// Pressing the mouse stops and starts the sound
public void mousePressed() {
if (tone.isPlaying()) {
tone.stop(); // The sound can be stopped with the function stop().
} else {
tone.repeat();
}
}
private void addSample(
Map<String, Map<String, Sample>> map,
String key,
String sample,
long len,
double depth,
String gene) {
if (map.containsKey(key)) {
Map<String, Sample> sampleMap = map.get(key);
if (sampleMap.containsKey(sample)) {
Sample sampleObj = sampleMap.get(sample);
sampleObj.addLen(len);
sampleObj.addCov(depth);
} else {
Sample sampleObj = new Sample(key, sample, gene, len, depth);
sampleMap.put(sample, sampleObj);
}
} else {
Sample sampleObj = new Sample(key, sample, gene, len, depth);
Map<String, Sample> sampleMap = new LinkedHashMap<>();
sampleMap.put(sample, sampleObj);
map.put(key, sampleMap);
}
}
public void updateModelWeight(List<Sample> sampleList) {
for (FeatureValue featureValue : featureMap.values()) {
featureValue.setTempWeight(0);
}
for (Sample sample : sampleList) {
Map<String, Double> probMap = predict(sample.getFeatures());
for (String feature : sample.getFeatures()) {
for (String label : labelSet) {
this.setTempWeight(
label,
feature,
this.getTempWeight(label, feature)
+ probMap.get(label) * (1.0 / sampleList.size()));
}
}
}
// GIS;
features.setLastWeight();
for (FeatureValue featureValue : featureMap.values()) {
featureValue.setModelWeight(
featureValue.getModelWeight()
+ 1.0
/ maxFeaturePerSample
* Math.log(featureValue.getEmpiricalWeight() / featureValue.getTempWeight()));
}
}
public void draw() {
if (tone.isPlaying()) {
background(255);
} else {
background(100);
}
// Set the volume to a range between 0 and 1.0
float ratio = (float) mouseX / width;
tone.setVolume(ratio);
// Set the rate to a range between 0 and 88,200
// Changing the rate alters the pitch
ratio = (float) mouseY / height;
// The rate is set according to the mouseY position.
tone.setRate(ratio * 88200);
// Draw some rectangles to show what is going on
stroke(0);
fill(175);
rect(0, 160, mouseX, 20);
stroke(0);
fill(175);
rect(160, 0, 20, mouseY);
}
private void printResult(List<String> bad) {
for (Map.Entry<String, Map<String, Sample>> entry : samples.entrySet()) {
if (!bad.contains(entry.getKey())) {
for (Map.Entry<String, Sample> entrySample : entry.getValue().entrySet()) {
Sample sample = entrySample.getValue();
String title = amplicon ? entry.getKey() : sample.getTitle(genes.get(sample.getGene()));
String result = sample.getResultString(title);
if (useControlSamples) {
addControlSamples(result, sample);
}
System.out.println(result);
}
}
}
}
private double getMedDepth(double[] depth, Set<String> samp) {
int i = 0;
for (Map.Entry<String, Map<String, Sample>> entry : samples.entrySet()) {
Map<String, Sample> sampleMap = entry.getValue();
for (Map.Entry<String, Sample> sampleEntry : sampleMap.entrySet()) {
Sample sample = sampleEntry.getValue();
double norm1 = Precision.round((sample.getCov() * factor.get(sample.getSample())), 2);
sample.setNorm1(norm1);
depth[i++] = norm1;
samp.add(sample.getSample());
}
}
return median.evaluate(depth);
}
private void setFactor2(double medDepth, List<String> bad, Map<String, Double> factor2) {
for (Map.Entry<String, Map<String, Sample>> entry : samples.entrySet()) {
if (!bad.contains(entry.getKey())) {
List<Double> list = new LinkedList<>();
for (Map.Entry<String, Sample> entrySample : entry.getValue().entrySet()) {
