Skip to content

Commit 0d4306e

Browse files
josemduartejosemduarte
committed
Fixing badly formatted page after automatic conversion
1 parent ed846ff commit 0d4306e

File tree

1 file changed

+70
-70
lines changed

1 file changed

+70
-70
lines changed

‎_wikis/BioJava:CookBook3:MSAProfiler.md‎

Lines changed: 70 additions & 70 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ title: BioJava:CookBook3:MSAProfiler
55
How to profile the time and memory used for Multiple Sequence Alignment in BioJava
66
==================================================================================
77

8-
<java>
8+
```java
99

1010
package org.biojava3.alignment;
1111

@@ -25,96 +25,96 @@ org.biojava.nbio.core.util.ConcurrencyTools;
2525

2626
public class CookbookMSAProfiler {
2727

28-
`   private static class Profiler {`
28+
   private static class Profiler {
2929

30-
`       private long maxMemoryUsed, timeCheckpoint;`
31-
`       private final long timeStart;`
30+
       private long maxMemoryUsed, timeCheckpoint;
31+
       private final long timeStart;
3232

33-
`       private Profiler() {`
34-
`           maxMemoryUsed = Runtime.getRuntime().totalMemory();`
35-
`           timeStart = timeCheckpoint = System.nanoTime();`
36-
`       }`
33+
       private Profiler() {
34+
           maxMemoryUsed = Runtime.getRuntime().totalMemory();
35+
           timeStart = timeCheckpoint = System.nanoTime();
36+
       }
3737

38-
`       private long getMaxMemoryUsed() {`
39-
`           return maxMemoryUsed = Math.max(maxMemoryUsed, Runtime.getRuntime().totalMemory());`
40-
`       }`
38+
       private long getMaxMemoryUsed() {
39+
           return maxMemoryUsed = Math.max(maxMemoryUsed, Runtime.getRuntime().totalMemory());
40+
       }
4141

42-
`       private long getTimeSinceCheckpoint() {`
43-
`           return System.nanoTime() - timeCheckpoint;`
44-
`       }`
42+
       private long getTimeSinceCheckpoint() {
43+
           return System.nanoTime() - timeCheckpoint;
44+
       }
4545

46-
`       private long getTimeSinceStart() {`
47-
`           return System.nanoTime() - timeStart;`
48-
`       }`
46+
       private long getTimeSinceStart() {
47+
           return System.nanoTime() - timeStart;
48+
       }
4949

50-
`       private void setCheckpoint() {`
51-
`           maxMemoryUsed = Math.max(maxMemoryUsed, Runtime.getRuntime().totalMemory());`
52-
`           timeCheckpoint = System.nanoTime();`
53-
`       }`
50+
       private void setCheckpoint() {
51+
           maxMemoryUsed = Math.max(maxMemoryUsed, Runtime.getRuntime().totalMemory());
52+
           timeCheckpoint = System.nanoTime();
53+
       }
5454

55-
`   }`
55+
   }
5656

57-
`   public static void main(String[] args) throws Exception {`
57+
   public static void main(String[] args) throws Exception {
5858

59-
`       if (args.length < 1) {`
60-
`           System.err.println("The first argument must be a fasta file of protein sequences.");`
61-
`           return;`
62-
`       }`
59+
       if (args.length < 1) {
60+
           System.err.println("The first argument must be a fasta file of protein sequences.");
61+
           return;
62+
       }
6363

64-
`       // ConcurrencyTools.setThreadPoolSingle();`
64+
       // ConcurrencyTools.setThreadPoolSingle();
6565

66-
`       PrintStream fout = new PrintStream("msa.txt");`
67-
`       Profiler profiler = new Profiler();`
66+
       PrintStream fout = new PrintStream("msa.txt");
67+
       Profiler profiler = new Profiler();
6868

69-
`       System.out.printf("Loading sequences from %s... ", args[0]);`
70-
`       List`<ProteinSequence>` list = new ArrayList`<ProteinSequence>`();`
71-
`       list.addAll(FastaReaderHelper.readFastaProteinSequence(new File(args[0])).values());`
72-
`       if (args.length > 1 && Integer.parseInt(args[1]) < list.size()) {`
73-
`           System.out.printf("%s/%d", args[1], list.size());`
74-
`           list = list.subList(0, Integer.parseInt(args[1]));`
75-
`       } else {`
76-
`           System.out.printf("%d", list.size());`
77-
`       }`
78-
`       System.out.printf(" sequences in %d ms using %d kB%n%n", profiler.getTimeSinceCheckpoint()/1000000,`
79-
`               profiler.getMaxMemoryUsed()/1024);`
69+
       System.out.printf("Loading sequences from %s... ", args[0]);
70+
       List<ProteinSequence> list = new ArrayList<ProteinSequence>();
71+
       list.addAll(FastaReaderHelper.readFastaProteinSequence(new File(args[0])).values());
72+
