umcg.genetica.io.probemapping

Class reading

java.lang.Object

umcg.genetica.io.probemapping.reading

public class reading
extends Object

Author:

MarcJan

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	ENCODING

Constructor Summary

Constructors

Constructor and Description
reading()

Method Summary

Modifier and Type	Method and Description
static HashMap<String,HashMap<String,String>>	readAnnotationFile(String annotationFile, int storingId, int sizeMap) Read annotation file.
static ArrayList<Triple<Integer,Integer,Integer>>	readAnnotationFileArrayList(String annotationFile, int col1, int col2, int col3, boolean firstRowAsHeader, int sizeMap) Read annotation file Supply int key and int for value
static HashMap<String,String>	readAnnotationFileHash(String annotationFile, boolean firstRowAsHeader, int key, int val, int sizeMap) Read annotation file Supply int key and int for value
static HashMap<String,Triple<Integer,Integer,Integer>>	readAnnotationFileHashMap(String annotationFile, boolean firstRowAsHeader, int key, int val1, int val2, int val3, int sizeMap) Read annotation file Supply int key and int for value
static HashMap<Integer,HashMap<String,Pair<Integer,Integer>>>	readAnnotationFileHashMap2(String annotationFile, boolean firstRowAsHeader, int key, int val1, int val2, int val3, int sizeMap)
static DoubleMatrixDataset<String,String>	readDoubleMatrixFile(String eigenVectorFile, Set<String> rowsToInclude) Read double matrix file restricting to given rows Eigenvector file / pc file / probe matrix
static HashSet<String>	readFilterHash(String probeFilteringFiles) Read one file into HashSet
static HashSet<String>	readFilterHash2(String[] probeFilteringFiles) Read multiple file into HashSet
static HashMap<String,String>	readGTFAnnotationFileHash(String annotationFile, int sizeMap) read GTF file (gene code information)
static HashMap<String,ArrayList<ArrayList<String>>>	readInMultipleSamFiles(String folderIn, String fileExtention) Read sam files
static HashMap<String,ArrayList<ArrayList<String>>>	readInMultipleSamFiles2(String folderIn, String fileExtention, int maxDiff) Read sam files if there are more than maxDiff differences in the read the row is skipped
static HashMap<String,ArrayList<ArrayList<String>>>	readInMultipleSamFiles2DG(String folderIn, String fileExtention, int maxDiff) Read sam files if there are more than maxDiff differences in the read the row is skipped Degenerate bases are not counted as a mismatch (removed from edit distance)
static ArrayList<String>	readListToArrayList(String probeFilteringFiles) Read one file into HashSet
static HashMap<String,Pair<String,Double>>	readMetaAnalysisResults(String metaAnalysisScores, boolean firstRowAsHeader, int key, int val1, int val2, int sizeMap)
static HashMap<String,LinkedHashMap<Integer,String>>	readMultipleSNPAnnotationFiles(String annotationFileFolder, double minMaf, boolean firstRowAsHeader) Read SNP information files
static HashMap<String,HashMap<Integer,String>>	readMultipleSNPAnnotationFiles2(String annotationFileFolder, double minMaf, boolean firstRowAsHeader) Read SNP information files
static HashMap<String,TreeMap<Integer,String>>	readMultipleSNPAnnotationFiles3(String annotationFileFolder, double minMaf, boolean firstRowAsHeader) Read SNP information files
static HashMap<String,HashSet<Integer>>	readMultipleSNPAnnotationFilesSmall(String annotationFileFolder, double minMaf, boolean firstRowAsHeader) Read SNP information files

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ENCODING

protected static final String ENCODING

See Also:

Constant Field Values

Constructor Detail

reading

public reading()

Method Detail

readInMultipleSamFiles

public static HashMap<String,ArrayList<ArrayList<String>>> readInMultipleSamFiles(String folderIn,
                                                                                  String fileExtention)

Read sam files

Parameters:

folderIn -

fileExtention -

Returns:

readInMultipleSamFiles2

public static HashMap<String,ArrayList<ArrayList<String>>> readInMultipleSamFiles2(String folderIn,
                                                                                   String fileExtention,
                                                                                   int maxDiff)

Read sam files if there are more than maxDiff differences in the read the row is skipped

Parameters:

folderIn -

fileExtention -

maxDiff -

Returns:

readInMultipleSamFiles2DG

public static HashMap<String,ArrayList<ArrayList<String>>> readInMultipleSamFiles2DG(String folderIn,
                                                                                     String fileExtention,
                                                                                     int maxDiff)

Read sam files if there are more than maxDiff differences in the read the row is skipped Degenerate bases are not counted as a mismatch (removed from edit distance)

Parameters:

folderIn -

fileExtention -

maxDiff -

Returns:

readAnnotationFile

public static HashMap<String,HashMap<String,String>> readAnnotationFile(String annotationFile,
                                                                        int storingId,
                                                                        int sizeMap)

