List of usage examples for java.util Map.Entry get
V get(Object key);
From source file:org.apache.hadoop.hbase.master.DefaultLoadBalancer.java
/** * Generate a global load balancing plan according to the specified map of * server information to the most loaded regions of each server. * * The load balancing invariant is that all servers are within 1 region of the * average number of regions per server. If the average is an integer number, * all servers will be balanced to the average. Otherwise, all servers will * have either floor(average) or ceiling(average) regions. * * HBASE-3609 Modeled regionsToMove using Guava's MinMaxPriorityQueue so that * we can fetch from both ends of the queue. * At the beginning, we check whether there was empty region server * just discovered by Master. If so, we alternately choose new / old * regions from head / tail of regionsToMove, respectively. This alternation * avoids clustering young regions on the newly discovered region server. * Otherwise, we choose new regions from head of regionsToMove. * //from w ww .ja va 2s.com * Another improvement from HBASE-3609 is that we assign regions from * regionsToMove to underloaded servers in round-robin fashion. * Previously one underloaded server would be filled before we move onto * the next underloaded server, leading to clustering of young regions. * * Finally, we randomly shuffle underloaded servers so that they receive * offloaded regions relatively evenly across calls to balanceCluster(). * * The algorithm is currently implemented as such: * * <ol> * <li>Determine the two valid numbers of regions each server should have, * <b>MIN</b>=floor(average) and <b>MAX</b>=ceiling(average). * * <li>Iterate down the most loaded servers, shedding regions from each so * each server hosts exactly <b>MAX</b> regions. Stop once you reach a * server that already has <= <b>MAX</b> regions. * <p> * Order the regions to move from most recent to least. * * <li>Iterate down the least loaded servers, assigning regions so each server * has exactly </b>MIN</b> regions. Stop once you reach a server that * already has >= <b>MIN</b> regions. * * Regions being assigned to underloaded servers are those that were shed * in the previous step. It is possible that there were not enough * regions shed to fill each underloaded server to <b>MIN</b>. If so we * end up with a number of regions required to do so, <b>neededRegions</b>. * * It is also possible that we were able to fill each underloaded but ended * up with regions that were unassigned from overloaded servers but that * still do not have assignment. * * If neither of these conditions hold (no regions needed to fill the * underloaded servers, no regions leftover from overloaded servers), * we are done and return. Otherwise we handle these cases below. * * <li>If <b>neededRegions</b> is non-zero (still have underloaded servers), * we iterate the most loaded servers again, shedding a single server from * each (this brings them from having <b>MAX</b> regions to having * <b>MIN</b> regions). * * <li>We now definitely have more regions that need assignment, either from * the previous step or from the original shedding from overloaded servers. * Iterate the least loaded servers filling each to <b>MIN</b>. * * <li>If we still have more regions that need assignment, again iterate the * least loaded servers, this time giving each one (filling them to * </b>MAX</b>) until we run out. * * <li>All servers will now either host <b>MIN</b> or <b>MAX</b> regions. * * In addition, any server hosting >= <b>MAX</b> regions is guaranteed * to end up with <b>MAX</b> regions at the end of the balancing. This * ensures the minimal number of regions possible are moved. * </ol> * * TODO: We can at-most reassign the number of regions away from a particular * server to be how many they report as most loaded. * Should we just keep all assignment in memory? Any objections? * Does this mean we need HeapSize on HMaster? Or just careful monitor? * (current thinking is we will hold all assignments in memory) * * @param clusterState Map of regionservers and their load/region information to * a list of their most loaded regions * @return a list of regions to be moved, including source and destination, * or null if cluster is already balanced */ public List<RegionPlan> balanceCluster(Map<ServerName, List<HRegionInfo>> clusterState) { boolean emptyRegionServerPresent = false; long startTime = System.currentTimeMillis(); int numServers = clusterState.size(); if (numServers == 0) { LOG.debug("numServers=0 so skipping load balancing"); return null; } NavigableMap<ServerAndLoad, List<HRegionInfo>> serversByLoad = new TreeMap<ServerAndLoad, List<HRegionInfo>>(); int numRegions = 0; // Iterate so we can count regions as we build the map for (Map.Entry<ServerName, List<HRegionInfo>> server : clusterState.entrySet()) { List<HRegionInfo> regions = server.getValue(); int sz = regions.size(); if (sz == 0) emptyRegionServerPresent = true; numRegions += sz; serversByLoad.put(new ServerAndLoad(server.getKey(), sz), regions); } // Check if we even need to do any load balancing float average = (float) numRegions / numServers; // for logging // HBASE-3681 check sloppiness first int floor = (int) Math.floor(average * (1 - slop)); int ceiling = (int) Math.ceil(average * (1 + slop)); if (serversByLoad.lastKey().getLoad() <= ceiling && serversByLoad.firstKey().getLoad() >= floor) { // Skipped because no server outside (min,max) range