Sample sample = entrySample.getValue();
list.add(sample.getNorm1());
}
double median = new Median().evaluate(toDoubleArray(list));
if (median != 0) {
factor2.put(entry.getKey(), medDepth / median);
} else {
factor2.put(entry.getKey(), 0.0);
}
}
}
}
private void validate() {
validatePedigreeIDUniqueness();
if (validationStrictness != PedigreeValidationType.SILENT) {
// check that samples in data sources are all annotated, if anything is annotated
if (!samplesFromPedigrees.isEmpty() && !samplesFromDataSources.isEmpty()) {
final Set<String> sampleNamesFromPedigrees =
samplesFromPedigrees.stream().map(Sample::getID).collect(Collectors.toSet());
for (final Sample dsSample : samplesFromDataSources)
if (!sampleNamesFromPedigrees.contains(dsSample.getID())) {
throw new UserException(
"Sample "
+ dsSample.getID()
+ " found in data sources but not in pedigree files with STRICT pedigree validation");
}
}
}
}
private void setNorm(
double medDepth,
List<String> bad,
Map<String, Double> factor2,
Map<String, Double> sampleMedian) {
for (Map.Entry<String, Map<String, Sample>> entry : samples.entrySet()) {
if (!bad.contains(entry.getKey())) {
for (Map.Entry<String, Sample> entrySample : entry.getValue().entrySet()) {
Sample sample = entrySample.getValue();
double norm1 = sample.getNorm1();
double fact2 = factor2.get(entry.getKey());
double smplMed = sampleMedian.get(sample.getSample());
sample.setNorm1b(Precision.round(norm1 * fact2 + 0.1, 2));
sample.setNorm2(
Precision.round(
medDepth != 0 ? log.value((norm1 * fact2 + 0.1) / medDepth) / log.value(2) : 0,
2));
sample.setNorm3(
Precision.round(
smplMed != 0 ? log.value((norm1 * fact2 + 0.1) / smplMed) / log.value(2) : 0, 2));
}
}
}
}
public void setup() {
size(200, 200);
// Start Sonia engine.
Sonia.start(this);
// Create a new sample object.
tone = new Sample("tone.wav");
// Loop the sound forever
// (well, at least until stop() is called)
tone.repeat();
smooth();
}
@Test
public void testSamples() {
try {
// get row count of experiments in the dataset
int expected = getDataSet().getTable("Sample").getRowCount();
// get number of experiments from the DAO
int actual = getSampleDAO().count();
// test data contains 2 experiments, check size of returned list
TestCase.assertEquals("Wrong number of Sample", expected, actual);
System.out.println("Expected number of Sample: " + expected + ", actual: " + actual);
for (Sample d : random(getSampleDAO(), actual, 5)) {
TestCase.assertNotNull(d);
TestCase.assertNotNull(d.getId());
}
} catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
}
private void addControlSamples(String result, Sample sample) {
List<Double> list = new LinkedList<>();
for (String s : controlSamples) {
for (Map.Entry<String, Map<String, Sample>> entry : samples.entrySet()) {
list.add(entry.getValue().get(s).getNorm1b());
}
}
if (!list.isEmpty()) {
double meanVal = mean.evaluate(toDoubleArray(list));
StringBuilder builder = new StringBuilder(result);
builder
.append("\t")
.append(
String.format(
"%.3f%n", meanVal == 0 ? sample.getNorm1b() / meanVal / log.value(2) : 0));
}
}
private Sample feedSampleData(Sample sample) throws Exception {
sample.setProjectId(projectId);
sample.setProjectName(projectName);
// set project level by adding 1 to selected parent project's level
if (sample.getParentSampleName() == null || sample.getParentSampleName().equals("0"))
sample.setParentSampleName(null);
String parentSampleName = sample.getParentSampleName();
