use of uk.ac.babraham.SeqMonk.DataTypes.DataSet in project SeqMonk by s-andrews.
the class DataCollectionTreeModel method dataSetsRemoved.
/* (non-Javadoc)
* @see uk.ac.babraham.SeqMonk.DataTypes.DataChangeListener#dataSetRemoved(uk.ac.babraham.SeqMonk.DataTypes.DataSet)
*/
public void dataSetsRemoved(DataSet[] d) {
// Find the indices of each of these datasets and sort them low to high
// before telling the listeners
Hashtable<Integer, DataSet> indices = new Hashtable<Integer, DataSet>();
for (int i = 0; i < d.length; i++) {
indices.put(getIndexOfChild(dataSetNode, d[i]), d[i]);
}
// We have to make an Integer object array before we can convert this
// to a primitive int array
Integer[] deleteIndices = indices.keySet().toArray(new Integer[0]);
Arrays.sort(deleteIndices);
DataSet[] deleteSets = new DataSet[deleteIndices.length];
for (int i = 0; i < deleteIndices.length; i++) {
deleteSets[i] = indices.get(deleteIndices[i]);
}
int[] delInd = new int[deleteIndices.length];
for (int i = 0; i < deleteIndices.length; i++) {
delInd[i] = deleteIndices[i];
}
TreeModelEvent me = new TreeModelEvent(d, getPathToRoot(dataSetNode), delInd, deleteSets);
Enumeration<TreeModelListener> e = listeners.elements();
while (e.hasMoreElements()) {
e.nextElement().treeNodesRemoved(me);
}
}
use of uk.ac.babraham.SeqMonk.DataTypes.DataSet in project SeqMonk by s-andrews.
the class ActiveProbeListParser method run.
/* (non-Javadoc)
* @see java.lang.Runnable#run()
*/
public void run() {
DataSet newData = processNormalDataStore(activeList);
processingFinished(new DataSet[] { newData });
}
use of uk.ac.babraham.SeqMonk.DataTypes.DataSet in project SeqMonk by s-andrews.
the class BedFileParser method run.
/* (non-Javadoc)
* @see java.lang.Runnable#run()
*/
public void run() {
// System.err.println("Started parsing BED files");
int extendBy = prefs.extendReads();
try {
File[] probeFiles = getFiles();
DataSet[] newData = new DataSet[probeFiles.length];
for (int f = 0; f < probeFiles.length; f++) {
BufferedReader br;
if (probeFiles[f].getName().toLowerCase().endsWith(".gz")) {
br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(probeFiles[f]))));
} else {
br = new BufferedReader(new FileReader(probeFiles[f]));
}
String line;
if (prefs.isHiC()) {
newData[f] = new PairedDataSet(probeFiles[f].getName(), probeFiles[f].getCanonicalPath(), prefs.removeDuplicates(), prefs.hiCDistance(), prefs.hiCIgnoreTrans());
} else {
newData[f] = new DataSet(probeFiles[f].getName(), probeFiles[f].getCanonicalPath(), prefs.removeDuplicates());
}
int lineCount = 0;
// Now process the file
while ((line = br.readLine()) != null) {
if (cancel) {
br.close();
progressCancelled();
return;
}
// Ignore blank lines
if (line.trim().length() == 0)
continue;
++lineCount;
if (lineCount % 100000 == 0) {
progressUpdated("Read " + lineCount + " lines from " + probeFiles[f].getName(), f, probeFiles.length);
}
String[] sections = line.split("\t");
// Check to see if we've got enough data to work with
if (sections.length < 3) {
progressWarningReceived(new SeqMonkException("Not enough data from line '" + line + "'"));
// Skip this line...
continue;
}
int strand;
int start;
int end;
try {
// The start is zero indexed so we need to add 1 to get genomic positions
start = Integer.parseInt(sections[1]) + 1;
// The end is zero indexed, but not included in the feature position so
// we need to add one to get genomic coordinates, but subtract one to not
// include the final base.
end = Integer.parseInt(sections[2]);
// End must always be later than start
if (start > end) {
progressWarningReceived(new SeqMonkException("End position " + end + " was lower than start position " + start));
int temp = start;
start = end;
end = temp;
}
if (sections.length >= 6) {
if (sections[5].equals("+")) {
strand = Location.FORWARD;
} else if (sections[5].equals("-")) {
strand = Location.REVERSE;
} else {
progressWarningReceived(new SeqMonkException("Unknown strand character '" + sections[5] + "' marked as unknown strand"));
strand = Location.UNKNOWN;
}
if (extendBy > 0) {
if (strand == Location.REVERSE) {
start -= extendBy;
} else if (strand == Location.FORWARD) {
end += extendBy;
}
}
} else {
strand = Location.UNKNOWN;
}
} catch (NumberFormatException e) {
progressWarningReceived(new SeqMonkException("Location " + sections[0] + "-" + sections[1] + " was not an integer"));
continue;
}
try {
ChromosomeWithOffset c = dataCollection().genome().getChromosome(sections[0]);
// We also don't allow readings which are beyond the end of the chromosome
start = c.position(start);
end = c.position(end);
if (end > c.chromosome().length()) {
int overrun = end - c.chromosome().length();
progressWarningReceived(new SeqMonkException("Reading position " + end + " was " + overrun + "bp beyond the end of chr" + c.chromosome().name() + " (" + c.chromosome().length() + ")"));
continue;
}
// We can now make the new reading
long read = SequenceRead.packPosition(start, end, strand);
newData[f].addData(c.chromosome(), read);
} catch (IllegalArgumentException iae) {
progressWarningReceived(iae);
} catch (SeqMonkException sme) {
progressWarningReceived(sme);
continue;
}
}
// We're finished with the file.
