--- /dev/null
+package jalview.analysis;
+
+import jalview.bin.Cache;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.StringTokenizer;
+
+/**
+ * A singleton that provides instances of genetic code translation tables
+ *
+ * @author gmcarstairs
+ * @see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
+ */
+public final class GeneticCodes
+{
+ private static final int CODON_LENGTH = 3;
+
+ private static final String QUOTE = "\"";
+
+ /*
+ * nucleotides as ordered in data file
+ */
+ private static final String NUCS = "TCAG";
+
+ private static final int NUCS_COUNT = NUCS.length();
+
+ private static final int NUCS_COUNT_SQUARED = NUCS_COUNT * NUCS_COUNT;
+
+ private static final int NUCS_COUNT_CUBED = NUCS_COUNT * NUCS_COUNT
+ * NUCS_COUNT;
+
+ private static final String AMBIGUITY_CODES_FILE = "/AmbiguityCodes.dat";
+
+ private static final String RESOURCE_FILE = "/GeneticCodes.dat";
+
+ private static GeneticCodes instance = new GeneticCodes();
+
+ private Map<String, String> ambiguityCodes;
+
+ /*
+ * loaded code tables, with keys in order of loading
+ */
+ private Map<String, GeneticCodeI> codeTables;
+
+ /**
+ * Private constructor enforces singleton
+ */
+ private GeneticCodes()
+ {
+ if (instance == null)
+ {
+ ambiguityCodes = new HashMap<>();
+
+ /*
+ * LinkedHashMap preserves order of addition of entries,
+ * so we can assume the Standard Code Table is the first
+ */
+ codeTables = new LinkedHashMap<>();
+ loadAmbiguityCodes(AMBIGUITY_CODES_FILE);
+ loadCodes(RESOURCE_FILE);
+ }
+ }
+
+ /**
+ * Returns the singleton instance of this class
+ *
+ * @return
+ */
+ public static GeneticCodes getInstance()
+ {
+ return instance;
+ }
+
+ /**
+ * Returns the known code tables, in order of loading.
+ *
+ * @return
+ */
+ public Iterable<GeneticCodeI> getCodeTables()
+ {
+ return codeTables.values();
+ }
+
+ /**
+ * Answers the code table with the given id
+ *
+ * @param id
+ * @return
+ */
+ public GeneticCodeI getCodeTable(String id)
+ {
+ return codeTables.get(id);
+ }
+
+ /**
+ * A convenience method that returns the standard code table (table 1). As
+ * implemented, this has to be the first table defined in the data file.
+ *
+ * @return
+ */
+ public GeneticCodeI getStandardCodeTable()
+ {
+ return codeTables.values().iterator().next();
+ }
+
+ /**
+ * Loads the code tables from a data file
+ */
+ protected void loadCodes(String fileName)
+ {
+ try
+ {
+ InputStream is = getClass().getResourceAsStream(fileName);
+ if (is == null)
+ {
+ System.err.println("Resource file not found: " + fileName);
+ return;
+ }
+ BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
+
+ /*
+ * skip comments and start of table
+ */
+ String line = "";
+ while (line != null && !line.startsWith("Genetic-code-table"))
+ {
+ line = readLine(dataIn);
+ }
+ line = readLine(dataIn);
+
+ while (line.startsWith("{"))
+ {
+ line = loadOneTable(dataIn);
+ }
+ } catch (IOException | NullPointerException e)
+ {
+ Cache.log.error(
+ "Error reading genetic codes data file " + fileName + ": "
+ + e.getMessage());
+ }
+ if (codeTables.isEmpty())
+ {
+ System.err.println(
+ "No genetic code tables loaded, check format of file "
+ + fileName);
+ }
+ }
+
+ /**
+ * Reads and saves Nucleotide ambiguity codes from a data file. The file may
+ * include comment lines (starting with #), a header 'DNA', and one line per
+ * ambiguity code, for example:
+ * <p>
+ * R<tab>AG
+ * <p>
+ * means that R is an ambiguity code meaning "A or G"
+ *
+ * @param fileName
+ */
+ protected void loadAmbiguityCodes(String fileName)
+ {
+ try
+ {
+ InputStream is = getClass().getResourceAsStream(fileName);
+ if (is == null)
+ {
+ System.err.println("Resource file not found: " + fileName);
+ return;
+ }
+ BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
+ String line = "";
+ while (line != null)
+ {
+ line = readLine(dataIn);
+ if (line != null && !"DNA".equals(line.toUpperCase()))
+ {
+ String[] tokens = line.split("\\t");
+ if (tokens.length == 2)
+ {
+ ambiguityCodes.put(tokens[0].toUpperCase(),
+ tokens[1].toUpperCase());
+ }
+ else
+ {
+ System.err.println(
+ "Unexpected data in " + fileName + ": " + line);
+ }
+ }
+ }
+ } catch (IOException e)
+ {
+ Cache.log.error(
+ "Error reading nucleotide ambiguity codes data file: "
+ + e.getMessage());
+ }
+ }
+
+ /**
+ * Reads up to and returns the next non-comment line, trimmed. Comment lines
+ * start with a #. Returns null at end of file.