LOG.info("Skipping load balancing because balanced cluster; " + "servers=" + numServers + " " + "regions=" + numRegions + " average=" + average + " " + "mostloaded=" + serversByLoad.lastKey().getLoad() + " leastloaded=" + serversByLoad.firstKey().getLoad()); return null; } int min = numRegions / numServers; int max = numRegions % numServers == 0 ? min : min + 1; // Using to check balance result. StringBuilder strBalanceParam = new StringBuilder(); strBalanceParam.append("Balance parameter: numRegions=").append(numRegions).append(", numServers=") .append(numServers).append(", max=").append(max).append(", min=").append(min); LOG.debug(strBalanceParam.toString()); // Balance the cluster // TODO: Look at data block locality or a more complex load to do this MinMaxPriorityQueue<RegionPlan> regionsToMove = MinMaxPriorityQueue.orderedBy(rpComparator).create(); List<RegionPlan> regionsToReturn = new ArrayList<RegionPlan>(); // Walk down most loaded, pruning each to the max int serversOverloaded = 0; // flag used to fetch regions from head and tail of list, alternately boolean fetchFromTail = false; Map<ServerName, BalanceInfo> serverBalanceInfo = new TreeMap<ServerName, BalanceInfo>(); for (Map.Entry<ServerAndLoad, List<HRegionInfo>> server : serversByLoad.descendingMap().entrySet()) { ServerAndLoad sal = server.getKey(); int regionCount = sal.getLoad(); if (regionCount <= max) { serverBalanceInfo.put(sal.getServerName(), new BalanceInfo(0, 0)); break; } serversOverloaded++; List<HRegionInfo> regions = server.getValue(); int numToOffload = Math.min(regionCount - max, regions.size()); // account for the out-of-band regions which were assigned to this server // after some other region server crashed Collections.sort(regions, riComparator); int numTaken = 0; for (int i = 0; i <= numToOffload;) { HRegionInfo hri = regions.get(i); // fetch from head if (fetchFromTail) { hri = regions.get(regions.size() - 1 - i); } i++; // Don't rebalance meta regions. if (hri.isMetaRegion()) continue; regionsToMove.add(new RegionPlan(hri, sal.getServerName(), null)); numTaken++; if (numTaken >= numToOffload) break; // fetch in alternate order if there is new region server if (emptyRegionServerPresent) { fetchFromTail = !fetchFromTail; } } serverBalanceInfo.put(sal.getServerName(), new BalanceInfo(numToOffload, (-1) * numTaken)); } int totalNumMoved = regionsToMove.size(); // Walk down least loaded, filling each to the min int neededRegions = 0; // number of regions needed to bring all up to min fetchFromTail = false; Map<ServerName, Integer> underloadedServers = new HashMap<ServerName, Integer>(); for (Map.Entry<ServerAndLoad, List<HRegionInfo>> server : serversByLoad.entrySet()) { int regionCount = server.getKey().getLoad(); if (regionCount >= min) { break; } underloadedServers.put(server.getKey().getServerName(), min - regionCount); } // number of servers that get new regions int serversUnderloaded = underloadedServers.size(); int incr = 1; List<ServerName> sns = Arrays .asList(underloadedServers.keySet().toArray(new ServerName[serversUnderloaded])); Collections.shuffle(sns, RANDOM); while (regionsToMove.size() > 0) { int cnt = 0; int i = incr > 0 ? 0 : underloadedServers.size() - 1; for (; i >= 0 && i < underloadedServers.size(); i += incr) { if (regionsToMove.isEmpty()) break; ServerName si = sns.get(i); int numToTake = underloadedServers.get(si); if (numToTake == 0) continue; addRegionPlan(regionsToMove, fetchFromTail, si, regionsToReturn); if (emptyRegionServerPresent) { fetchFromTail = !fetchFromTail; } underloadedServers.put(si, numToTake - 1); cnt++; BalanceInfo bi = serverBalanceInfo.get(si); if (bi == null) { bi = new BalanceInfo(0, 0); serverBalanceInfo.put(si, bi); } bi.setNumRegionsAdded(bi.getNumRegionsAdded() + 1); } if (cnt == 0) break; // iterates underloadedServers in the other direction incr = -incr; } for (Integer i : underloadedServers.values()) { // If we still want to take some, increment needed neededRegions += i; } // If none needed to fill all to min and none left to drain all to max, // we are done if (neededRegions == 0 && regionsToMove.isEmpty()) { long endTime = System.currentTimeMillis(); LOG.info("Calculated a load balance in " + (endTime - startTime) + "ms. " + "Moving " + totalNumMoved + " regions off of " + serversOverloaded + " overloaded servers onto " + serversUnderloaded + " less loaded servers"); return regionsToReturn; } // Need to do a second pass. // Either more regions to assign out or servers that are still underloaded // If we need more to fill min, grab one from each most loaded until enough if (neededRegions != 0) { // Walk down most loaded, grabbing one from each until we get enough for (Map.Entry<ServerAndLoad, List<HRegionInfo>> server : serversByLoad.descendingMap().entrySet()) { BalanceInfo balanceInfo = serverBalanceInfo.get(server.getKey().getServerName()); int idx = balanceInfo == null ? 