Read annotation file. General read in

Parameters:

annotationFile -

storingId -

sizeMap -

Returns:

readAnnotationFileHash

public static HashMap<String,String> readAnnotationFileHash(String annotationFile,
                                                            boolean firstRowAsHeader,
                                                            int key,
                                                            int val,
                                                            int sizeMap)

Read annotation file Supply int key and int for value

Parameters:

annotationFile -

firstRowAsHeader -

key -

val -

sizeMap -

Returns:

readAnnotationFileHashMap

public static HashMap<String,Triple<Integer,Integer,Integer>> readAnnotationFileHashMap(String annotationFile,
                                                                                        boolean firstRowAsHeader,
                                                                                        int key,
                                                                                        int val1,
                                                                                        int val2,
                                                                                        int val3,
                                                                                        int sizeMap)

Read annotation file Supply int key and int for value

Parameters:

annotationFile -

firstRowAsHeader -

key -

val -

sizeMap -

Returns:

readAnnotationFileArrayList

public static ArrayList<Triple<Integer,Integer,Integer>> readAnnotationFileArrayList(String annotationFile,
                                                                                     int col1,
                                                                                     int col2,
                                                                                     int col3,
                                                                                     boolean firstRowAsHeader,
                                                                                     int sizeMap)

Read annotation file Supply int key and int for value

Parameters:

annotationFile -

firstRowAsHeader -

key -

val -

sizeMap -

Returns:

readGTFAnnotationFileHash

public static HashMap<String,String> readGTFAnnotationFileHash(String annotationFile,
                                                               int sizeMap)

read GTF file (gene code information)

Parameters:

annotationFile -

sizeMap -

Returns:

readMultipleSNPAnnotationFilesSmall

public static HashMap<String,HashSet<Integer>> readMultipleSNPAnnotationFilesSmall(String annotationFileFolder,
                                                                                   double minMaf,
                                                                                   boolean firstRowAsHeader)

Read SNP information files

Parameters:

annotationFileFolder -

minMaf -

firstRowAsHeader -

Returns:

readMultipleSNPAnnotationFiles

public static HashMap<String,LinkedHashMap<Integer,String>> readMultipleSNPAnnotationFiles(String annotationFileFolder,
                                                                                           double minMaf,
                                                                                           boolean firstRowAsHeader)

Read SNP information files

Parameters:

annotationFileFolder -

minMaf -

firstRowAsHeader -

Returns:

readMultipleSNPAnnotationFiles2

public static HashMap<String,HashMap<Integer,String>> readMultipleSNPAnnotationFiles2(String annotationFileFolder,
                                                                                      double minMaf,
                                                                                      boolean firstRowAsHeader)

Read SNP information files

Parameters:

annotationFileFolder -

minMaf -

firstRowAsHeader -

Returns:

readMultipleSNPAnnotationFiles3

public static HashMap<String,TreeMap<Integer,String>> readMultipleSNPAnnotationFiles3(String annotationFileFolder,
                                                                                      double minMaf,
                                                                                      boolean firstRowAsHeader)

Read SNP information files

Parameters:

annotationFileFolder -

minMaf -

firstRowAsHeader -

Returns:

readFilterHash

public static HashSet<String> readFilterHash(String probeFilteringFiles)

Read one file into HashSet

Parameters:

fileWithAnnotation -

Returns:

Sample annotation

readListToArrayList

public static ArrayList<String> readListToArrayList(String probeFilteringFiles)

Read one file into HashSet

Parameters:

fileWithAnnotation -

Returns:

Sample annotation

readFilterHash2

public static HashSet<String> readFilterHash2(String[] probeFilteringFiles)

Read multiple file into HashSet

Parameters:

fileWithAnnotation -

Returns:

Sample annotation

readDoubleMatrixFile

public static DoubleMatrixDataset<String,String> readDoubleMatrixFile(String eigenVectorFile,
                                                                      Set<String> rowsToInclude)

Read double matrix file restricting to given rows Eigenvector file / pc file / probe matrix

Parameters:

eigenVectorFile -

Returns:

readMetaAnalysisResults

public static HashMap<String,Pair<String,Double>> readMetaAnalysisResults(String metaAnalysisScores,
                                                                          boolean firstRowAsHeader,
                                                                          int key,
                                                                          int val1,
                                                                          int val2,
                                                                          int sizeMap)

readAnnotationFileHashMap2

public static HashMap<Integer,HashMap<String,Pair<Integer,Integer>>> readAnnotationFileHashMap2(String annotationFile,
                                                                                                boolean firstRowAsHeader,
                                                                                                int key,
                                                                                                int val1,
                                                                                                int val2,
                                                                                                int val3,
                                                                                                int sizeMap)