+ *
+ * @param dataIn
+ * @return
+ * @throws IOException
+ */
+ protected String readLine(BufferedReader dataIn) throws IOException
+ {
+ String line = dataIn.readLine();
+ while (line != null && line.startsWith("#"))
+ {
+ line = readLine(dataIn);
+ }
+ return line == null ? null : line.trim();
+ }
+
+ /**
+ * Reads the lines of the data file describing one translation table, and
+ * creates and stores an instance of GeneticCodeI. Returns the '{' line
+ * starting the next table, or the '}' line at end of all tables. Data format
+ * is
+ *
+ * <pre>
+ * {
+ * name "Vertebrate Mitochondrial" ,
+ * name "SGC1" ,
+ * id 2 ,
+ * ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
+ * sncbieaa "----------**--------------------MMMM----------**---M------------"
+ * -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ * -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ * -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ * },
+ * </pre>
+ *
+ * of which we parse the first name, the id, and the ncbieaa translations for
+ * codons as ordered by the Base1/2/3 lines. Note Base1/2/3 are included for
+ * readability and are in a fixed order, these are not parsed. The sncbieaa
+ * line marks alternative start codons, these are not parsed.
+ *
+ * @param dataIn
+ * @return
+ * @throws IOException
+ */
+ protected String loadOneTable(BufferedReader dataIn) throws IOException
+ {
+ String name = null;
+ String id = null;
+ Map<String, String> codons = new HashMap<>();
+
+ String line = readLine(dataIn);
+
+ while (line != null && !line.startsWith("}"))
+ {
+ if (line.startsWith("name") && name == null)
+ {
+ name = line.substring(line.indexOf(QUOTE) + 1,
+ line.lastIndexOf(QUOTE));
+ }
+ else if (line.startsWith("id"))
+ {
+ id = new StringTokenizer(line.substring(2)).nextToken();
+ }
+ else if (line.startsWith("ncbieaa"))
+ {
+ String aminos = line.substring(line.indexOf(QUOTE) + 1,
+ line.lastIndexOf(QUOTE));
+ if (aminos.length() != NUCS_COUNT_CUBED) // 4 * 4 * 4 combinations
+ {
+ Cache.log.error("wrong data length in code table: " + line);
+ }
+ else
+ {
+ for (int i = 0; i < aminos.length(); i++)
+ {
+ String peptide = String.valueOf(aminos.charAt(i));
+ char codon1 = NUCS.charAt(i / NUCS_COUNT_SQUARED);
+ char codon2 = NUCS
+ .charAt((i % NUCS_COUNT_SQUARED) / NUCS_COUNT);
+ char codon3 = NUCS.charAt(i % NUCS_COUNT);
+ String codon = new String(
+ new char[]
+ { codon1, codon2, codon3 });
+ codons.put(codon, peptide);
+ }
+ }
+ }
+ line = readLine(dataIn);
+ }
+
+ registerCodeTable(id, name, codons);
+ return readLine(dataIn);
+ }
+
+ /**
+ * Constructs and registers a GeneticCodeI instance with the codon
+ * translations as defined in the data file. For all instances except the
+ * first, any undeclared translations default to those in the standard code
+ * table.
+ *
+ * @param id
+ * @param name
+ * @param codons
+ */
+ protected void registerCodeTable(final String id, final String name,
+ final Map<String, String> codons)
+ {
+ codeTables.put(id, new GeneticCodeI()
+ {
+ /*
+ * map of ambiguous codons to their 'product'
+ * (null if not all possible translations match)
+ */
+ Map<String, String> ambiguous = new HashMap<>();
+
+ @Override
+ public String translateCanonical(String codon)
+ {
+ return codons.get(codon.toUpperCase());
+ }
+
+ @Override
+ public String translate(String codon)
+ {
+ String upper = codon.toUpperCase();
+ String peptide = translateCanonical(upper);
+
+ /*
+ * if still not translated, check for ambiguity codes
+ */
+ if (peptide == null)
+ {
+ peptide = getAmbiguousTranslation(upper, ambiguous, this);
+ }
+ return peptide;
+ }
+
+ @Override
+ public String getId()
+ {
+ return id;
+ }
+
+ @Override
+ public String getName()
+ {
+ return name;
+ }
+ });
+ }
+
+ /**
+ * Computes all possible translations of a codon including one or more
+ * ambiguity codes, and stores and returns the result (null if not all
+ * translations match). If the codon includes no ambiguity codes, simply
+ * returns null.
+ *
+ * @param codon
+ * @param ambiguous
+ * @param codeTable
+ * @return
+ */
+ protected String getAmbiguousTranslation(String codon,
+ Map<String, String> ambiguous, GeneticCodeI codeTable)
+ {
+ if (codon.length() != CODON_LENGTH)
+ {
+ return null;
+ }
+
+ boolean isAmbiguous = false;
+
+ char[][] expanded = new char[CODON_LENGTH][];
+ for (int i = 0; i < CODON_LENGTH; i++)
+ {
+ String base = String.valueOf(codon.charAt(i));
+ if (ambiguityCodes.containsKey(base))
+ {
+ isAmbiguous = true;
+ base = ambiguityCodes.get(base);
+ }
+ expanded[i] = base.toCharArray();
+ }
+
+ if (!isAmbiguous)
+ {
+ // no ambiguity code involved here
+ return null;
+ }
+
+ /*
+ * generate and translate all permutations of the ambiguous codon
+ * only return the translation if they all agree, else null
+ */
+ String peptide = null;
+ for (char c1 : expanded[0])
+ {
+ for (char c2 : expanded[1])
+ {
+ for (char c3 : expanded[2])
+ {
+ char[] cdn = new char[] { c1, c2, c3 };
+ String possibleCodon = String.valueOf(cdn);
+ String pep = codeTable.translate(possibleCodon);
+ if (pep == null || (peptide != null && !pep.equals(peptide)))
+ {
+ ambiguous.put(codon, null);
+ return null;
+ }
+ peptide = pep;
+ }
+ }
+ }
+
+ /*
+ * all translations of ambiguous codons matched!
+ */
+ ambiguous.put(codon, peptide);
+ return peptide;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff