To test the TreeSummary class, we need for the main function to create a TreeSummary object and call its readTreeFile and showSummary functions. We also need a tree file to read, and need to link in the Nexus Class Library to do the work of parsing this tree file.
Create a tree file
Create a file named test.tre (use the “Empty” template under the “Other” category for this file because it is not a header file) and fill it with the following text:
#NEXUS
[ID: 1234567]
begin taxa;
dimensions ntax=33;
taxlabels
'Bracteacoccus minor UTEX66'
'Bracteacoccus aerius UTEX1250'
'Pseudomuriella engadinensis UTEX58'
'Pseudomuriella schumacherensis SAG2137'
'Bracteamorpha trainori CC1VF5A'
'Radiococcus polycoccus SAG217 1c'
'Planktosphaeria gelatinosa SAG262 1b'
'Planktosphaeria texensis UTEX1241'
'Planktosphaeria botryoides UTEXLB951'
'Chromochloris zofingiensis UTEX56'
'Pediastrum duplex UTEX1364'
'Parapediastrum biradiatum UTEX37'
'Ankistrodesmus falcatus UTEX101'
'Neochloris aquatica UTEX138'
'Botryococcus sudeticus'
'Characiopodium hindakii'
'Scenedesmus obliquus UTEX393'
'Scenedesmus rotundus SEV3VF49'
'Hariotina reticulata UTEX1365'
'Schizochlamys gelatinosa SAG66 94'
'Dictyococcus varians UTEXLB62'
'Dictyochloris fragrans UTEX127'
'Mychonastes homosphaera CAUPH6502'
'Mychonastes jurisii SAG3798'
'Schroederia setigera UTEXLB2454'
'Chlorotetraedron incus SAG4381'
'Kirchneriella aperta SAG2004'
'Sphaeroplea robusta UTEX2350'
'Ankyra judai SAG17 84'
'Tumidella tumida SAG2265'
'Rotundella rotunda WJT54VFNP11'
'Rotundella sp ZNP1VF31'
'Ourococcus multisporus';
end;
begin trees;
translate
1 'Bracteacoccus minor UTEX66',
2 'Bracteacoccus aerius UTEX1250',
3 'Pseudomuriella engadinensis UTEX58',
4 'Pseudomuriella schumacherensis SAG2137',
5 'Bracteamorpha trainori CC1VF5A',
6 'Radiococcus polycoccus SAG217 1c',
7 'Planktosphaeria gelatinosa SAG262 1b',
8 'Planktosphaeria texensis UTEX1241',
9 'Planktosphaeria botryoides UTEXLB951',
10 'Chromochloris zofingiensis UTEX56',
11 'Pediastrum duplex UTEX1364',
12 'Parapediastrum biradiatum UTEX37',
13 'Ankistrodesmus falcatus UTEX101',
14 'Neochloris aquatica UTEX138',
15 'Botryococcus sudeticus',
16 'Characiopodium hindakii',
17 'Scenedesmus obliquus UTEX393',
18 'Scenedesmus rotundus SEV3VF49',
19 'Hariotina reticulata UTEX1365',
20 'Schizochlamys gelatinosa SAG66 94',
21 'Dictyococcus varians UTEXLB62',
22 'Dictyochloris fragrans UTEX127',
23 'Mychonastes homosphaera CAUPH6502',
24 'Mychonastes jurisii SAG3798',
25 'Schroederia setigera UTEXLB2454',
26 'Chlorotetraedron incus SAG4381',
27 'Kirchneriella aperta SAG2004',
28 'Sphaeroplea robusta UTEX2350',
29 'Ankyra judai SAG17 84',
30 'Tumidella tumida SAG2265',
31 'Rotundella rotunda WJT54VFNP11',
32 'Rotundella sp ZNP1VF31',
33 'Ourococcus multisporus';
