@Override
public String process(File page, Map<String, String> query) {
loadContigs();
if (query.get("contigName").matches("^[ACGT]+$")) {
contigs.put("manual", query.get("contigName"));
query.put("contigName", "manual");
} else if (query.get("contigName").matches("^Pf3D7.+$")) {
String[] pieces = query.get("contigName").split("[:-]");
int start = Integer.valueOf(pieces[1].replaceAll(",", ""));
int end = Integer.valueOf(pieces[2].replaceAll(",", ""));
ReferenceSequence rseq = REF.getSubsequenceAt(pieces[0], start, end);
contigs.put("manual", new String(rseq.getBases()));
query.put("contigName", "manual");
}
if (query.containsKey("contigName")
&& contigs.containsKey(query.get("contigName"))
&& graphs.containsKey(query.get("graphName"))) {
boolean showLinks = query.get("showLinks").equals("links_on");
String contig = contigs.get(query.get("contigName"));
String originalContig = contigs.get(query.get("contigName"));
String refFormattedString = "";
String kmerOrigin = "";
if (metrics.containsKey(query.get("contigName"))) {
String[] loc = metrics.get(query.get("contigName")).get("canonicalLocus").split("[:-]");
if (!loc[0].equals("*")) {
boolean isRc = metrics.get(query.get("contigName")).get("isRcCanonical").equals("1");
if (isRc) {
contig = SequenceUtils.reverseComplement(contig);
originalContig = SequenceUtils.reverseComplement(originalContig);
}
int locStart = Integer.valueOf(loc[1]);
int locEnd = Integer.valueOf(loc[2]);
Cigar cigar =
cigarStringToCigar(metrics.get(query.get("contigName")).get("cigarCanonical"));
if (cigar.getCigarElement(0).getOperator().equals(CigarOperator.S)) {
locStart -= cigar.getCigarElement(0).getLength();
}
if (cigar
.getCigarElement(cigar.getCigarElements().size() - 1)
.getOperator()
.equals(CigarOperator.S)) {
locEnd += cigar.getCigarElement(cigar.getCigarElements().size() - 1).getLength();
}
String ref = new String(REF.getSubsequenceAt(loc[0], locStart, locEnd).getBases());
StringBuilder refFormatted = new StringBuilder();
int pos = 0;
for (CigarElement ce : cigar.getCigarElements()) {
CigarOperator co = ce.getOperator();
switch (co) {
case S:
refFormatted.append(ref.substring(pos, pos + ce.getLength()).toLowerCase());
break;
case M:
refFormatted.append(ref.substring(pos, pos + ce.getLength()));
break;
case I:
refFormatted.append(StringUtils.repeat("-", ce.getLength()));
break;
}
if (ce.getOperator().consumesReferenceBases()) {
pos += ce.getLength();
}
}
refFormattedString = refFormatted.toString();
kmerOrigin = metrics.get(query.get("contigName")).get("kmerOrigin");
}
}
CortexGraph cg = graphs.get(query.get("graphName"));
String sampleName = cg.getColor(0).getSampleName();
Set<CortexLinksMap> links = new HashSet<CortexLinksMap>();
if (LINKS != null && !LINKS.isEmpty()) {
for (CortexLinksMap link : LINKS) {
if (sampleName.equals(link.getCortexLinks().getColor(0).getSampleName())) {
links.add(link);
}
}
}
Set<String> contigKmers = new HashSet<String>();
for (int i = 0; i <= contig.length() - cg.getKmerSize(); i++) {
String curKmer = contig.substring(i, i + cg.getKmerSize());
contigKmers.add(curKmer);
}
StringBuilder firstFlank = new StringBuilder();
String firstKmer = contig.substring(0, cg.getKmerSize());
Set<String> pks = CortexUtils.getPrevKmers(cg, firstKmer, 0);
Set<String> usedPrevKmers = new HashSet<String>();
usedPrevKmers.add(firstKmer);
while (pks.size() == 1 && usedPrevKmers.size() <= 100) {
String kmer = pks.iterator().next();
firstFlank.insert(0, kmer.charAt(0));
if (usedPrevKmers.contains(kmer)) {
break;
}
usedPrevKmers.add(kmer);
pks = CortexUtils.getPrevKmers(cg, kmer, 0);
}
StringBuilder lastFlank = new StringBuilder();
String lastKmer = contig.substring(contig.length() - cg.getKmerSize(), contig.length());
Set<String> nks = CortexUtils.getNextKmers(cg, lastKmer, 0);
Set<String> usedNextKmers = new HashSet<String>();
usedNextKmers.add(lastKmer);
while (nks.size() == 1 && usedNextKmers.size() <= 100) {
String kmer = nks.iterator().next();
lastFlank.append(kmer.charAt(kmer.length() - 1));
if (usedNextKmers.contains(kmer)) {
break;
}
usedNextKmers.add(kmer);
nks = CortexUtils.getNextKmers(cg, kmer, 0);
}
contig = firstFlank.toString() + contig + lastFlank.toString();
DirectedGraph<CtxVertex, MultiEdge> g =