br.close();
// Cache the data in the new dataset
progressUpdated("Caching data from " + probeFiles[f].getName(), f, probeFiles.length);
newData[f].finalise();
}
processingFinished(newData);
} catch (Exception ex) {
progressExceptionReceived(ex);
return;
}
}
use of uk.ac.babraham.SeqMonk.DataTypes.DataSet in project SeqMonk by s-andrews.
the class GenericSeqReadParser method run.
/* (non-Javadoc)
* @see java.lang.Runnable#run()
*/
public void run() {
try {
// This call just makes sure that the options panel exists if
// it's never been called for before.
getOptionsPanel();
int removeDuplicates = optionsPanel.removeDuplicates();
int extendBy = optionsPanel.extendBy();
File[] probeFiles = getFiles();
DataSet[] newData = new DataSet[probeFiles.length];
for (int f = 0; f < probeFiles.length; f++) {
BufferedReader br;
if (probeFiles[f].getName().toLowerCase().endsWith(".gz")) {
br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(probeFiles[f]))));
} else {
br = new BufferedReader(new FileReader(probeFiles[f]));
}
String line;
// First skip the header lines
for (int i = 0; i < startRowValue; i++) {
line = br.readLine();
if (line == null) {
br.close();
throw new Exception("Ran out of file before skipping all of the header lines");
}
}
int maxIndexValue = 0;
if (chrColValue > maxIndexValue)
maxIndexValue = chrColValue;
if (startColValue > maxIndexValue)
maxIndexValue = startColValue;
if (endColValue > maxIndexValue)
maxIndexValue = endColValue;
if (strandColValue > maxIndexValue)
maxIndexValue = strandColValue;
if (countColValue > maxIndexValue)
maxIndexValue = countColValue;
if (optionsPanel.isHiC()) {
int distance = 0;
if (optionsPanel.hiCDistance.getText().length() > 0) {
distance = Integer.parseInt(optionsPanel.hiCDistance.getText());
}
// TODO: Add an option to remove trans hits when importing from the generic parser.
newData[f] = new PairedDataSet(probeFiles[f].getName(), probeFiles[f].getCanonicalPath(), removeDuplicates, distance, false);
} else {
newData[f] = new DataSet(probeFiles[f].getName(), probeFiles[f].getCanonicalPath(), removeDuplicates);
}
int lineCount = 0;
// Now process the rest of the file
while ((line = br.readLine()) != null) {
if (cancel) {
br.close();
progressCancelled();
return;
}
++lineCount;
if (lineCount % 100000 == 0) {
progressUpdated("Read " + lineCount + " lines from " + probeFiles[f].getName(), f, probeFiles.length);
}
String[] sections = line.split(delimitersValue);
// Check to see if we've got enough data to work with
if (maxIndexValue >= sections.length) {
progressWarningReceived(new SeqMonkException("Not enough data (" + sections.length + ") to get a probe name on line '" + line + "'"));
// Skip this line...
continue;
}
int strand;
int start;
int end;
int count = 1;
try {
start = Integer.parseInt(sections[startColValue].replaceAll(" ", ""));
end = Integer.parseInt(sections[endColValue].replaceAll(" ", ""));
// End must always be later than start
if (end < start) {
int temp = start;
start = end;
end = temp;
}
if (countColValue != -1 && sections[countColValue].length() > 0) {
try {
count = Integer.parseInt(sections[countColValue].replaceAll(" ", ""));
} catch (NumberFormatException e) {
progressWarningReceived(new SeqMonkException("Count value " + sections[countColValue] + " was not an integer"));
continue;
}
}
if (useStrand) {
sections[strandColValue] = sections[strandColValue].replaceAll(" ", "");
if (sections[strandColValue].equals("+") || sections[strandColValue].equals("1") || sections[strandColValue].equals("FF") || sections[strandColValue].equals("F")) {
strand = Location.FORWARD;
} else if (sections[strandColValue].equals("-") || sections[strandColValue].equals("-1") || sections[strandColValue].equals("RF") || sections[strandColValue].equals("R")) {
strand = Location.REVERSE;
} else {
progressWarningReceived(new SeqMonkException("Unknown strand character '" + sections[strandColValue] + "' marked as unknown strand"));
strand = Location.UNKNOWN;
}
} else {
strand = Location.UNKNOWN;
}
if (extendBy > 0) {
if (strand == Location.REVERSE) {
start -= extendBy;
} else {
end += extendBy;
}
}
} catch (NumberFormatException e) {
progressWarningReceived(new SeqMonkException("Location '" + sections[startColValue] + "'-'" + sections[endColValue] + "' was not an integer"));
continue;
}
ChromosomeWithOffset c;
try {
c = dataCollection().genome().getChromosome(sections[chrColValue]);
} catch (IllegalArgumentException sme) {
progressWarningReceived(sme);
continue;
}
start = c.position(start);
end = c.position(end);
// We also don't allow readings which are beyond the end of the chromosome
if (end > c.chromosome().length()) {
int overrun = end - c.chromosome().length();
progressWarningReceived(new SeqMonkException("Reading position " + end + " was " + overrun + "bp beyond the end of chr" + c.chromosome().name() + " (" + c.chromosome().length() + ")"));
continue;
}
if (start < 1) {
progressWarningReceived(new SeqMonkException("Reading start position " + start + " was less than 1"));
continue;
}
// We can now make the new reading
try {
long read = SequenceRead.packPosition(start, end, strand);
for (int i = 0; i < count; i++) {
newData[f].addData(c.chromosome(), read);
}
} catch (SeqMonkException e) {
progressWarningReceived(e);
continue;
}
// System.out.println("Added probe "+newProbe.name()+" on "+newProbe.chromosome()+" at pos "+newProbe.position());
}
// We're finished with the file.