0 : balanceInfo.getNextRegionForUnload(); if (idx >= server.getValue().size()) break; HRegionInfo region = server.getValue().get(idx); if (region.isMetaRegion()) continue; // Don't move meta regions. regionsToMove.add(new RegionPlan(region, server.getKey().getServerName(), null)); totalNumMoved++; if (--neededRegions == 0) { // No more regions needed, done shedding break; } } } // Now we have a set of regions that must be all assigned out // Assign each underloaded up to the min, then if leftovers, assign to max // Walk down least loaded, assigning to each to fill up to min for (Map.Entry<ServerAndLoad, List<HRegionInfo>> server : serversByLoad.entrySet()) { int regionCount = server.getKey().getLoad(); if (regionCount >= min) break; BalanceInfo balanceInfo = serverBalanceInfo.get(server.getKey().getServerName()); if (balanceInfo != null) { regionCount += balanceInfo.getNumRegionsAdded(); } if (regionCount >= min) { continue; } int numToTake = min - regionCount; int numTaken = 0; while (numTaken < numToTake && 0 < regionsToMove.size()) { addRegionPlan(regionsToMove, fetchFromTail, server.getKey().getServerName(), regionsToReturn); numTaken++; if (emptyRegionServerPresent) { fetchFromTail = !fetchFromTail; } } } // If we still have regions to dish out, assign underloaded to max if (0 < regionsToMove.size()) { for (Map.Entry<ServerAndLoad, List<HRegionInfo>> server : serversByLoad.entrySet()) { int regionCount = server.getKey().getLoad(); if (regionCount >= max) { break; } addRegionPlan(regionsToMove, fetchFromTail, server.getKey().getServerName(), regionsToReturn); if (emptyRegionServerPresent) { fetchFromTail = !fetchFromTail; } if (regionsToMove.isEmpty()) { break; } } } long endTime = System.currentTimeMillis(); if (!regionsToMove.isEmpty() || neededRegions != 0) { // Emit data so can diagnose how balancer went astray. LOG.warn("regionsToMove=" + totalNumMoved + ", numServers=" + numServers + ", serversOverloaded=" + serversOverloaded + ", serversUnderloaded=" + serversUnderloaded); StringBuilder sb = new StringBuilder(); for (Map.Entry<ServerName, List<HRegionInfo>> e : clusterState.entrySet()) { if (sb.length() > 0) sb.append(", "); sb.append(e.getKey().toString()); sb.append(" "); sb.append(e.getValue().size()); } LOG.warn("Input " + sb.toString()); } // All done! LOG.info("Done. Calculated a load balance in " + (endTime - startTime) + "ms. " + "Moving " + totalNumMoved + " regions off of " + serversOverloaded + " overloaded servers onto " + serversUnderloaded + " less loaded servers"); return regionsToReturn; }
From source file:base.BasePlayer.FileRead.java
static void removeNonListVariants() { VarNode node = FileRead.head.getNext(); VarNode tempNode;/*w w w.j a v a 2 s .c om*/ Map.Entry<String, ArrayList<SampleNode>> entry; int mutcount = 0; while (node != null) { if (!node.inVarList || Main.drawCanvas.hideNode(node)) { tempNode = node.getNext(); node.removeNode(); node = tempNode; } else { for (int v = 0; v < node.vars.size(); v++) { entry = node.vars.get(v); mutcount = 0; for (int m = 0; m < entry.getValue().size(); m++) { if (entry.getValue().get(m).alleles != null) { break; } if (!Main.drawCanvas.hideVar(entry.getValue().get(m), entry.getKey().length() > 1)) { if (VariantHandler.onlyselected.isSelected()) { if (!entry.getValue().get(m).getSample().equals(Main.drawCanvas.selectedSample)) { entry.getValue().remove(m); m--; continue; } } mutcount++; } else { entry.getValue().remove(m); m--; } } } if (mutcount == 0) { tempNode = node.getNext(); node.removeNode(); node = tempNode; } else { node = node.getNext(); } } } node = null; tempNode = null; entry = null; Main.drawCanvas.current = FileRead.head; Draw.updatevars = true; Main.drawCanvas.repaint(); }
From source file:base.BasePlayer.FileRead.java
VarNode annotateVariant(VarNode vardraw) {
if (Main.drawCanvas.hideNode(vardraw)) {
returnnode = vardraw.getNext();/*from w ww .j ava2s . c o m*/
if (VariantHandler.allChroms.isSelected()) {
vardraw.removeNode();
}
return returnnode;
}
Map.Entry<String, ArrayList<SampleNode>> entry = null;
String base = null, amino = null;
int pretrack = -1, preI = -1;
Main.drawCanvas.loadbarAll = (int) ((vardraw.getPosition()
/ (double) (Main.drawCanvas.splits.get(0).chromEnd)) * 100);
Main.drawCanvas.loadBarSample = Main.drawCanvas.loadbarAll;
boolean recessivefound = false;
for (int v = 0; v < vardraw.vars.size(); v++) {
entry = vardraw.vars.get(v);
if (Main.drawCanvas.hideNodeVar(vardraw, entry)) {
if (VariantHandler.allChroms.isSelected()) {
vardraw.vars.remove(v);
v--;
}
continue;
}
if (Main.drawCanvas.annotationOn) {
if (vardraw.vars.size() == 1 && vardraw.vars.get(0).getValue().size() == 1
&& vardraw.vars.get(0).getValue().get(0).getSample().annotation) {
if (VariantHandler.allChroms.isSelected()) {
vardraw.vars.remove(v);
v--;
}
continue;
}
}
recessivefound = false;
base = entry.getKey();
mutcount = 0;
if (!VariantHandler.none.isSelected()) {
if (VariantHandler.recessiveHomo.isSelected()) {
if (!checkRecessiveHomo(vardraw, entry))
continue;
} else if (VariantHandler.denovo.isSelected()) {
if (!checkDeNovo(vardraw, entry))
continue;
} else if (VariantHandler.dominant.isSelected()) {
if (!checkDominant(vardraw, entry))
continue;
} else if (VariantHandler.xLinked.isSelected()) {
if (!checkXlinked(vardraw, entry))
continue;
} else if (VariantHandler.compound.isSelected()) {
if (!checkCompound(vardraw, entry))
continue;
} else if (VariantHandler.recessive.isSelected()) {
recessivefound = checkRecessiveHomo(vardraw, entry);
if (!recessivefound) {
if (Main.chromosomeDropdown.getSelectedItem().equals("X")) {
recessivefound = checkXlinked(vardraw, entry);
}
}
if (!recessivefound) {
if (!checkCompound(vardraw, entry)) {
continue;
}
}
}
}
for (int m = 0; m < entry.getValue().size(); m++) {
if (entry.getValue().get(m).alleles != null) {
break;
}
if (Main.drawCanvas.hideVar(entry.getValue().get(m), entry.getKey().length() > 1)) {
if (VariantHandler.allChroms.isSelected()) {
entry.getValue().remove(m);
m--;
}
continue;
}
if (entry.getValue().get(m).getSample().annotation) {
continue;
