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Merge branch 'master' of github.com:biojava/biojava.github.io
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‎_wikis/BioJava:CookBook3:PSA.md‎

Lines changed: 104 additions & 104 deletions
Original file line numberDiff line numberDiff line change
@@ -23,29 +23,29 @@ import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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public class CookbookAlignPairGlobal {
2525

26-
` public static void main(String[] args) {`
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` String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
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` try {`
29-
` alignPairGlobal(ids[0], ids[1]);`
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` } catch (Exception e){`
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` e.printStackTrace();`
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` }`
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` }`
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35-
` private static void alignPairGlobal(String id1, String id2) throws Exception {`
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` ProteinSequence s1 = getSequenceForId(id1), s2 = getSequenceForId(id2);`
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` SubstitutionMatrix`<AminoAcidCompound>` matrix = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
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` 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 {`
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` 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);`
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` System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
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` return seq;`
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` }`
26+
public static void main(String[] args) {
27+
String[] ids = new String[] {"Q21691", "Q21495", "O48771"};
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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);
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System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());
47+
return seq;
48+
}
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}
5151

@@ -69,29 +69,29 @@ import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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public class CookbookAlignPairLocal {
7171

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-
` }`
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", 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+
}
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}
9797

@@ -121,35 +121,35 @@ import org.biojava.nbio.core.util.ConcurrencyTools;
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122122
public class CookbookAlignAllGlobal {
123123

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-
` }`
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", 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+
}
153153

154154
}
155155

@@ -176,35 +176,35 @@ 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", 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
}
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