br.close();
// Cache the data in the new dataset
progressUpdated("Caching data from " + probeFiles[f].getName(), f, probeFiles.length);
newData[f].finalise();
}
processingFinished(newData);
} catch (Exception ex) {
progressExceptionReceived(ex);
return;
}
}
use of uk.ac.babraham.SeqMonk.DataTypes.DataSet in project SeqMonk by s-andrews.
the class MethylKitFileParser method run.
/* (non-Javadoc)
* @see java.lang.Runnable#run()
*/
public void run() {
try {
File[] methylKitFiles = getFiles();
DataSet[] newData = new DataSet[methylKitFiles.length];
for (int f = 0; f < methylKitFiles.length; f++) {
BufferedReader br;
if (methylKitFiles[f].getName().toLowerCase().endsWith(".gz")) {
br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(methylKitFiles[f]))));
} else {
br = new BufferedReader(new FileReader(methylKitFiles[f]));
}
String line;
newData[f] = new DataSet(methylKitFiles[f].getName(), methylKitFiles[f].getCanonicalPath(), prefs.removeDuplicates());
int lineCount = 0;
// Now process the file
while ((line = br.readLine()) != null) {
if (cancel) {
br.close();
progressCancelled();
return;
}
// Ignore blank lines
if (line.trim().length() == 0)
continue;
// In case it has comments
if (line.startsWith("#"))
continue;
// This is the start of the header
if (line.startsWith("chrBase"))
continue;
++lineCount;
if (lineCount % 100000 == 0) {
progressUpdated("Read " + lineCount + " lines from " + methylKitFiles[f].getName(), f, methylKitFiles.length);
}
String[] sections = line.split("\t");
// Check to see if we've got enough data to work with
if (sections.length < 6) {
progressWarningReceived(new SeqMonkException("Not enough data from line '" + line + "'"));
// Skip this line...
continue;
}
int position;
int totalCount;
int methCount;
int unmethCount;
try {
position = Integer.parseInt(sections[2]);
totalCount = Integer.parseInt(sections[4]);
methCount = Math.round((Float.parseFloat(sections[5]) / 100) * totalCount);
unmethCount = Math.round((Float.parseFloat(sections[6]) / 100) * totalCount);
} catch (NumberFormatException e) {
progressWarningReceived(new SeqMonkException("Failed to parse position and counts from " + line));
continue;
}
try {
ChromosomeWithOffset c = dataCollection().genome().getChromosome(sections[1]);
// We also don't allow readings which are beyond the end of the chromosome
if (position > c.chromosome().length()) {
int overrun = position - c.chromosome().length();
progressWarningReceived(new SeqMonkException("Reading position " + position + " was " + overrun + "bp beyond the end of chr" + c.chromosome().name() + " (" + c.chromosome().length() + ")"));
continue;
}
// We can now make the new reads
long methRead = SequenceRead.packPosition(position, position, Location.FORWARD);
long unmethRead = SequenceRead.packPosition(position, position, Location.REVERSE);
for (int i = 0; i < methCount; i++) {
newData[f].addData(c.chromosome(), methRead);
}
for (int i = 0; i < unmethCount; i++) {
newData[f].addData(c.chromosome(), unmethRead);
}
} catch (IllegalArgumentException iae) {
progressWarningReceived(iae);
} catch (SeqMonkException sme) {
progressWarningReceived(sme);
continue;
}
}
// We're finished with the file.
br.close();
// Cache the data in the new dataset
progressUpdated("Caching data from " + methylKitFiles[f].getName(), f, methylKitFiles.length);
newData[f].finalise();
}
processingFinished(newData);
} catch (Exception ex) {
progressExceptionReceived(ex);
return;
}
}
Aggregations