public class Utils extends Object
Modifier and Type | Method and Description |
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static TreeMap<String,Integer> |
computeTupleFrequencies(File[] files,
int n)
Loads a FASTA file and returns the n-tuple frequencies of its letters.
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static TreeMap<String,Integer> |
computeTupleFrequencies(File file,
int n,
char[] base)
Loads a FASTA file and returns the n-tuple frequencies of its letters.
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static TreeMap<String,Integer> |
computeTupleFrequencies(int n)
Loads a FASTA file and returns the n-tuple frequencies of its letters.
|
static TreeMap<String,Integer> |
computeTupleFrequencies(int n,
char[] base)
Asks the user to select a FASTA file, loads it and returns the n-tuple
frequencies of its letters.
|
static String |
getAsCSVTable(Map<String,Integer> map)
Returns the specified map as a CSV data table string, with data aligned in columns.
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static String |
getAsCSVTable(Map<String,Integer> map,
int minimum)
Returns the specified map as a CSV data table string, with data aligned in columns.
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protected static String |
getAsCSVTableRows(Map<String,Integer> map)
Returns the specified map as a CSV data table string, with data aligned in rows.
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static String |
getFrequenciesAsHTMLGraph(Map<String,Integer> frequencies)
Returns the frequency distribution of amino acid triplets as HTML graph.
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static void |
save(String fileName,
CharSequence string)
Saves the specified character sequence.
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static void |
saveOccurrencesAsText(String fileName,
TreeMap<String,Integer> distribution,
int frequency)
Saves those occurrences of a frequency distribution which have the specified
frequency into a text file.
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static void |
saveOccurrencesAsText(String fileName,
TreeMap<String,Integer> distribution,
int frequency,
char[] ignore)
Saves those occurrences of a frequency distribution which have the specified
frequency into a text file.
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static void |
saveWordFrequenciesAsCSV()
This method asks the user to select a list of files,
computes the word frequencies and saves them in a CSV file.
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static File[] |
selectFASTAFiles()
Asks the user to select a directory and returns a list of FASTA files.
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public static String getAsCSVTable(Map<String,Integer> map)
map
- the map to be savedpublic static String getAsCSVTable(Map<String,Integer> map, int minimum)
map
- the map to be savedminimum
- the minimum frequency number to be savedprotected static String getAsCSVTableRows(Map<String,Integer> map)
map
- a map of datapublic static String getFrequenciesAsHTMLGraph(Map<String,Integer> frequencies)
frequencies
- frequency distributionpublic static TreeMap<String,Integer> computeTupleFrequencies(int n)
n
- the tuple sizepublic static TreeMap<String,Integer> computeTupleFrequencies(int n, char[] base)
n
- the tuple sizebase
- the base alphabet (important for finding zero occurrences)public static File[] selectFASTAFiles()
public static TreeMap<String,Integer> computeTupleFrequencies(File[] files, int n)
files
- an array of FASTA filen
- the tuple sizepublic static TreeMap<String,Integer> computeTupleFrequencies(File file, int n, char[] base)
file
- a FASTA filen
- the tuple sizebase
- the base alphabet (important for finding zero occurrences)public static void saveOccurrencesAsText(String fileName, TreeMap<String,Integer> distribution, int frequency)
fileName
- the file name (without extension) in which the text is storeddistribution
- the frequency distributionfrequency
- the frequency which filters the occurrencespublic static void saveOccurrencesAsText(String fileName, TreeMap<String,Integer> distribution, int frequency, char[] ignore)
fileName
- the file name (without extension) in which the text is storeddistribution
- the frequency distributionfrequency
- the frequency which filters the occurrencesignore
- list of characters to be ignoredpublic static void saveWordFrequenciesAsCSV()
public static void save(String fileName, CharSequence string)
fileName
- name of the filestring
- a sequence of characters