if (parentSampleName != null && !parentSampleName.isEmpty() && !parentSampleName.equals("0")) {
Sample selectedParentSample = readPersister.getSample(projectId, parentSampleName);
sample.setSampleLevel(selectedParentSample.getSampleLevel() + 1);
} else {
sample.setParentSampleId(null);
sample.setSampleLevel(1);
}
return sample;
}
private MultiLoadParameter createMultiLoadParameter(
String projectName, Project project, Sample sample, List<FileReadAttributeBean> frab)
throws Exception {
MultiLoadParameter loadParameter = new MultiLoadParameter();
boolean isSampleRegistration = false;
boolean isProjectRegistration = false;
if (this.eventName.equals(Constants.EVENT_PROJECT_REGISTRATION)
&& project.getProjectName() != null
&& !project.getProjectName().isEmpty()) {
isProjectRegistration = true;
List<Project> projectList = new ArrayList<Project>();
projectList.add(feedProjectData(project));
loadParameter.addProjects(projectList);
/*
* loads all event meta attributes from the parent
* by hkim 6/11/13
*/
List<EventMetaAttribute> emas =
this.readPersister.getEventMetaAttributes(
projectName, null); // , Constants.EVENT_PROJECT_REGISTRATION);
if (emas != null && emas.size() > 0) {
List<EventMetaAttribute> newEmas = new ArrayList<EventMetaAttribute>(emas.size());
for (EventMetaAttribute ema : emas) {
EventMetaAttribute newEma = new EventMetaAttribute();
newEma.setProjectName(project.getProjectName());
newEma.setEventName(ema.getEventName());
newEma.setEventTypeLookupId(ema.getEventTypeLookupId());
newEma.setAttributeName(ema.getAttributeName());
newEma.setNameLookupId(ema.getNameLookupId());
newEma.setActive(ema.isActive());
newEma.setRequired(ema.isRequired());
newEma.setDesc(ema.getDesc());
newEma.setDataType(ema.getDataType());
newEma.setLabel(ema.getLabel());
newEma.setOntology(ema.getOntology());
newEma.setOptions(ema.getOptions());
newEma.setSampleRequired(ema.isSampleRequired());
newEmas.add(newEma);
}
loadParameter.addEventMetaAttributes(newEmas);
} else {
throw new Exception(
String.format(
"Event Metadata has not been set up for the parent project and the '%s' event type.",
Constants.EVENT_PROJECT_REGISTRATION));
}
List<SampleMetaAttribute> smas = this.readPersister.getSampleMetaAttributes(projectId);
if (smas != null && smas.size() > 0) {
List<SampleMetaAttribute> newSmas = new ArrayList<SampleMetaAttribute>(smas.size());
for (SampleMetaAttribute sma : smas) {
SampleMetaAttribute newSma = new SampleMetaAttribute();
newSma.setProjectName(project.getProjectName());
newSma.setAttributeName(sma.getAttributeName());
newSma.setNameLookupId(sma.getNameLookupId());
newSma.setDataType(sma.getDataType());
newSma.setDesc(sma.getDesc());
newSma.setLabel(sma.getLabel());
newSma.setOntology(sma.getOntology());
newSma.setOptions(sma.getOptions());
newSma.setRequired(sma.isRequired());
newSma.setActive(sma.isActive());
newSmas.add(newSma);
}
loadParameter.addSampleMetaAttributes(newSmas);
}
List<ProjectMetaAttribute> pmas = this.readPersister.getProjectMetaAttributes(projectName);
if (pmas != null && pmas.size() > 0) {
List<ProjectMetaAttribute> newPmas = new ArrayList<ProjectMetaAttribute>(pmas.size());
for (ProjectMetaAttribute pma : pmas) {
ProjectMetaAttribute newPma = new ProjectMetaAttribute();
newPma.setProjectName(project.getProjectName());
newPma.setAttributeName(pma.getAttributeName());
newPma.setDataType(pma.getDataType());
newPma.setDesc(pma.getDesc());
newPma.setLabel(pma.getLabel());
newPma.setNameLookupId(pma.getNameLookupId());
newPma.setOntology(pma.getOntology());
newPma.setOptions(pma.getOptions());
newPma.setRequired(pma.isRequired());
newPma.setActive(pma.isActive());
newPmas.add(newPma);
}
loadParameter.addProjectMetaAttributes(newPmas);
}
} else if (this.eventName.equals(Constants.EVENT_SAMPLE_REGISTRATION)
&& sample.getSampleName() != null
&& !sample.getSampleName().isEmpty()) {
isSampleRegistration = true;
List<Sample> sampleList = new ArrayList<Sample>();
sampleList.add(feedSampleData(sample));
loadParameter.addSamples(sampleList);
}
List<FileReadAttributeBean> loadingList = null;
if (frab != null && frab.size() > 0) {
loadingList =
processFileReadBeans(
isProjectRegistration ? project.getProjectName() : projectName,
isSampleRegistration ? sample.getSampleName() : this.sampleName,
frab);
}
if (loadingList != null && loadingList.size() > 0) {
if (isProjectRegistration) {
loadParameter.addProjectRegistrations(Constants.EVENT_PROJECT_REGISTRATION, loadingList);
} else if (isSampleRegistration) {
loadParameter.addSampleRegistrations(Constants.EVENT_SAMPLE_REGISTRATION, loadingList);
} else {
loadParameter.addEvents(this.eventName, loadingList);
}
}
return loadParameter;
}
public String execute() {
String rtnVal = SUCCESS;
UserTransaction tx = null;
try {
sampleName = sampleName != null && sampleName.equals("0") ? null : sampleName;
if (jobType != null) {
boolean isProjectRegistration = eventName.equals(Constants.EVENT_PROJECT_REGISTRATION);
boolean isSampleRegistration = eventName.equals(Constants.EVENT_SAMPLE_REGISTRATION);
if (projectName == null
|| projectName.equals("0")
|| eventName == null
|| eventName.equals("0")) throw new Exception("Project or Event type is not selected.");
if (jobType.equals("insert")) { // loads single event
tx = (UserTransaction) new InitialContext().lookup("java:comp/UserTransaction");
tx.begin();
psewt.loadAll(
null,
this.createMultiLoadParameter(projectName, loadingProject, loadingSample, beanList));
this.reset();
} else if (jobType.equals("grid")) { // loads multiple events from grid view
tx = (UserTransaction) new InitialContext().lookup("java:comp/UserTransaction");
tx.begin();
for (GridBean gBean : gridList) {
if (gBean != null) {
if (isProjectRegistration
&& gBean.getProjectName() != null
&& gBean.getProjectPublic() != null) {
loadingProject = new Project();
loadingProject.setProjectName(gBean.getProjectName());
loadingProject.setIsPublic(Integer.valueOf(gBean.getProjectPublic()));
} else if (isSampleRegistration
&& gBean.getSampleName() != null
&& gBean.getSamplePublic() != null) {
loadingSample = new Sample();
loadingSample.setSampleName(gBean.getSampleName());
loadingSample.setParentSampleName(gBean.getParentSampleName());
loadingSample.setIsPublic(Integer.valueOf(gBean.getSamplePublic()));
} else {
if (gBean.getSampleName() != null) {
this.sampleName = gBean.getSampleName();
}
}
List<FileReadAttributeBean> fBeanList = gBean.getBeanList();
if (fBeanList != null && fBeanList.size() > 0) {
psewt.loadAll(
null,
this.createMultiLoadParameter(
projectName, loadingProject, loadingSample, fBeanList));
}
}
}
this.reset();
} else if (jobType.equals("file")) { // loads data from a CSV file to grid view
if (!this.uploadFile.canRead()) {
throw new Exception("Error in reading the file.");
} else {
try {
CSVReader reader = new CSVReader(new FileReader(this.uploadFile));
