#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
+#include "sharedjackknife.h"
+#include "whittaker.h"
string fileNameRoot;
fileNameRoot = getRootName(globaldata->inputFileName);
format = globaldata->getFormat();
+ convert(globaldata->getFreq(), freq);
validCalculator = new ValidCalculators();
util = new SharedUtil();
cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
}else if (globaldata->Estimators[i] == "sharednseqs") {
cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
+
}else if (globaldata->Estimators[i] == "ochiai") {
cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
}else if (globaldata->Estimators[i] == "anderberg") {
//if the users entered no valid calculators don't execute command
if (cDisplays.size() == 0) { return 0; }
- if (format == "sharedfile") {
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
- input = globaldata->ginput;
- order = input->getSharedOrderVector();
- }else {
- //you are using a list and a groupfile
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
- }
- set<string> orderList;
+ input = globaldata->ginput;
+ order = input->getSharedOrderVector();
+ SharedOrderVector* lastOrder = order;
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = globaldata->labels;
+ set<int> userLines = globaldata->lines;
+
//set users groups
util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
- while(order != NULL){
- orderList.insert(order->getLabel());
+ while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+
//create collectors curve
cCurve = new Collect(order, cDisplays);
- convert(globaldata->getFreq(), freq);
cCurve->getSharedCurve(freq);
-
delete cCurve;
cout << order->getLabel() << '\t' << count << endl;
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
+ userLines.erase(count);
+
+ //you have a label the user want that is smaller than this line and the last line has not already been processed
+ }
+
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
+ //create collectors curve
+ cCurve = new Collect(lastOrder, cDisplays);
+ cCurve->getSharedCurve(freq);
+ delete cCurve;
+
+ cout << lastOrder->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lastOrder->getLabel());
+ userLabels.erase(lastOrder->getLabel());
}
+ if (count != 1) { delete lastOrder; }
+ lastOrder = order;
+
//get next line to process
- if (format == "sharedfile") {
- order = input->getSharedOrderVector();
+ order = input->getSharedOrderVector();
+ count++;
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastOrder->getLabel()) != 1) {
+ cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ needToRun = true;
}else {
- //you are using a list and a groupfile
- SharedList = input->getSharedListVector(); //get new list vector to process
- if (SharedList != NULL) {
- order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
- }else {
- break;
- }
+ cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
}
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cCurve = new Collect(lastOrder, cDisplays);
+ cCurve->getCurve(freq);
+ delete cCurve;
- count++;
+ cout << lastOrder->getLabel() << '\t' << count << endl;
}
- set<string>::iterator i;
- for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
- if(orderList.count(*i) == 0)
- cout << "'" << *i << "'" << " is not a valid label.\n";
+
+ delete lastOrder;
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
//reset groups parameter