centers, R - rextester

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hamming <- function(s1, s2) {
  distances <- NA
  
  # Ensure the strings are equal length.
  if (nchar(s1) == nchar(s2)) {
    # Split the strings into characters.
    s1 <- unlist(strsplit(s1, ''))
    s2 <- unlist(strsplit(s2, ''))
    
    # Mark characters that do not match.
    distances <- sapply(seq_along(s1), function(index) {
      s1[index] == s2[index]
    })
  }
  
  # Return the number of different characters.
  length(which(!distances))
}

center <- function(input) {
  distances <- data.frame()
  
  # Compare string combinations, summing their distances.
  for (i in 1:length(input)) {
    totalDistance <- 0
    
    for (j in 1:length(input)) {
      if (j != i) {
        s1 <- input[i]
        s2 <- input[j]
        
        # Get hamming distance between the strings.
        distance <- hamming(s1, s2)

# Add to the total distance from all other strings.
        totalDistance <- totalDistance + distance
      }
    }
    
    # Record the total distance for this string against all other strings in the set.
    distances <- rbind(distances, data.frame(s1=s1, totalDistance=totalDistance))
  }
  
  distances[distances$totalDistance == min(distances$totalDistance),]$s1
}

inputs <- list(
  c('ATCAATATCAA',
  'ATTAAATAACT',
  'AATCCTTAAAC',
  'CTACTTTCTTT',
  'TCCCATCCTTT',
  'ACTTCAATATA'),
  c('CTCCATCACAC',
    'AATATCTACAT',
    'ACATTCTCCAT',
    'CCTCCCCACTC'),
  c('AACACCCTATA',
    'CTTCATCCACA',
    'TTTCAATTTTC',
    'ACAATCAAACC',
    'ATTCTACAACT',
    'ATTCCTTATTC',
    'ACTTCTCTATT',
    'TAAAACTCACC',
    'CTTTTCCCACC',
    'ACCTTTTCTCA',
    'TACCACTACTT'),
  c('ACAAAATCCTATCAAAAACTACCATACCAAT',
    'ACTATACTTCTAATATCATTCATTACACTTT',
    'TTAACTCCCATTATATATTATTAATTTACCC',
    'CCAACATACTAAACTTATTTTTTAACTACCA',
    'TTCTAAACATTACTCCTACACCTACATACCT',
    'ATCATCAATTACCTAATAATTCCCAATTTAT',
    'TCCCTAATCATACCATTTTACACTCAAAAAC',
    'AATTCAAACTTTACACACCCCTCTCATCATC',
    'CTCCATCTTATCATATAATAAACCAAATTTA',
    'AAAAATCCATCATTTTTTAATTCCATTCCTT',
    'CCACTCCAAACACAAAATTATTACAATAACA',
    'ATATTTACTCACACAAACAATTACCATCACA',
    'TTCAAATACAAATCTCAAAATCACCTTATTT',
    'TCCTTTAACAACTTCCCTTATCTATCTATTC',
    'CATCCATCCCAAAACTCTCACACATAACAAC',
    'ATTACTTATACAAAATAACTACTCCCCAATA',
    'TATATTTTAACCACTTACCAAAATCTCTACT',
    'TCTTTTATATCCATAAATCCAACAACTCCTA',
    'CTCTCAAACATATATTTCTATAACTCTTATC',
    'ACAAATAATAAAACATCCATTTCATTCATAA',
    'CACCACCAAACCTTATAATCCCCAACCACAC')
)

centers <- sapply(inputs, function(input) {
  center(input)
})
print(centers)

[ + ] Show input
Absolute running time: 1.33 sec, cpu time: 0.76 sec, memory peak: 31 Mb, absolute service time: 1,34 sec