> alig = Alignments.getAllPairsAlignments(lst,`
140+
` PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), matrix);`
141+
` for (SequencePair`<ProteinSequence, AminoAcidCompound>` pair : alig) {`
142+
` System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
143+
` }`
144+
` ConcurrencyTools.shutdown();`
145+
` }`
146+
147+
` private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
148+
` URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
149+
` ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
150+
` System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
151+
` return seq;`
152+
` }`
154153

155154
}
156155

157-
</java>
156+
```
158157

159158
Local alignments
160159
----------------
161160

162-
<java>
161+
```java
163162

164163
package org.biojava3.alignment;
165164

166-
import java.net.URL; import java.util.ArrayList; import java.util.List;
165+
import java.net.URL;
166+
import java.util.ArrayList;
167+
import java.util.List;
167168

168-
import
169-
org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
170-
import org.biojava.nbio.alignment.template.SequencePair; import
171-
org.biojava.nbio.alignment.template.SubstitutionMatrix; import
172-
org.biojava.nbio.core.sequence.ProteinSequence; import
173-
org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
174-
org.biojava.nbio.core.sequence.io.FastaReaderHelper; import
175-
org.biojava.nbio.core.util.ConcurrencyTools;
169+
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
170+
import org.biojava.nbio.alignment.template.SequencePair;
171+
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
172+
import org.biojava.nbio.core.sequence.ProteinSequence;
173+
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
174+
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
175+
import 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-
`       }`
186-
`   }`
187-
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();`
200-
`   }`
201-
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;`
207-
`   }`
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+
` }`
186+
` }`
187+
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();`
200+
` }`
201+
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;`
207+
` }`
208208

209209
}
210210

211-
</java>
211+
```

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