}
sample = entry.getValue().get(m).getSample();
if (VariantHandler.onlyselected.isSelected()) {
if (!sample.equals(Main.drawCanvas.selectedSample)) {
continue;
}
}
sample.varcount++;
mutcount++;
VariantHandler.stattable.variants++;
if (vardraw.coding) {
sample.coding++;
}
sample.callrates += entry.getValue().get(m).getAlleleFraction();
if (entry.getValue().get(m).isHomozygous()) {
sample.homozygotes++;
} else {
sample.heterozygotes++;
}
if (entry.getKey().length() > 1) {
if (entry.getKey().contains("del")) {
sample.indels++;
} else {
sample.ins++;
}
} else {
//TODO
//System.out.println((int)(MethodLibrary.round(entry.getValue().get(m).getAlleleFraction(),4)*10000));
//array[entry.getValue().get(m).getSample().getIndex()][(int)(MethodLibrary.round(entry.getValue().get(m).getAlleleFraction(),5)*10000)]++;
/*if(sample.getName().contains("161")) {
if(Main.getBase.get(vardraw.getRefBase()).equals("C")) {
if(base.equals("A")) {
System.out.println(vardraw.getChrom() +":" +vardraw.getPosition());
}
}
}*/
if (VariantHandler.onlyStats.isSelected()) {
if (VariantHandler.outputContexts.isSelected()) {
String context = Main.chromDraw.getSeq(Main.drawCanvas.splits.get(0).chrom,
vardraw.getPosition() - 1, vardraw.getPosition() + 2, Main.referenceFile)
.toString();
//boolean set = false;
if (contexts == null) {
contexts = new HashMap<String, Integer[]>();
//contextQuals = new HashMap<String, Float[]>();
}
/*
if(base.equals("T")) {
if(context.endsWith("CG")) {
set = true;
}
}
if(base.equals("A")) {
if(context.startsWith("CG")) {
set = true;
}
}*/
// if(set) {
basecontext = base + context;
if (contexts.containsKey(base + context)) {
if (contexts.get(base + context)[sample.getIndex()] == null) {
contexts.get(base + context)[sample.getIndex()] = 1;
//contextQuals.get(base+context)[0]++;
// contextQuals.get(base+context)[1] += entry.getValue().get(m).getQuality();
} else {
contexts.get(base + context)[sample.getIndex()]++;
//contextQuals.get(base+context)[0]++;
//contextQuals.get(base+context)[1] += entry.getValue().get(m).getQuality();
}
} else {
if (contexts.containsKey(MethodLibrary.reverseComplement(base)
+ MethodLibrary.reverseComplement(context))) {
if (contexts.get(MethodLibrary.reverseComplement(base)
+ MethodLibrary.reverseComplement(context))[sample
.getIndex()] == null) {
contexts.get(MethodLibrary.reverseComplement(base)
+ MethodLibrary.reverseComplement(context))[sample.getIndex()] = 1;
//contextQuals.get(MethodLibrary.reverseComplement(base)+MethodLibrary.reverseComplement(context))[0] = 1F;
//contextQuals.get(MethodLibrary.reverseComplement(base)+MethodLibrary.reverseComplement(context))[1] = entry.getValue().get(m).getQuality();
} else {
contexts.get(MethodLibrary.reverseComplement(base)
+ MethodLibrary.reverseComplement(context))[sample.getIndex()]++;
//contextQuals.get(MethodLibrary.reverseComplement(base)+MethodLibrary.reverseComplement(context))[0]++;
//contextQuals.get(MethodLibrary.reverseComplement(base)+MethodLibrary.reverseComplement(context))[1] += entry.getValue().get(m).getQuality();
}
} else {
contexts.put(base + context, new Integer[Main.drawCanvas.sampleList.size()]);
contexts.get(base + context)[sample.getIndex()] = 1;
//contextQuals.put(base+context, new Float[2]);
//contextQuals.get(base+context)[0] = 1F;
//contextQuals.get(base+context)[1] = entry.getValue().get(m).getQuality();
}
}
}
// }
}
sample.snvs++;
try {
if (!Main.getBase.get(vardraw.getRefBase()).equals("N") && !entry.getKey().equals("N")
&& !entry.getKey().equals(".")) {
sample.mutationTypes[Main.mutTypes
.get(Main.getBase.get(vardraw.getRefBase()) + entry.getKey())]++;
}
} catch (Exception e) {
System.out.println(
sample.getName() + " " + vardraw.getPosition() + " " + (char) vardraw.getRefBase()
+ " " + Main.getBase.get(vardraw.getRefBase()) + " " + entry.getKey());
e.printStackTrace();
}
if (((char) vardraw.getRefBase() == 'A' && entry.getKey().equals("G"))
|| ((char) vardraw.getRefBase() == 'G' && entry.getKey().equals("A"))
|| ((char) vardraw.getRefBase() == 'C' && entry.getKey().equals("T"))
|| ((char) vardraw.getRefBase() == 'T' && entry.getKey().equals("C"))) {
sample.sitioRate++;
} else {
sample.versioRate++;
}
}
}
if (mutcount == 0) {
continue;
}
// INTRONIC
if (VariantHandler.intronic.isSelected() && vardraw.isInGene() && vardraw.getTranscripts() != null
&& vardraw.getExons() == null) {
for (int t = 0; t < vardraw.getTranscripts().size(); t++) {
for (int i = 0; i < entry.getValue().size(); i++) {
if (entry.getValue().get(i).alleles != null) {
break;
}
if (entry.getValue().get(i).getSample().annotation) {
continue;
}
if (Main.drawCanvas.hideVar(entry.getValue().get(i), entry.getKey().length() > 1)) {
if (VariantHandler.allChroms.isSelected()) {
entry.getValue().remove(i);
i--;
}
continue;
}
if (VariantHandler.onlyselected.isSelected()) {
if (!entry.getValue().get(i).getSample().equals(Main.drawCanvas.selectedSample)) {
continue;
}
}
if (!vardraw.getTranscripts().get(t).getGene().samples
.contains(entry.getValue().get(i).getSample())) {
vardraw.getTranscripts().get(t).getGene().samples
.add(entry.getValue().get(i).getSample());
}
}
if (!VariantHandler.onlyStats.isSelected()) {
boolean add = true;
if (VariantHandler.recessive.isSelected()) {
if (!recessivefound) {
add = checkCompoundGene(vardraw.getTranscripts().get(t).getGene(), vardraw);
}
} else if (VariantHandler.compound.isSelected()) {
add = checkCompoundGene(vardraw.getTranscripts().get(t).getGene(), vardraw);
}