new DefaultDirectedGraph<CtxVertex, MultiEdge>(MultiEdge.class);
for (int i = 0; i <= contig.length() - cg.getKmerSize(); i++) {
String curKmer = contig.substring(i, i + cg.getKmerSize());
CortexKmer ck = new CortexKmer(curKmer);
CtxVertex curVer =
new CtxVertex(
curKmer,
i,
contigKmers.contains(curKmer) ? VertexType.CONTIG : VertexType.CLIPPED,
cg.findRecord(ck));
g.addVertex(curVer);
String expectedPrevKmer =
(i > 0) ? contig.substring(i - 1, i - 1 + cg.getKmerSize()) : "";
String expectedNextKmer =
(i < contig.length() - cg.getKmerSize())
? contig.substring(i + 1, i + 1 + cg.getKmerSize())
: "";
Set<String> prevKmers = CortexUtils.getPrevKmers(cg, curKmer, 0);
for (String prevKmer : prevKmers) {
if (!expectedPrevKmer.equals(prevKmer)) {
CortexKmer pk = new CortexKmer(prevKmer);
CtxVertex prevVer = new CtxVertex(prevKmer, i - 1, VertexType.IN, cg.findRecord(pk));
MultiEdge me =
g.containsEdge(prevVer, curVer) ? g.getEdge(prevVer, curVer) : new MultiEdge();
me.addGraphName(cg.getCortexFile().getName());
g.addVertex(prevVer);
g.addEdge(prevVer, curVer, me);
}
}
Set<String> nextKmers = CortexUtils.getNextKmers(cg, curKmer, 0);
for (String nextKmer : nextKmers) {
if (!expectedNextKmer.equals(nextKmer)) {
CortexKmer nk = new CortexKmer(nextKmer);
CtxVertex nextVer = new CtxVertex(nextKmer, i + 1, VertexType.OUT, cg.findRecord(nk));
MultiEdge me =
g.containsEdge(curVer, nextVer) ? g.getEdge(curVer, nextVer) : new MultiEdge();
me.addGraphName(cg.getCortexFile().getName());
g.addVertex(nextVer);
g.addEdge(curVer, nextVer, me);
}
}
}
Set<Map<String, Object>> verticesWithLinks = new HashSet<Map<String, Object>>();
DataFrame<String, String, Integer> hv = new DataFrame<String, String, Integer>(0);
for (int q = 0; q <= contig.length() - cg.getKmerSize(); q++) {
// String sk = cv.getBinaryKmer();
String sk = contig.substring(q, q + cg.getKmerSize());
CortexKmer ck = new CortexKmer(sk);
for (CortexLinksMap link : links) {
if (link.containsKey(ck)) {
CortexLinksRecord clr = link.get(ck);
Map<String, Integer> lc =
(!showLinks)
? new HashMap<String, Integer>()
: CortexUtils.getKmersAndCoverageInLink(cg, sk, clr);
Map<String, Object> entry = new HashMap<String, Object>();
entry.put("kmer", sk);
entry.put("lc", lc);
verticesWithLinks.add(entry);
if (showLinks) {
for (CortexJunctionsRecord cjr : clr.getJunctions()) {
List<String> lk = CortexUtils.getKmersInLink(cg, sk, cjr);
for (int i = 0; i < lk.size(); i++) {
String kili = lk.get(i);
for (int j = 0; j < lk.size(); j++) {
String kilj = lk.get(j);
if (i != j) {
hv.set(kili, kilj, hv.get(kili, kilj) + cjr.getCoverage(0));
}
}
}
}
}
}
}
}
/*
int hvMax = 0;
Map<String, Integer> hvlin = new HashMap<String, Integer>();
if (showLinks) {
for (String kili : hv.getRowNames()) {
for (String kilj : hv.getColNames()) {
int cov = hv.get(kili, kilj);
String id = kili + "_" + kilj;
hvlin.put(id, cov);
if (cov > hvMax) {
hvMax = cov;
}
}
}
}
*/
JSONObject jo = new JSONObject();
jo.put("contig", contig);
jo.put("originalContig", originalContig);
jo.put("ref", refFormattedString);
jo.put("kmerOrigin", kmerOrigin);
jo.put("kmerSize", cg.getKmerSize());
jo.put("clipStart", firstFlank.length());
jo.put("clipEnd", contig.length() - lastFlank.length());
List<Map<String, Object>> va = new ArrayList<Map<String, Object>>();
for (CtxVertex v : g.vertexSet()) {
Map<String, Object> vm = new HashMap<String, Object>();
vm.put("base", v.getBase());
vm.put("kmer", v.getKmer());
vm.put("pos", v.getPos());
vm.put("type", v.getVertexType().name());
vm.put("missing", v.isMissingFromGraph());
vm.put("cov", v.getCoverage());
va.add(vm);
}
jo.put("vertices", va);
jo.put("verticesWithLinks", verticesWithLinks);
// jo.put("hvlin", hvlin);
// jo.put("hvmax", hvMax);
return jo.toString();
}
return null;
}
static {
try {
String platform;
if (isWindows()) {
platform = "windows";
} else if (isUnix()) {
platform = "linux";
} else if (isMac()) {
platform = "mac";
} else {
platform = null;
}
String propertiesFile = "undefined";
if (platform != null) {
propertiesFile = "org/python/pydev/core/TestDependent." + platform + ".properties";
InputStream stream =
TestDependent.class.getClassLoader().getResourceAsStream(propertiesFile);
if (stream != null) {
// Initialize the static contents of the class.
