X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylosummary.cpp;h=5f7bbc3c73a2161417a1841f567719a4bd1f8c4a;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=58274b3ec365c573eacc9644a446c209f35f63ff;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git diff --git a/phylosummary.cpp b/phylosummary.cpp index 58274b3..5f7bbc3 100644 --- a/phylosummary.cpp +++ b/phylosummary.cpp @@ -25,7 +25,7 @@ PhyloSummary::PhyloSummary(string refTfile, string groupFile){ } //check for necessary files - string taxFileNameTest = refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"; + string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum")); ifstream FileTest(taxFileNameTest.c_str()); if (!FileTest) { @@ -71,22 +71,18 @@ PhyloSummary::PhyloSummary(string groupFile){ } /**************************************************************************************************/ -void PhyloSummary::summarize(string userTfile){ +int PhyloSummary::summarize(string userTfile){ try { - - ifstream in; - m->openInputFile(userTfile, in); - - //read in users taxonomy file and add sequences to tree - string name, tax; - while(!in.eof()){ - in >> name >> tax; m->gobble(in); - - addSeqToTree(name, tax); - - if (m->control_pressed) { break; } - } - in.close(); + map temp; + m->readTax(userTfile, temp); + + for (map::iterator itTemp = temp.begin(); itTemp != temp.end();) { + addSeqToTree(itTemp->first, itTemp->second); + numSeqs++; + temp.erase(itTemp++); + } + + return numSeqs; } catch(exception& e) { m->errorOut(e, "PhyloSummary", "summarize"); @@ -117,6 +113,7 @@ string PhyloSummary::getNextTaxon(string& heirarchy){ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){ try { + numSeqs++; map::iterator childPointer; @@ -126,6 +123,9 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){ int level = 0; + //are there confidence scores, if so remove them + if (seqTaxonomy.find_first_of('(') != -1) { m->removeConfidences(seqTaxonomy); } + while (seqTaxonomy != "") { if (m->control_pressed) { return 0; } @@ -141,7 +141,7 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){ //find out the sequences group string group = groupmap->getGroup(seqName); - if (group == "not found") { m->mothurOut(seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); } + if (group == "not found") { m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); } //do you have a count for this group? map::iterator itGroup = tree[childPointer->second].groupCount.find(group); @@ -176,7 +176,7 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){ //find out the sequences group string group = groupmap->getGroup(seqName); - if (group == "not found") { m->mothurOut(seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); } + if (group == "not found") { m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); } //do you have a count for this group? map::iterator itGroup = tree[index].groupCount.find(group); @@ -221,6 +221,9 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector names){ int level = 0; + //are there confidence scores, if so remove them + if (seqTaxonomy.find_first_of('(') != -1) { m->removeConfidences(seqTaxonomy); } + while (seqTaxonomy != "") { if (m->control_pressed) { return 0; } @@ -244,7 +247,7 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector names){ //find out the sequences group string group = groupmap->getGroup(names[k]); - if (group == "not found") { m->mothurOut(names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); } + if (group == "not found") { m->mothurOut("[WARNING]: " + names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); } else { containsGroup[group] = true; } @@ -286,7 +289,7 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector names){ //find out the sequences group string group = groupmap->getGroup(names[k]); - if (group == "not found") { m->mothurOut(names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); } + if (group == "not found") { m->mothurOut("[WARNING]: " + names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); } else { containsGroup[group] = true; } @@ -361,16 +364,25 @@ void PhyloSummary::print(ofstream& out){ out << endl; int totalChildrenInTree = 0; + map::iterator itGroup; map::iterator it; for(it=tree[0].children.begin();it!=tree[0].children.end();it++){ - if (tree[it->second].total != 0) { totalChildrenInTree++; } + if (tree[it->second].total != 0) { + totalChildrenInTree++; + tree[0].total += tree[it->second].total; + + if (groupmap != NULL) { + vector mGroups = groupmap->getNamesOfGroups(); + for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; } + } + } } //print root out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t"; - map::iterator itGroup; + if (groupmap != NULL) { //for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) { // out << itGroup->second << '\t'; @@ -472,11 +484,10 @@ void PhyloSummary::readTreeStruct(ifstream& in){ } catch(exception& e) { - m->errorOut(e, "PhyloSummary", "print"); + m->errorOut(e, "PhyloSummary", "readTreeStruct"); exit(1); } } - /**************************************************************************************************/