int lineCount = 0;
List<String> columns = new ArrayList<String>();
String currProjectName = null;
gridList = new ArrayList<GridBean>();
boolean hasSampleName = false;
String[] line;
while ((line = reader.readNext()) != null) {
if (lineCount != 1) {
if (lineCount == 0) {
Collections.addAll(columns, line);
hasSampleName = columns.indexOf("SampleName") >= 0;
} else {
int colIndex = 0;
currProjectName = line[colIndex++];
if (!isProjectRegistration && !currProjectName.equals(this.projectName)) {
throw new Exception(MULTIPLE_SUBJECT_IN_FILE_MESSAGE);
}
GridBean gBean = new GridBean();
gBean.setProjectName(currProjectName);
if (hasSampleName) {
gBean.setSampleName(line[(colIndex++)]);
}
if (isProjectRegistration) {
gBean.setProjectName(currProjectName);
gBean.setProjectPublic(line[(colIndex++)]);
} else if (isSampleRegistration) {
gBean.setParentSampleName(line[(colIndex++)]);
gBean.setSamplePublic(line[(colIndex++)]);
}
gBean.setBeanList(new ArrayList<FileReadAttributeBean>());
for (; colIndex < columns.size(); colIndex++) {
FileReadAttributeBean fBean = new FileReadAttributeBean();
fBean.setProjectName(
isProjectRegistration ? currProjectName : this.projectName);
fBean.setAttributeName(columns.get(colIndex));
fBean.setAttributeValue(line[colIndex]);
gBean.getBeanList().add(fBean);
}
this.gridList.add(gBean);
}
}
lineCount++;
}
jobType = "grid";
} catch (Exception ex) {
throw ex;
}
}
} else if (jobType.equals("template")) { // download template
List<EventMetaAttribute> emaList =
readPersister.getEventMetaAttributes(projectName, eventName);
/*
* removing the sanity check on sample requirement since multiple sample support is in action
* by hkim 5/2/13
ModelValidator validator = new ModelValidator();
validator.validateEventTemplateSanity(emaList, projectName, sampleName, eventName);
*/
TemplatePreProcessingUtils cvsUtils = new TemplatePreProcessingUtils();
String templateType = jobType.substring(jobType.indexOf("_") + 1);
downloadStream =
cvsUtils.buildFileContent(templateType, emaList, projectName, sampleName, eventName);
downloadContentType = templateType.equals("c") ? "csv" : "vnd.ms-excel";
rtnVal = Constants.FILE_DOWNLOAD_MSG;
}
}
} catch (Exception ex) {
logger.error("Exception in EventLoader : " + ex.toString());
ex.printStackTrace();
if (ex.getClass() == ForbiddenResourceException.class) {
addActionError(Constants.DENIED_USER_EDIT_MESSAGE);
return Constants.FORBIDDEN_ACTION_RESPONSE;
} else if (ex.getClass() == ForbiddenResourceException.class) {
addActionError(Constants.DENIED_USER_EDIT_MESSAGE);
return LOGIN;
} else if (ex.getClass() == ParseException.class)
addActionError(Constants.INVALID_DATE_MESSAGE);
else {
addActionError(ex.toString());
}
// deletes uploaded files in event of error
if (loadedFiles != null && loadedFiles.size() > 0) {
for (String filePath : loadedFiles) {
File tempFile = new File(fileStoragePath + filePath);
if (tempFile.exists()) tempFile.delete();
}
}
try {
if (tx != null) tx.rollback();
} catch (SystemException se) {
addActionError(se.toString());
}
rtnVal = ERROR;
} finally {
try {
// get project list for the drop down box
List<String> projectNameList = new ArrayList<String>();
if (projectNames == null || projectNames.equals("")) {
projectNameList.add("ALL");
} else if (projectNames.contains(",")) {
projectNameList.addAll(Arrays.asList(projectNames.split(",")));
} else {
projectNameList.add(projectNames);
}
projectList = readPersister.getProjects(projectNameList);
if (tx != null && tx.getStatus() != Status.STATUS_NO_TRANSACTION) {
tx.commit();
}
if (jobType != null && jobType.equals("grid") && this.uploadFile != null) {
this.uploadFile.delete();
}
} catch (Exception ex) {
ex.printStackTrace();
}
}
return rtnVal;
}
public void run() {
String line;
String id = null;
config.refgenes = new ArrayList<RefGene>();
config.dbsnp = new ArrayList<dbSNP>();
try {
// System.err.println("quality read start"); // debug
boolean need_ruler_rebuild = false;
boolean need_title = false;
SAMRegion sr = null;
while (true) {
line = br.readLine();
if (line == null) break;
// EOF
String[] stuff = line.split("\t");
if (stuff[0].equals("sample2id")) {
Sample sample = Sample.get_sample(stuff[1]);
for (int i = 2; i < stuff.length; i++) {
config.read2sample.put(new String(stuff[i]), sample);
}
} else if (stuff[0].equals("consensus_label")) {
config.CONSENSUS_TAG = new String(stuff[1]);
} else if (stuff[0].equals("ruler_start")) {
config.ruler_start = Integer.parseInt(stuff[1]);
need_ruler_rebuild = true;
} else if (stuff[0].equals("title")) {
config.title = stuff[1];
need_title = true;
} else if (stuff[0].equals("refGene")) {
config.refgenes.add(new RefGene(stuff));
} else if (stuff[0].equals("dbsnp")) {
config.dbsnp.add(new dbSNP(stuff));
} else if (stuff[0].toUpperCase().indexOf("SAM_") == 0) {
// FUGLY
SAMResourceTags v = SAMResourceTags.valueOf(stuff[0].toUpperCase());
if (v.equals(SAMResourceTags.SAM_URL)) config.sams.add(new SAMResource());
config.sams.get(config.sams.size() - 1).import_data(v, stuff[1]);
} else if (stuff[0].equals("reference_sequence")) {
StringBuffer target_sequence = new StringBuffer();
while (true) {
line = br.readLine();
if (line.equals(">")) {
// config.target_sequence = target_sequence.toString().toCharArray();
config.target_sequence = target_sequence.toString().getBytes();
break;
} else {
target_sequence.append(line);
}
}
} else if (stuff[0].equals("target_region")) {
sr = new SAMRegion();
sr.tname = new String(stuff[1]);
sr.range = new Range(Integer.parseInt(stuff[2]), Integer.parseInt(stuff[3]));
// System.err.println("range " + sr.tname + " " + sr.range.start + " " + sr.range.end);
// // debug
} else {
System.err.println("error, don't recognize tag " + stuff[0]); // debug
}
}
if (config.ruler_start > 0) {
for (dbSNP snp : config.dbsnp) {
snp.consensus_adjust(config.ruler_start);
}
for (RefGene rg : config.refgenes) {
rg.consensus_adjust(config.ruler_start);
}
}
if (config.dbsnp != null) {
for (dbSNP snp : config.dbsnp) {
// System.err.println("adding snp at " + snp.start + " = " + (snp.start +
// config.ruler_start)); // debug
}
config.snp_config.snp_query = new dbSNPSet(config.dbsnp);
}
for (SAMResource sre : config.sams) {
sre.set_region(sr);
}
if (av != null) {
while (av.get_acepanel().is_built() == false) {
// spin until dependency built
try {
System.err.println("MarkupReader spin..."); // debug
Thread.sleep(50);
} catch (Exception e) {
}
}
PadMap pm = av.get_acepanel().get_assembly().get_padmap();
for (RefGene rg : config.refgenes) {
rg.consensus_setup(pm);
}
Runnable later;
if (need_title) {
// System.err.println("title="+config.title); // debug
later =
new Runnable() {
public void run() {
av.setTitle(config.title);
av.repaint();
}
};
javax.swing.SwingUtilities.invokeLater(later);
}
if (need_ruler_rebuild) {
//
// ruler labeling has changed.
//
later =
new Runnable() {
public void run() {
// av.get_acepanel().get_canvas().build_ruler();
if (config.start_unpadded_offset != 0) {
AcePanel ap = av.get_acepanel();
PadMap pm = ap.get_assembly().get_padmap();
int upo = (config.start_unpadded_offset - config.ruler_start) + 1;
// +1: convert to 1-based offset
int po = pm.get_unpadded_to_padded(upo);
System.err.println("upo=" + upo + " po=" + po); // debug
SNPList sl = new SNPList();
sl.addElement(new SNP(po, 0.0));
ap.ace.set_snps(sl);
ap.get_canvas().center_on(po);
ap.get_canvas().repaint();
}
}
};
javax.swing.SwingUtilities.invokeLater(later);
}
if (config.enable_exon_navigation) {
if (false) {
System.err.println("DEBUG: exon nav disabled");
} else {
av.get_acepanel().init_exon_navigation();
}
}
av.get_acepanel().get_assembly().build_summary_info();
// group samples by tumor/normal, if applicable
// av.repaint();
later =
new Runnable() {
public void run() {
av.repaint();
}
};
javax.swing.SwingUtilities.invokeLater(later);
}
// System.err.println("quality read end"); // debug
} catch (Exception e) {
e.printStackTrace(); // debug
}
}
public final List<Sample> parse(
Reader reader, EnumSet<MissingPedField> missingFields, SampleDB sampleDB) {
final List<String> lines = new XReadLines(reader).readLines();
// What are the record offsets?
final int familyPos = missingFields.contains(MissingPedField.NO_FAMILY_ID) ? -1 : 0;
final int samplePos = familyPos + 1;
final int paternalPos = missingFields.contains(MissingPedField.NO_PARENTS) ? -1 : samplePos + 1;
final int maternalPos =
missingFields.contains(MissingPedField.NO_PARENTS) ? -1 : paternalPos + 1;
final int sexPos =
missingFields.contains(MissingPedField.NO_SEX) ? -1 : Math.max(maternalPos, samplePos) + 1;
final int phenotypePos =
missingFields.contains(MissingPedField.NO_PHENOTYPE)
? -1
: Math.max(sexPos, Math.max(maternalPos, samplePos)) + 1;
final int nExpectedFields =
MathUtils.arrayMaxInt(
Arrays.asList(samplePos, paternalPos, maternalPos, sexPos, phenotypePos))
+ 1;
// go through once and determine properties
int lineNo = 1;
boolean isQT = false;
final List<String[]> splits = new ArrayList<String[]>(lines.size());
for (final String line : lines) {
if (line.startsWith(commentMarker)) continue;
if (line.trim().equals("")) continue;
final String[] parts = line.split("\\s+");
if (parts.length != nExpectedFields)
throw new UserException.MalformedFile(
reader.toString(), "Bad PED line " + lineNo + ": wrong number of fields");
if (phenotypePos != -1) {
isQT = isQT || !CATAGORICAL_TRAIT_VALUES.contains(parts[phenotypePos]);
}
splits.add(parts);
lineNo++;
}
logger.info("Phenotype is other? " + isQT);
// now go through and parse each record
lineNo = 1;
final List<Sample> samples = new ArrayList<Sample>(splits.size());
for (final String[] parts : splits) {
String familyID = null, individualID, paternalID = null, maternalID = null;
Gender sex = Gender.UNKNOWN;
String quantitativePhenotype = Sample.UNSET_QT;
Affection affection = Affection.UNKNOWN;
if (familyPos != -1) familyID = maybeMissing(parts[familyPos]);
individualID = parts[samplePos];
if (paternalPos != -1) paternalID = maybeMissing(parts[paternalPos]);
if (maternalPos != -1) maternalID = maybeMissing(parts[maternalPos]);
if (sexPos != -1) {
if (parts[sexPos].equals(SEX_MALE)) sex = Gender.MALE;
else if (parts[sexPos].equals(SEX_FEMALE)) sex = Gender.FEMALE;
else sex = Gender.UNKNOWN;
}
if (phenotypePos != -1) {
if (isQT) {
if (parts[phenotypePos].equals(MISSING_VALUE1)) affection = Affection.UNKNOWN;
else {
affection = Affection.OTHER;
quantitativePhenotype = parts[phenotypePos];
}
} else {
if (parts[phenotypePos].equals(MISSING_VALUE1)) affection = Affection.UNKNOWN;
else if (parts[phenotypePos].equals(MISSING_VALUE2)) affection = Affection.UNKNOWN;
else if (parts[phenotypePos].equals(PHENOTYPE_UNAFFECTED))
affection = Affection.UNAFFECTED;
else if (parts[phenotypePos].equals(PHENOTYPE_AFFECTED)) affection = Affection.AFFECTED;
else
throw new ReviewedGATKException(
"Unexpected phenotype type " + parts[phenotypePos] + " at line " + lineNo);
}
}
final Sample s =
new Sample(
individualID,
sampleDB,
familyID,
paternalID,
maternalID,
sex,
affection,
quantitativePhenotype);
samples.add(s);
sampleDB.addSample(s);
lineNo++;
}
for (final Sample sample : new ArrayList<Sample>(samples)) {
Sample dad =
maybeAddImplicitSample(
sampleDB, sample.getPaternalID(), sample.getFamilyID(), Gender.MALE);
if (dad != null) samples.add(dad);
Sample mom =
maybeAddImplicitSample(
sampleDB, sample.getMaternalID(), sample.getFamilyID(), Gender.FEMALE);
if (mom != null) samples.add(mom);
}
return samples;
}
public static void main(String[] args) {
System.loadLibrary(Core.NATIVE_LIBRARY_NAME);
// Mat mat = Mat.eye( 3, 3, CvType.CV_8UC1 );
// System.out.println( "mat = " + mat.dump() );
Sample n = new Sample();
// n.templateMatching();
// put text in image
// Mat data= Highgui.imread("images/erosion.jpg");
// Core.putText(data, "Sample", new Point(50,80), Core.FONT_HERSHEY_SIMPLEX, 1, new
// Scalar(0,0,0),2);
//
// Highgui.imwrite("images/erosion2.jpg", data);
// getting dct of an image
String path = "images/croppedfeature/go (20).jpg";
path = "images/wordseg/img1.png";
Mat image = Highgui.imread(path, Highgui.IMREAD_GRAYSCALE);
ArrayList<MatOfPoint> contours = new ArrayList<MatOfPoint>();
Imgproc.threshold(image, image, 0, 255, Imgproc.THRESH_OTSU);
Imgproc.threshold(image, image, 220, 128, Imgproc.THRESH_BINARY_INV);
Mat newImg = new Mat(45, 100, image.type());
newImg.setTo(new Scalar(0));
n.copyMat(image, newImg);
int vgap = 25;
int hgap = 45 / 3;
Moments m = Imgproc.moments(image, false);
Mat hu = new Mat();
Imgproc.HuMoments(m, hu);
System.out.println(hu.dump());
// //divide the mat into 12 parts then get the features of each part
// int count=1;
// for(int j=0; j<45; j+=hgap){
// for(int i=0;i<100;i+=vgap){
// Mat result = newImg.submat(j, j+hgap, i, i+vgap);
//
//
// Moments m= Imgproc.moments(result, false);
// double m01= m.get_m01();
// double m00= m.get_m00();
// double m10 = m.get_m10();
// int x= m00!=0? (int)(m10/m00):0;
// int y= m00!=0? (int)(m01/m00):0;
// Mat hu= new Mat();
// Imgproc.HuMoments(m, hu);
// System.out.println(hu.dump());
// System.out.println(count+" :"+x+" and "+y);
// Imgproc.threshold(result, result, 0,254, Imgproc.THRESH_BINARY_INV);
// Highgui.imwrite("images/submat/"+count+".jpg", result);
// count++;
//
// }
// }
//
// for(int i=vgap;i<100;i+=vgap){
// Point pt1= new Point(i, 0);
// Point pt2= new Point(i, 99);
// Core.line(newImg, pt1, pt2, new Scalar(0,0,0));
// }
// for(int i=hgap;i<45;i+=hgap){
// Point pt1= new Point(0, i);
// Point pt2= new Point(99, i);
// Core.line(newImg, pt1, pt2, new Scalar(0,0,0));
// }
// Highgui.imwrite("images/submat/copyto.jpg", newImg);
}