String streamContents = REF.getStreamContents(stream, null, null);
Properties props = PropertiesHelper.createPropertiesFromString(streamContents);
Map<String, String> map = PropertiesHelper.createMapFromProperties(props);
Set<Entry<String, String>> entrySet = map.entrySet();
for (Entry<String, String> entry : entrySet) {
String key = entry.getKey();
try {
Field field = TestDependent.class.getField(key);
if (field != null) {
String value = entry.getValue();
if (!value.equals("null")) {
field.set(null, value);
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
} else {
System.err.println(
"Could not get stream to: "
+ propertiesFile
+ " to initialize TestDependent.java values.");
}
}
// Checking and setting variables that do not exist (if possible).
if (PYTHON_INSTALL == null) {
System.err.println(
"PYTHON_INSTALL variable MUST be set in " + propertiesFile + " to run tests.");
} else if (!new File(PYTHON_INSTALL).exists()) {
System.err.println(
"PYTHON_INSTALL variable points to path that does NOT exist: " + PYTHON_INSTALL);
}
if (TEST_PYDEV_BASE_LOC == null) {
System.err.println(
"TEST_PYDEV_BASE_LOC variable MUST be set in " + propertiesFile + " to run tests.");
} else if (!new File(TEST_PYDEV_BASE_LOC).exists()) {
System.err.println(
"TEST_PYDEV_BASE_LOC variable points to path that does NOT exist: "
+ TEST_PYDEV_BASE_LOC);
}
if (PYTHON_EXE == null) {
if (isWindows()) {
PYTHON_EXE = PYTHON_INSTALL + "python.exe";
} else {
PYTHON_EXE = PYTHON_INSTALL + "python";
}
}
if (!new File(PYTHON_EXE).exists()) {
System.err.println("PYTHON_EXE variable points to path that does NOT exist: " + PYTHON_EXE);
}
if (PYTHON_LIB == null) {
PYTHON_LIB = PYTHON_INSTALL + "Lib/";
}
if (PYTHON_DLLS == null) {
PYTHON_DLLS = PYTHON_INSTALL + "DLLs/";
}
if (PYTHON_SITE_PACKAGES == null) {
PYTHON_SITE_PACKAGES = PYTHON_LIB + "site-packages/";
}
if (PYTHON_TEST_PACKAGES == null) {
if (new File(TestDependent.PYTHON_LIB + "test/").exists()) {
PYTHON_TEST_PACKAGES = TestDependent.PYTHON_LIB + "test/";
}
}
if (TEST_PYSRC_LOC == null) {
TEST_PYSRC_LOC = TEST_PYDEV_BASE_LOC + "org.python.pydev/tests/pysrc/";
}
if (TEST_PYSRC_NAVIGATOR_LOC == null) {
TEST_PYSRC_NAVIGATOR_LOC = TEST_PYDEV_BASE_LOC + "org.python.pydev/tests_navigator/pysrc/";
}
if (TEST_PYSRC_LOC2 == null) {
TEST_PYSRC_LOC2 = TEST_PYDEV_BASE_LOC + "org.python.pydev/tests/pysrc2/";
}
if (TEST_PYDEV_PLUGIN_LOC == null) {
TEST_PYDEV_PLUGIN_LOC = TEST_PYDEV_BASE_LOC + "org.python.pydev/";
}
if (TEST_PYDEV_DEBUG_PLUGIN_LOC == null) {
TEST_PYDEV_DEBUG_PLUGIN_LOC = TEST_PYDEV_BASE_LOC + "org.python.pydev.debug/";
}
if (TEST_PYDEV_JYTHON_PLUGIN_LOC == null) {
TEST_PYDEV_JYTHON_PLUGIN_LOC = TEST_PYDEV_BASE_LOC + "org.python.pydev.jython/";
}
if (TEST_PYDEV_PARSER_PLUGIN_LOC == null) {
TEST_PYDEV_PARSER_PLUGIN_LOC = TEST_PYDEV_BASE_LOC + "org.python.pydev.parser/";
}
if (TEST_PYDEV_REFACTORING_PLUGIN_LOC == null) {
TEST_PYDEV_REFACTORING_PLUGIN_LOC = TEST_PYDEV_BASE_LOC + "org.python.pydev.refactoring/";
}
if (TEST_COM_REFACTORING_PYSRC_LOC == null) {
TEST_COM_REFACTORING_PYSRC_LOC =
TEST_PYDEV_BASE_LOC + "com.python.pydev.refactoring/tests/pysrcrefactoring/";
}
} catch (Exception e) {
System.err.println(
"--- Error getting contents to properly initialize TestDependent.java values ---");
e.printStackTrace();
}
}