       if (args.length > 1 && Integer.parseInt(args[1]) < list.size()) {
73+
           System.out.printf("%s/%d", args[1], list.size());
74+
           list = list.subList(0, Integer.parseInt(args[1]));
75+
       } else {
76+
           System.out.printf("%d", list.size());
77+
       }
78+
       System.out.printf(" sequences in %d ms using %d kB%n%n", profiler.getTimeSinceCheckpoint()/1000000,
79+
               profiler.getMaxMemoryUsed()/1024);
8080

81-
`       profiler.setCheckpoint();`
81+
       profiler.setCheckpoint();
8282

83-
`       System.out.print("Stage 1: pairwise similarity calculation... ");`
84-
`       GapPenalty gaps = new SimpleGapPenalty();`
85-
`       SubstitutionMatrix`<AminoAcidCompound>` blosum62 = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
86-
`       List`<PairwiseSequenceScorer<ProteinSequence, AminoAcidCompound>`> scorers = Alignments.getAllPairsScorers(list,`
87-
`               PairwiseSequenceScorerType.GLOBAL_IDENTITIES, gaps, blosum62);`
88-
`       Alignments.runPairwiseScorers(scorers);`
89-
`       System.out.printf("%d scores in %d ms using %d kB%n%n", scorers.size(),`
90-
`               profiler.getTimeSinceCheckpoint()/1000000, profiler.getMaxMemoryUsed()/1024);`
83+
       System.out.print("Stage 1: pairwise similarity calculation... ");
84+
       GapPenalty gaps = new SimpleGapPenalty();
85+
       SubstitutionMatrix<AminoAcidCompound> blosum62 = new SimpleSubstitutionMatrix<AminoAcidCompound>();
86+
       List<PairwiseSequenceScorer<ProteinSequence, AminoAcidCompound>> scorers = Alignments.getAllPairsScorers(list,
87+
               PairwiseSequenceScorerType.GLOBAL_IDENTITIES, gaps, blosum62);
88+
       Alignments.runPairwiseScorers(scorers);
89+
       System.out.printf("%d scores in %d ms using %d kB%n%n", scorers.size(),
90+
               profiler.getTimeSinceCheckpoint()/1000000, profiler.getMaxMemoryUsed()/1024);
9191

92-
`       profiler.setCheckpoint();`
92+
       profiler.setCheckpoint();
9393

94-
`       System.out.print("Stage 2: hierarchical clustering into a guide tree... ");`
95-
`       GuideTree`<ProteinSequence, AminoAcidCompound>` tree = new GuideTree`<ProteinSequence, AminoAcidCompound>`(list,`
96-
`               scorers);`
97-
`       scorers = null;`
98-
`       System.out.printf("%d ms using %d kB%n%n%s%n%n", profiler.getTimeSinceCheckpoint()/1000000,`
99-
`               profiler.getMaxMemoryUsed()/1024, tree);`
94+
       System.out.print("Stage 2: hierarchical clustering into a guide tree... ");
95+
       GuideTree<ProteinSequence, AminoAcidCompound> tree = new GuideTree<ProteinSequence, AminoAcidCompound>(list,
96+
               scorers);
97+
       scorers = null;
98+
       System.out.printf("%d ms using %d kB%n%n%s%n%n", profiler.getTimeSinceCheckpoint()/1000000,
99+
               profiler.getMaxMemoryUsed()/1024, tree);
100100

101-
`       profiler.setCheckpoint();`
101+
       profiler.setCheckpoint();
102102

103-
`       System.out.print("Stage 3: progressive alignment... ");`
104-
`       Profile`<ProteinSequence, AminoAcidCompound>` msa = Alignments.getProgressiveAlignment(tree,`
105-
`               ProfileProfileAlignerType.GLOBAL, gaps, blosum62);`
106-
`       System.out.printf("%d profile-profile alignments in %d ms using %d kB%n%n", list.size() - 1,`
107-
`               profiler.getTimeSinceCheckpoint()/1000000, profiler.getMaxMemoryUsed()/1024);`
108-
`       fout.print(msa);`
109-
`       fout.close();`
103+
       System.out.print("Stage 3: progressive alignment... ");
104+
       Profile<ProteinSequence, AminoAcidCompound> msa = Alignments.getProgressiveAlignment(tree,
105+
               ProfileProfileAlignerType.GLOBAL, gaps, blosum62);
106+
       System.out.printf("%d profile-profile alignments in %d ms using %d kB%n%n", list.size() - 1,
107+
               profiler.getTimeSinceCheckpoint()/1000000, profiler.getMaxMemoryUsed()/1024);
108+
       fout.print(msa);
109+
       fout.close();
110110

111-
`       ConcurrencyTools.shutdown();`
111+
       ConcurrencyTools.shutdown();
112112

113-
`       System.out.printf("Total time: %d ms%nMemory use: %d kB%n", profiler.getTimeSinceStart()/1000000,`
114-
`               profiler.getMaxMemoryUsed()/1024);`
113+
       System.out.printf("Total time: %d ms%nMemory use: %d kB%n", profiler.getTimeSinceStart()/1000000,
114+
               profiler.getMaxMemoryUsed()/1024);
115115

116-
`   }`
116+
   }
117117

118118
}
119119

120-
</java>
120+
```

0 commit comments

Comments
 (0)