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java.lang.Objectutil.io.FileParser
public class FileParser
Utility class for parsing and extracting data from files
Constructor Summary | |
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FileParser()
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Method Summary | |
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FastaFileData |
extractDataFromFastaEmblFile(java.io.File file)
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FastaFileData |
extractDataFromFastaFile(java.io.File file)
Reads all the fasta data from a fastafile. |
SecondaryStructureData |
extractRandomSecondaryStructuresFromFile(java.lang.String fileName,
int number)
Extracts a given amount of secondary structure data from a given file. |
java.util.List<java.lang.String> |
extractRandomSequencesFromFile(java.lang.String fileName,
int number)
This method extracts at random a certain number of unique lines from a file. |
SecondaryStructureData |
extractSecondaryStructuresFromFile(java.lang.String fileName)
Extracts the secondarystructure data from a file, according to the way it was written in the file by RNAfold. |
java.util.List<java.lang.String> |
extractSequencesFromFile(java.lang.String fileName)
Static method for extracting all DNA sequences (simple format, one sequence on each line, those sequences should all have their (pseudo-) splicesites aligned at the same position (defined in main.Jaspr.SPLICESITE). |
java.io.BufferedReader |
getReader(java.lang.String fileName)
Extracts the secondarystructure data from a file, according to the way it was written in the file by RNAfold. |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public FileParser()
Method Detail |
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public java.io.BufferedReader getReader(java.lang.String fileName) throws java.io.IOException
fileName
- The name of the file
java.io.IOException
- If the reading from the file fails for a reason.
public SecondaryStructureData extractSecondaryStructuresFromFile(String fileName) throws IOException{
Listpublic SecondaryStructureData extractSecondaryStructuresFromFile(java.lang.String fileName) throws java.io.IOException
fileName
- The name of the file
java.io.IOException
- If the reading from the file fails for a reason.public SecondaryStructureData extractRandomSecondaryStructuresFromFile(java.lang.String fileName, int number) throws java.io.IOException, java.lang.Exception
fileName
- The name of the filenumber
- The number of files to be extracted
java.io.IOException
- Thrown when reading the file goes wrong
java.lang.Exception
- When number>lines in filepublic java.util.List<java.lang.String> extractSequencesFromFile(java.lang.String fileName) throws java.io.IOException
fileName
- The name of the file
java.io.IOException
- Thrown when the reading failspublic java.util.List<java.lang.String> extractRandomSequencesFromFile(java.lang.String fileName, int number) throws java.io.IOException, java.lang.Exception
fileName
- The name of the filenumber
- The expected number of lines
java.io.IOException
- Possibly thrown when reading the file.
java.lang.Exception
public FastaFileData extractDataFromFastaFile(java.io.File file) throws java.io.IOException
file
- The fastafile
java.io.IOException
- Fileoperations are prone to errorspublic FastaFileData extractDataFromFastaEmblFile(java.io.File file) throws java.io.IOException
java.io.IOException
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