if (add && vardraw.getTranscripts().get(t).getGene().mutations == 0
&& vardraw.getTranscripts().get(t).getGene().samples
.size() >= VariantHandler.geneSlider.getValue()) {
VariantHandler.table.addEntry(vardraw.getTranscripts().get(t).getGene());
VariantHandler.table.revalidate();
VariantHandler.table.repaint();
}
}
vardraw.getTranscripts().get(t).getGene().intronic += mutcount;
vardraw.inVarList = true;
if (vardraw.inVarList) {
if (!vardraw.getTranscripts().get(t).getGene().varnodes.contains(vardraw)) {
if (!VariantHandler.onlyStats.isSelected()) {
vardraw.getTranscripts().get(t).getGene().varnodes.add(vardraw);
}
preI = -1;
}
if (v != preI) {
VariantHandler.table.variants += mutcount;
vardraw.getTranscripts().get(t).getGene().mutations += mutcount;
preI = v;
}
}
}
}
/*if(vardraw.getPosition() == 70117871) {
System.out.println(vardraw.getExons());
}*/
if (vardraw != null && vardraw.getExons() != null) {
ArrayList<Gene> calcgene = new ArrayList<Gene>();
for (int exon = 0; exon < vardraw.getExons().size(); exon++) {
amino = Main.chromDraw.getAminoChange(vardraw, base, vardraw.getExons().get(exon));
if (amino.contains("UTR")) {
if (VariantHandler.utr.isSelected()) {
if (!VariantHandler.table.genearray
.contains(vardraw.getExons().get(exon).getTranscript().getGene())
&& vardraw.getExons().get(exon).getTranscript().getGene().samples
.size() >= VariantHandler.geneSlider.getValue()) {
if (!VariantHandler.onlyStats.isSelected()) {
boolean add = true;
if (VariantHandler.recessive.isSelected()) {
if (!recessivefound) {
add = checkCompoundGene(
vardraw.getExons().get(exon).getTranscript().getGene(),
vardraw);
}
} else if (VariantHandler.compound.isSelected()) {
add = checkCompoundGene(
vardraw.getExons().get(exon).getTranscript().getGene(), vardraw);
}
if (add) {
VariantHandler.table
.addEntry(vardraw.getExons().get(exon).getTranscript().getGene());
}
}
}
vardraw.inVarList = true;
vardraw.getExons().get(exon).getTranscript().getGene().utr += mutcount;
} else {
continue;
}
}
if (VariantHandler.nonsense.isSelected()) {
if (!MethodLibrary.aminoEffect(amino).contains("nonsense")) {
continue;
}
}
if (VariantHandler.synonymous.isSelected()) {
if (MethodLibrary.aminoEffect(amino).contains("synonymous")) {
continue;
}
}
for (int i = 0; i < entry.getValue().size(); i++) {
if (entry.getValue().get(i).alleles != null) {
break;
}
if (entry.getValue().get(i).getSample().annotation) {
continue;
}
if (Main.drawCanvas.hideVar(entry.getValue().get(i), entry.getKey().length() > 1)) {
continue;
}
if (VariantHandler.onlyselected.isSelected()) {
if (!entry.getValue().get(i).getSample().equals(Main.drawCanvas.selectedSample)) {
continue;
}
}
if (!vardraw.getExons().get(exon).getTranscript().getGene().samples
.contains(entry.getValue().get(i).getSample())) {
if (!VariantHandler.onlyStats.isSelected()) {
vardraw.getExons().get(exon).getTranscript().getGene().samples
.add(entry.getValue().get(i).getSample());
}
}
}
boolean add = true;
if (!VariantHandler.onlyStats.isSelected()) {
if (VariantHandler.recessive.isSelected()) {
if (!recessivefound) {
add = checkCompoundGene(vardraw.getExons().get(exon).getTranscript().getGene(),
vardraw);
}
} else if (VariantHandler.compound.isSelected()) {
add = checkCompoundGene(vardraw.getExons().get(exon).getTranscript().getGene(),
vardraw);
}
if (add && !VariantHandler.table.genearray
.contains(vardraw.getExons().get(exon).getTranscript().getGene())
&& vardraw.getExons().get(exon).getTranscript().getGene().samples
.size() >= VariantHandler.geneSlider.getValue()) {
VariantHandler.table.addEntry(vardraw.getExons().get(exon).getTranscript().getGene());
}
}
if (MethodLibrary.aminoEffect(amino).contains("nonsense")) {
if (!calcgene.contains(vardraw.getExons().get(exon).getTranscript().getGene())) {
for (int i = 0; i < entry.getValue().size(); i++) {
if (entry.getValue().get(i).alleles != null) {
break;
}
if (entry.getValue().get(i).getSample().annotation) {
continue;
}
if (Main.drawCanvas.hideVar(entry.getValue().get(i), entry.getKey().length() > 1)) {
continue;
}
entry.getValue().get(i).getSample().nonsense++;
if (entry.getKey().length() > 1) {
entry.getValue().get(i).getSample().fshift++;
}
if (amino.contains("spl")) {
entry.getValue().get(i).getSample().splice++;
} else {
entry.getValue().get(i).getSample().nonsyn++;
}
}
}
vardraw.getExons().get(exon).getTranscript().getGene().nonsense += mutcount;
} else if (MethodLibrary.aminoEffect(amino).contains("missense")) {
if (!calcgene.contains(vardraw.getExons().get(exon).getTranscript().getGene())) {
for (int i = 0; i < entry.getValue().size(); i++) {
if (entry.getValue().get(i).alleles != null) {
break;
}
if (entry.getValue().get(i).getSample().annotation) {
continue;
}
if (Main.drawCanvas.hideVar(entry.getValue().get(i), entry.getKey().length() > 1)) {
continue;
}
if (entry.getKey().length() > 1) {
entry.getValue().get(i).getSample().inframe++;
}
entry.getValue().get(i).getSample().missense++;
entry.getValue().get(i).getSample().nonsyn++;
}
}
vardraw.getExons().get(exon).getTranscript().getGene().missense += mutcount;
} else if (MethodLibrary.aminoEffect(amino).contains("synonymous")) {
if (!calcgene.contains(vardraw.getExons().get(exon).getTranscript().getGene())) {
for (int i = 0; i < entry.getValue().size(); i++) {
if (entry.getValue().get(i).alleles != null) {
break;
}
if (entry.getValue().get(i).getSample().annotation) {
continue;
}
if (Main.drawCanvas.hideVar(entry.getValue().get(i), entry.getKey().length() > 1)) {
continue;
}
entry.getValue().get(i).getSample().syn++;
}
}
vardraw.getExons().get(exon).getTranscript().getGene().synonymous += mutcount;
}
vardraw.inVarList = true;
if (!vardraw.getExons().get(exon).getTranscript().getGene().varnodes.contains(vardraw)) {
if (!VariantHandler.onlyStats.isSelected()) {
vardraw.getExons().get(exon).getTranscript().getGene().varnodes.add(vardraw);
}
preI = -1;
}
if (v != preI) {
vardraw.getExons().get(exon).getTranscript().getGene().mutations += mutcount;
VariantHandler.table.variants += mutcount;
preI = v;
}
VariantHandler.table.revalidate();
VariantHandler.table.repaint();
if (!calcgene.contains(vardraw.getExons().get(exon).getTranscript().getGene())) {
calcgene.add(vardraw.getExons().get(exon).getTranscript().getGene());
}
}
}
preI = v;
if (!vardraw.isInGene() && VariantHandler.intergenic.isSelected()) {
/*
for(int v = 0; v<vardraw.vars.size(); v++) {
entry = vardraw.vars.get(v);
if(Main.drawCanvas.hideNodeVar(vardraw, entry)) {
continue;
}
base = entry.getKey();
mutcount = 0;
for(int m = 0; m<entry.getValue().size(); m++) {
if(entry.getValue().get(m).alleles != null) {
break;
}
if(Main.drawCanvas.hideVar(entry.getValue().get(m))) {
continue;
}
mutcount++;
}
*/
if (mutcount > 0) {
if (VariantHandler.table.genearray.size() == 0
|| !VariantHandler.table.genearray
.get(VariantHandler.table.genearray.size() - 1).intergenic
|| !VariantHandler.table.genearray.get(VariantHandler.table.genearray.size() - 1)
.getName().equals(vardraw.getTranscripts().get(0).getGene().getName())) {
Gene addgene = null;
try {
addgene = new Gene(vardraw.getTranscripts().get(0).getGene());
} catch (Exception e) {
e.printStackTrace();
//Main.drawCanvas.ready("all");
break;
}
addgene.intergenic = true;
addgene.mutations = mutcount;
VariantHandler.table.variants += mutcount;
if (!VariantHandler.onlyStats.isSelected()) {
addgene.varnodes.add(vardraw);
boolean add = true;
if (VariantHandler.recessive.isSelected()) {
if (!recessivefound) {
add = checkCompoundGene(addgene, vardraw);
}
} else if (VariantHandler.compound.isSelected()) {
add = checkCompoundGene(addgene, vardraw);
}
if (add) {
VariantHandler.table.addEntry(addgene);
}
}
for (int m = 0; m < entry.getValue().size(); m++) {
if (entry.getValue().get(m).alleles != null) {
break;
}
if (entry.getValue().get(m).getSample().annotation) {
continue;
}
if (Main.drawCanvas.hideVar(entry.getValue().get(m), entry.getKey().length() > 1)) {
continue;
}
if (!addgene.samples.contains(entry.getValue().get(m).getSample())) {
if (!VariantHandler.onlyStats.isSelected()) {
addgene.samples.add(entry.getValue().get(m).getSample());
}
}
}
} else {
if (!VariantHandler.onlyStats.isSelected()) {
VariantHandler.table.genearray
.get(VariantHandler.table.genearray.size() - 1).mutations += mutcount;
if (!VariantHandler.table.genearray
.get(VariantHandler.table.genearray.size() - 1).varnodes.contains(vardraw)) {
VariantHandler.table.genearray
.get(VariantHandler.table.genearray.size() - 1).varnodes.add(vardraw);
}
}
VariantHandler.table.variants += mutcount;
for (int m = 0; m < entry.getValue().size(); m++) {
if (entry.getValue().get(m).alleles != null) {
break;
}
if (entry.getValue().get(m).getSample().annotation) {
continue;
}
if (Main.drawCanvas.hideVar(entry.getValue().get(m), entry.getKey().length() > 1)) {
continue;
}
if (!VariantHandler.table.genearray
.get(VariantHandler.table.genearray.size() - 1).samples
.contains(entry.getValue().get(m).getSample())) {
if (!VariantHandler.onlyStats.isSelected()) {
VariantHandler.table.genearray
.get(VariantHandler.table.genearray.size() - 1).samples
.add(entry.getValue().get(m).getSample());
}
}
}
// }
}
vardraw.inVarList = true;
}
}
//TODO TAHAN
// System.out.println(vardraw.getTranscripts().get(0).getGenename() +"..." +vardraw.getTranscripts().get(1).getGenename() );
}
if (!vardraw.inVarList) {
returnnode = vardraw.getNext();
if (VariantHandler.allChroms.isSelected()) {
vardraw.removeNode();
}
return returnnode;
} else {
mutcount = 0;
for (int v = 0; v < vardraw.vars.size(); v++) {
entry = vardraw.vars.get(v);
if (Main.drawCanvas.hideNodeVar(vardraw, entry)) {
if (VariantHandler.allChroms.isSelected()) {
vardraw.vars.remove(v);
v--;
}
continue;
}
base = entry.getKey();
for (int m = 0; m < entry.getValue().size(); m++) {
if (entry.getValue().get(m).alleles != null) {
break;
}
if (entry.getValue().get(m).getSample().annotation) {
continue;
}
if (Main.drawCanvas.hideVar(entry.getValue().get(m), entry.getKey().length() > 1)) {
if (VariantHandler.allChroms.isSelected()) {
entry.getValue().remove(m);
m--;
}
continue;
}
mutcount++;
}
}
if (VariantHandler.commonSlider.getValue() > 1 && VariantHandler.clusterSize > 0) {
if (Main.drawCanvas.clusterNodes.size() == 0) {
ClusterNode cluster = new ClusterNode();
cluster.nodecount = mutcount;
cluster.ID = vardraw.clusterId;
vardraw.clusterNode = cluster;
cluster.varnodes.add(vardraw);
cluster.width = 1;
Main.drawCanvas.clusterNodes.add(cluster);
} else if (Main.drawCanvas.clusterNodes
.get(Main.drawCanvas.clusterNodes.size() - 1).ID != vardraw.clusterId) {
Main.drawCanvas.clusterNodes
.get(Main.drawCanvas.clusterNodes.size() - 1).width = Main.drawCanvas.clusterNodes
.get(Main.drawCanvas.clusterNodes.size() - 1).varnodes
.get(Main.drawCanvas.clusterNodes
.get(Main.drawCanvas.clusterNodes.size() - 1).varnodes.size()
- 1)
.getPosition()
- Main.drawCanvas.clusterNodes
.get(Main.drawCanvas.clusterNodes.size() - 1).varnodes.get(0)
.getPosition()
+ 1;
ClusterNode cluster = new ClusterNode();
cluster.nodecount += mutcount;
cluster.ID = vardraw.clusterId;
vardraw.clusterNode = cluster;
cluster.varnodes.add(vardraw);
cluster.width = 1;
Main.drawCanvas.clusterNodes.add(cluster);
} else {
vardraw.clusterNode = Main.drawCanvas.clusterNodes.get(Main.drawCanvas.clusterNodes.size() - 1);
Main.drawCanvas.clusterNodes.get(Main.drawCanvas.clusterNodes.size() - 1).nodecount += mutcount;
Main.drawCanvas.clusterNodes.get(Main.drawCanvas.clusterNodes.size() - 1).varnodes.add(vardraw);
}
VariantHandler.clusterTable.variants += mutcount;
}
if (!VariantHandler.writetofile.isSelected()) {
if (vardraw != null && vardraw.inVarList && vardraw.bedhit && vardraw.getBedHits() != null) {
pretrack = -1;
for (int i = 0; i < vardraw.getBedHits().size(); i++) {
vardraw.getBedHits().get(i).inVarlist = true;
if (pretrack != vardraw.getBedHits().get(i).getTrack().trackIndex) {
vardraw.getBedHits().get(i).getTrack().getTable().variants += mutcount;
pretrack = vardraw.getBedHits().get(i).getTrack().trackIndex;
}
if (vardraw.getBedHits().get(i).getTrack().getTable().bedarray == null) {
vardraw.getBedHits().get(i).getTrack().getTable().bedarray = new ArrayList<BedNode>();
}
if (!vardraw.getBedHits().get(i).getTrack().getTable().bedarray
.contains(vardraw.getBedHits().get(i))) {
vardraw.getBedHits().get(i).mutations += mutcount;
vardraw.getBedHits().get(i).getTrack().getTable().bedarray
.add(vardraw.getBedHits().get(i));
vardraw.getBedHits().get(i).getTrack().getTable()
.setPreferredSize(new Dimension(
vardraw.getBedHits().get(i).getTrack().getTable().tablescroll
.getViewport().getWidth(),
(vardraw.getBedHits().get(i).getTrack().getTable().getTableSize() + 2
+ samplecount)
* vardraw.getBedHits().get(i).getTrack().getTable().rowHeight));
vardraw.getBedHits().get(i).getTrack().getTable().revalidate();
// vardraw.inVarList = true;
} else {
vardraw.getBedHits().get(i).mutations += mutcount;
// vardraw.inVarList = true;
}
}
}
}
}
if (VariantHandler.writetofile.isSelected()) {
writeToFile(vardraw, output, outputgz);
}
lastVar = vardraw;
return vardraw.getNext();
// }
}
From source file:sos.settings.SOSSettingsDialog.java
/** * Dokumentation anzeigen// w w w .j av a2s. c o m * * @throws Exception */ private void showDocumentation() throws Exception { this.debug(3, "showDocumentation"); StringBuffer sqlStmt = new StringBuffer( "select \"TITLE\",\"APPLICATION\",\"SECTION\",\"NAME\",\"VALUE\",\"DISPLAY_TYPE\",\"INPUT_TYPE\" from " + this.settings.source); String sqlAnd = " where "; String[] display_type_entries = this.rb.getMessage("sos.settings.dialog.listbox_display_type_entries") .split(";"); String[] input_type_entries = this.rb.getMessage("sos.settings.dialog.listbox_input_type_entries") .split(";"); if (this.settings.section.equals(this.settings.entrySchemaSection)) { this.settings.section = this.settings.entrySchemaSection; } if (!this.settings.application.equals("")) { sqlStmt.append(sqlAnd + " \"" + this.settings.entryApplication + "\" = " + this.dbQuoted(this.settings.application)); sqlAnd = " and "; } if (!this.settings.section.equals("")) { sqlStmt.append( sqlAnd + " \"" + this.settings.entrySection + "\" = " + this.dbQuoted(this.settings.section)); sqlAnd = " and "; } sqlStmt.append(" order by \"" + this.settings.entryApplication + "\",\"" + this.settings.entrySection + "\",\"" + this.settings.entryName + "\""); try { Vector results = this.connection.getArrayAsVector(sqlStmt.toString()); LinkedHashMap applications = new LinkedHashMap(); LinkedHashMap sections = new LinkedHashMap(); LinkedHashMap entries = new LinkedHashMap(); for (Enumeration el = results.elements(); el.hasMoreElements();) { HashMap result = (HashMap) el.nextElement(); if (result.get("application").toString().equals(result.get("section").toString()) && result.get("application").toString().equals(result.get("name").toString())) { applications.put(result.get("application").toString(), result); } else if (result.get("section").toString().equals(result.get("name").toString()) && !result.get("section").toString().equals(result.get("application").toString())) { String key = result.get("application").toString(); LinkedHashMap section = new LinkedHashMap(); if (sections.containsKey(key)) { section = (LinkedHashMap) sections.get(key); } section.put(result.get("section").toString(), result); sections.put(key, section); } else { String appKey = result.get("application").toString(); String secKey = result.get("section").toString(); LinkedHashMap section = new LinkedHashMap(); LinkedHashMap entry = new LinkedHashMap(); if (entries.containsKey(appKey)) { section = (LinkedHashMap) entries.get(appKey); if (section.containsKey(secKey)) { entry = (LinkedHashMap) section.get(secKey); } } entry.put(result.get("name").toString(), result); section.put(secKey, entry); entries.put(appKey, section); } } //out.print(entries); results = null; this.styleBorder = "1\" bgcolor=\"#ffffff\" bordercolorlight=\"#D2D2D2\" bordercolordark=\"#ffffff"; this.showTableBegin(); if (applications.size() != 0) { Iterator appIt = applications.entrySet().iterator(); while (appIt.hasNext()) { Map.Entry application = (Map.Entry) appIt.next(); String app_key = application.getKey().toString(); HashMap app_value = (HashMap) application.getValue(); this.out.println("<tr>"); this.out.println(" <td colspan=\"3\" nowrap style=\"color:#808080;font-weight:bold;\">" + app_value.get("title") + "</td>"); this.out.println(" <td nowrap>" + app_value.get("name") + "</td>"); this.out.println(" <td nowrap> </td>"); this.out.println("</tr>"); if (sections.containsKey(app_key)) { HashMap appSections = (HashMap) sections.get(app_key); Iterator secIt = appSections.entrySet().iterator(); while (secIt.hasNext()) { Map.Entry section = (Map.Entry) secIt.next(); String sec_key = section.getKey().toString(); HashMap sec_value = (HashMap) section.getValue(); if (!sec_value.get("name").toString().equals(this.settings.entrySchemaSection)) { this.out.println("<tr>"); this.out.println(" <td nowrap> </td>"); this.out.println( " <td colspan=\"2\" nowrap style=\"color:#808080;font-weight:bold;\">" + sec_value.get("title") + "</td>"); this.out.println(" <td nowrap>" + sec_value.get("name") + "</td>"); this.out.println(" <td nowrap> </td>"); this.out.println("</tr>"); if (entries.containsKey(app_key)) { HashMap secEntrie = (HashMap) entries.get(app_key); if (secEntrie.containsKey(sec_key)) { HashMap secEntries = (HashMap) secEntrie.get(sec_key); Iterator entIt = secEntries.entrySet().iterator(); while (entIt.hasNext()) { Map.Entry entry = (Map.Entry) entIt.next(); String ent_key = entry.getKey().toString(); HashMap ent_value = (HashMap) entry.getValue(); this.out.println("<tr>"); this.out.println(" <td width=\"20\" nowrap> </td>"); this.out.println(" <td width=\"20\" nowrap> </td>"); this.out.println(" <td width=\"35%\" nowrap valign=\"top\">" + ent_value.get("title") + "</td>"); this.out.println(" <td width=\"10%\" nowrap valign=\"top\">" + ent_value.get("name") + "</td>"); this.out.println(" <td nowrap valign=\"top\">"); if (ent_value.get("input_type").toString().equals("5")) { // long_value this.out.println("[ " + this.rb.getMessage( "sos.settings.dialog.dialog_long_value_title") + " ]"); if (ent_value.get("display_type").toString().equals("4")) { this.out.println(" " + display_type_entries[4]); } } else if (ent_value.get("input_type").toString().equals("6")) { // binary versteckt this.out.println("[ " + input_type_entries[6] + " ]"); } else { if (ent_value.get("display_type").toString().endsWith("3")) { this.out.println("<pre>" + this.htmlSpecialChars( ent_value.get("value").toString()) + "</pre>"); } else { this.out.println( this.htmlSpecialChars(ent_value.get("value").toString()) + " "); } } this.out.println(" </td>"); this.out.println("</tr>"); } } } } } } } } // if applications else if (sections.size() != 0) { try { HashMap application = this.connection.getSingle("select \"TITLE\",\"NAME\" from " + this.settings.source + " where \"" + this.settings.entryApplication + "\" = " + this.dbQuoted(this.settings.application) + " and \"" + this.settings.entrySection + "\" = " + this.dbQuoted(this.settings.application) + " and \"" + this.settings.entryName + "\" = " + this.dbQuoted(this.settings.application)); Iterator secIt = sections.entrySet().iterator(); if (sections.containsKey(this.settings.application)) { HashMap appSections = (HashMap) sections.get(this.settings.application); Iterator secI = appSections.entrySet().iterator(); while (secI.hasNext()) { Map.Entry section = (Map.Entry) secI.next(); String sec_key = section.getKey().toString(); HashMap sec_value = (HashMap) section.getValue(); this.out.println("<tr>"); this.out.println( " <td colspan=\"3\" nowrap style=\"color:#808080;font-weight:bold;\">" + application.get("title") + "</td>"); this.out.println(" <td nowrap>" + application.get("name") + "</td>"); this.out.println(" <td nowrap> </td>"); this.out.println("</tr>"); this.out.println("<tr>"); this.out.println(" <td nowrap> </td>"); this.out.println( " <td colspan=\"2\" nowrap style=\"color:#808080;font-weight:bold;\">" + sec_value.get("title") + "</td>"); this.out.println(" <td nowrap>" + sec_value.get("name") + "</td>"); this.out.println(" <td nowrap> </td>"); this.out.println("</tr>"); if (entries.containsKey(this.settings.application)) { HashMap secEntrie = (HashMap) entries.get(this.settings.application); if (secEntrie.containsKey(sec_key)) { HashMap secEntries = (HashMap) secEntrie.get(sec_key); Iterator entI = secEntries.entrySet().iterator(); while (entI.hasNext()) { Map.Entry entry = (Map.Entry) entI.next(); String ent_key = entry.getKey().toString(); HashMap ent_value = (HashMap) entry.getValue(); this.out.println("<tr>"); this.out.println(" <td width=\"3%\" nowrap> </td>"); this.out.println(" <td width=\"3%\" nowrap> </td>"); this.out.println(" <td width=\"35%\" nowrap valign=\"top\">" + ent_value.get("title") + "</td>"); this.out.println(" <td width=\"10%\" nowrap valign=\"top\">" + ent_value.get("name") + "</td>"); this.out.println(" <td nowrap valign=\"top\">"); if (ent_value.get("input_type").toString().equals("5")) { // long_value this.out.println("[ " + this.rb.getMessage( "sos.settings.dialog.dialog_long_value_title") + " ]"); if (ent_value.get("display_type").toString().equals("4")) { this.out.println(" " + display_type_entries[4]); } } else if (ent_value.get("input_type").toString().equals("6")) { // binary versteckt this.out.println("[ " + input_type_entries[6] + " ]"); } else { if (ent_value.get("display_type").toString().endsWith("3")) { this.out.println("<pre>" + this.htmlSpecialChars(ent_value.get("value").toString()) + "</pre>"); } else { this.out.println( this.htmlSpecialChars(ent_value.get("value").toString())); } } this.out.println(" </td>"); this.out.println("</tr>"); } } } } //out.print(section); } } catch (Exception e) { this.setError(e.getMessage(), SOSClassUtil.getMethodName()); return; } } this.showTableEnd(); } catch (Exception e) { this.setError(e.getMessage(), SOSClassUtil.getMethodName()); return; } }