From 59c2827ee568dcc9293faef40e5d67499bc68bc3 Mon Sep 17 00:00:00 2001 From: westcott Date: Mon, 18 Oct 2010 16:14:10 +0000 Subject: [PATCH] fixed unifrac.unweighted --- mothur | Bin 6840072 -> 6840072 bytes unweighted.cpp | 25 +++++++++++++++++-------- 2 files changed, 17 insertions(+), 8 deletions(-) diff --git a/mothur b/mothur index 484ba58b9f04e78a155e4f2a450adebabf45f45c..f8b951d224cb8db0e1facc8b191cd3f5ad233e36 100755 GIT binary patch delta 9956 zcmZ`<30#!b+MnSa7MC25MMM#B$pH~j^a^Rpi;yhCxLhkOQE@>m6Wr1)91JI%#xb?% zcyF3Zb=7XB-ZIog!4((G+_ywc;~mitvvOmZ@Bf_h4x-<8{rw&e|MM*8InVQ)^PHDj zw0o_z2(+ctLwl^C%%iZ(Lkn^PNgy4_9YphYM z)B_X^>Iv!viUIWo^#T12)E5*BiUYj>>Ido%dJ!}LG!PVDT;?J7DeHB$&goQwck49C z)=I_t9mWZ(6wD>tN{E$wC~1QR{}jVku;TXV3#Kzex!hiRl_izSuW5B`O}Xr+EoIxv zcUTrwRc_n00N#CZ^Bw6kxS`B)O-d&@yC2fzh48M zBXal%A5Sv4O;sXylyl!>;X||sl6RI`leWwKUK*;m_kx8ciznK=k}QYy3y(E8ohjBc zDFp|H8m%?Tyl+{4h1|>MGqP-Ne}?Q(sAe(!QMrRQgGC*c!_5QB`R+9ECE1>L$Y>qs zrG#vuxox3N+ML+H{XKl@E|$O)cW)G?9K~94g$G<&w+S-g`=FUjn)dV!$<~W5=D?kh zF2J@dm-GwCmp}9oc4Iv|dsGfFpE>CX{90+2KFa;@aZkUy;dQIc<@3$$jlXTOxxSKrxz;SubN;B9{2=kH?r$6?7#S_ zB&wq;s+w}07}1vd`h|L`1Y8KOB#Tqq?@`w`o5T<#X|`mlPZeuVpe zB(+KLv&YA=i7rCl5)B0?Y8;8RPA7{$F8c-liKBy3$=uOWGtWc6@W^AQQ!c32>Mf=C zjfqX_CHbWdIX&jiM`sWN5)jzh3isz}~e`B>M{)1!?#lIV4<5h#=-?@s4|Ea4%#>vK1 z)2rdj9SEkSC4B8>xm_3MbjDfeLe($KqNuCaW&w|t7hRu;w!kFZ3zol-VYO5o84uJ{ zHrrw1sq9$6N`8{t#1ubtI(wEnexR%9NwwLqNvbw}iW`f~o5Gd5>C+Q(f^TOs6Xm|_ z2T?RJFe6H(KAqdoI`&i%qFhDc_*eqTN+m85x@HLQa%_Nu%Jf}2jWU&fOvaBC>%rs+ zC#|QR2}k61L}&tL`LVX1Qqs|_oJVI3G+G}h@0!2RX{@Jk<3L;aZ6g;YT%%lYfoCE< zS=g&)Mtj~-*uaIiRGEwG*l0xqIH;s;pkE*3o;x+lou_dUEa5{W*3jH&ADLP`MgqG+e;?j)7E$ zJQR-R__c9!H@@bZb3|ei7Rl8I8+2xFbv3Wn8l{SR=2SicR=z=ZcU`a9?Ld?01>wN}Wm=wWWB7ox^)tm!rTrx>9!7s;H)$TH3w}P`3 zf7o>-V#?8-oVMp35$o0eORP5mtfl&pcnvE(Ehof%Nz--<9W|;=>!D<;Wh6wDV0wgL z%M&guACQc#gr@OES%JW5lt|X^jNGLg7cIlRhcmJW{5=nG*V=}Uuoj&rBV9^FiCGUR zCz8dn;kwWy%MG^XtlUc*!A_l(J9$oA2N~;Lwk6QJYs8Fao))=35;G|u zw1{FQ8eY;;WdSptlT);7*@|;=mv|pkJkBXO{z<1g-fZX7+reI>;ek7cmsmD!cm-wE zZi(iz6w7fmyN1=Dlf#DD0_n^kUM@68wX_|hQn!xHyevlqln>%fqvu}UG}NNVX5U?w4Zh29MyOR# za(Sy5R>wkqkpqGA-YpfZ!!L3huV`WPAMC|nEHre5wlJ9N{O65tXbZu?}B$Xnz{TF$V zPYM}~a{u9L;pW4~+FNV?eLo<9 zulU#Bsp{`=<0`vY=@r?}d}$R#3oLixhL^G5CK_k|s(b-SqkZ-PEP}4NMOi>t7#XpW ze!YjDcsX5k&1o=!u6fYaHG6Rh>YCwkqG=jw5u0Txj2o?@X*TetdBL15y5`Gd16{Ko zo>Nax;`o7b2Uv8?NpL~zvlibd*!5AR;h+4Me8oZb(bkS&0p2kWDLU2QH>$xuxl<36 zmB7jlSa58Ha0)wFDYrI<(~S=O`7~uc#9t;&?}%aayrT~J%tf(T?bI*Py7s(d!oN5y zLDAn1Q%GGko)dY;xml$HSk)E4jVChC2cfo^H7dy9ZyyI3*uhzP=gO`{SrSm`k{QYU35wuK5atreV1;}2~4-vC0qZf zZpm8)8~sRr1Nw&^$-&xqcJq-OW)@B9YbXM^hGA^K##p#PnAbmNpHv$b_{M;P2+Cy(zN!oL_!pkfkH zGW?G+>!9zDxsmHG*VZq>iI{^q(b(cyM!g)3Y%QsmJ9gmNTKI}+h&(I{-^EU>dlAFz z$4tH?8+^Jy(~IY`W)0}YlbNAGHfU4Xum;&zj>y9*Rj`8sad_dr)myxH>&rMmPiJ?q zk*+P=4Ll3!ffGwvm|sZCRVugGR}HA|SLf-NZ9`IT|4^>18;;(2fSx8Klg&b$a+tO? 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z9#>#(%aU(xqgtC-i>wJd>=*EVTl#*;l06TB|0p0hsrUgwoHwz&9*iIp5S*74_?C1| zC~zCVFF*ykJ?WSg5IX%3BFYl6*ZW{fL@%4<@(F=eNT5i8PssL81%!nt6-pr%uYeHS zuE0lRpbvgUkA+WSp_SxR!yevMK)C&3GenPALTQs?34abM0H&seAe8MfmSNPNQgLmA zg|s;e1QU2mfeRS5zcuA-P(bJmhAb`m9mW>gvkFzUV0~LX)2<{tdqR${eLh`~EOq!x z2$U$~2>hf6#prg{_8Ut(h+khppui(WpwBjY&}hMP99#M}vcFx2Nxh=1@m zoSU{>g{+Ri1_gEz_@pUkp8~%XPJU@Z$>f(NzVq1I&4T{9b>jM`Ol5@|{3n%c@Si;U zd3)Wl)>?g*-vt`TvGfRId1<|j%#Y=xb#1AJat8m zqy8($+~4FFcTJm$MD;79PS$` sHZVRwj&aT9xW0uPvs=nBFi4ICPitDo!j&^8gQkG8N> > namesOfGroupCombo for (int h = start; h < (start+num); h++) { - + //cout << namesOfGroupCombos[h][0] << '\t' << namesOfGroupCombos[h][1] << endl; if (m->control_pressed) { return results; } double UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group @@ -203,12 +203,14 @@ EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombo nodePcountSize[i] = pcountSize; - if (pcountSize == 0) { ; } + //cout << i << '\t' << t->tree[i].getName() << " br = " << abs(t->tree[i].getBranchLength()) << '\t'; + if (pcountSize == 0) { } else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); } - + //if you are a leaf from a users group add to total if (i < numLeaves) { - if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) { + if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) { + //cout << "added to total" << endl; totalBL += abs(t->tree[i].getBranchLength()); } tempTotals[i] = 0.0; //we don't care about you, or we have already added you @@ -220,17 +222,21 @@ EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombo //if yes, add your childrens tempTotals if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) { totalBL += tempTotals[lc] + tempTotals[rc]; + //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl; if (t->tree[i].getBranchLength() != -1) { tempTotals[i] = abs(t->tree[i].getBranchLength()); }else { tempTotals[i] = 0.0; } + }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0; //we don't care about you }else { //if no, your tempTotal is your childrens temp totals + your branch length tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength()); } + //cout << "temptotal = "<< tempTotals[i] << endl; } + } - cout << UniqueBL << '\t' << totalBL << endl; + //cout << UniqueBL << '\t' << totalBL << endl; UW = (UniqueBL / totalBL); if (isnan(UW) || isinf(UW)) { UW = 0; } @@ -446,13 +452,13 @@ EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombo } nodePcountSize[i] = pcountSize; - + if (pcountSize == 0) { } - else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); } + else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); } //if you are a leaf from a users group add to total if (i < numLeaves) { - if ((copyTree->tree[i].getBranchLength() != -1) && pcountSize != 0) { + if ((copyTree->tree[i].getBranchLength() != -1) && pcountSize != 0) { totalBL += abs(copyTree->tree[i].getBranchLength()); } tempTotals[i] = 0.0; //we don't care about you, or we have already added you @@ -464,14 +470,17 @@ EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombo //if yes, add your childrens tempTotals if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) { totalBL += tempTotals[lc] + tempTotals[rc]; + if (copyTree->tree[i].getBranchLength() != -1) { tempTotals[i] = abs(copyTree->tree[i].getBranchLength()); }else { tempTotals[i] = 0.0; } + }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0; //we don't care about you }else { //if no, your tempTotal is your childrens temp totals + your branch length tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength()); } + } } -- 2.39.2