tree 2topo212 = (1:0.15627210,(30:0.17162998,(((5:0.25666877,((6:0.25918524,(8:0.04890046,9:0.02103898):0.16393496):0.07744044,(((13:0.24662238,27:0.17921628):0.03452417,33:0.21951314):0.12422514,(24:0.05135497,23:0.08634639):0.29672639):0.02603509):0.04301592):0.02147069,((((17:0.11304779,(19:0.19230870,18:0.17106424):0.04876048):0.06024803,(((26:0.12528321,(12:0.14811074,11:0.10159416):0.12450103):0.11574026,(14:0.17432556,(15:0.14378088,16:0.16952013):0.07100215):0.11501679):0.06325832,(32:0.05236326,31:0.03443277):0.35846911):0.01210282):0.05449317,(((28:0.11725934,29:0.10772249):0.27946445,25:0.38458363):0.00596258,22:0.37338675):0.04813972):0.03168543,(10:0.34204294,(4:0.06438535,3:0.05207162):0.17721564):0.09167346):0.03102114):0.05358973,((7:0.21563145,20:0.25535189):0.04878285,21:0.45456205):0.10424236):0.04005845):0.13566845,2:0.15577441);
tree 37topo212 = (1:0.19535319,(30:0.21396159,(((((4:0.06681961,3:0.05541859):0.20988915,10:0.33177384):0.07063769,(((17:0.10503839,(19:0.18486713,18:0.13774763):0.07906941):0.05218904,((32:0.04101216,31:0.02770287):0.34559869,((14:0.21037724,(15:0.14385916,16:0.20516275):0.03494270):0.14087560,((12:0.15299548,11:0.09111928):0.15599325,26:0.12149992):0.03630639):0.05173516):0.00399992):0.07032845,((25:0.40721998,(28:0.10814417,29:0.13006267):0.35070553):0.00810781,22:0.48605529):0.02915788):0.00443725):0.03465077,(((6:0.33026531,(8:0.03452133,9:0.03577985):0.14055156):0.07528730,((24:0.07724682,23:0.04864349):0.26668853,((13:0.25391435,27:0.14815373):0.03760906,33:0.17433277):0.11920613):0.01382651):0.04943612,5:0.26938200):0.04605544):0.05798100,(21:0.45881190,(20:0.25293709,7:0.13093373):0.02727468):0.14226066):0.01826858):0.15905419,2:0.12223918);
tree 177topo212 = (1:0.17263901,(30:0.20992067,(((20:0.18697491,7:0.20783012):0.02022342,21:0.55912126):0.15786325,((5:0.32191893,((((13:0.22120673,27:0.14088151):0.12466135,33:0.20099223):0.10429643,(24:0.04519368,23:0.10657649):0.26923351):0.04840972,(6:0.34311725,(8:0.06647765,9:0.02513638):0.12167059):0.09308608):0.03699157):0.03553243,(((22:0.41515488,(25:0.40934369,(28:0.07315304,29:0.14252246):0.28599405):0.02714662):0.04648712,((17:0.10241118,(19:0.15187746,18:0.13872898):0.07522029):0.07677836,(((14:0.21666447,(16:0.17464475,15:0.10474928):0.03565734):0.14916653,((12:0.12576209,11:0.09283544):0.12182421,26:0.10155592):0.06173464):0.07438984,(32:0.03727526,31:0.00825297):0.40050603):0.02452030):0.06175045):0.01611106,(10:0.30285524,(4:0.09298016,3:0.06285482):0.21244857):0.05596027):0.02822623):0.02385617):0.03964512):0.12164953,2:0.13314206);
tree 817topo212 = (1:0.19215872,(((((((((26:0.20396310,(12:0.17477873,11:0.10084075):0.13460141):0.08771374,(14:0.21573087,(15:0.18461346,16:0.15407304):0.08978479):0.15596104):0.04588627,(32:0.06028829,31:0.01004081):0.41204051):0.00982853,((19:0.21149271,18:0.17387892):0.05163667,17:0.14656430):0.08237560):0.08025059,(22:0.52381962,(25:0.40330052,(28:0.10940880,29:0.15724750):0.26358713):0.05715116):0.03890461):0.01082136,((4:0.09774546,3:0.04765817):0.21833378,10:0.39081571):0.06929534):0.04574448,((((33:0.22267066,(27:0.13682667,13:0.25232487):0.10200532):0.18416847,(24:0.05246640,23:0.08160045):0.31519901):0.06970887,(6:0.35894655,(8:0.03974742,9:0.04956770):0.16531089):0.08256358):0.05406209,5:0.33414002):0.03053482):0.03697446,((7:0.20220552,20:0.29151778):0.04382592,21:0.74201221):0.11221562):0.01333178,30:0.22124048):0.18243369,2:0.14916207);
tree 846topo212 = (1:0.21513445,(30:0.26663916,(((7:0.20473226,20:0.25328580):0.05298203,21:0.57646513):0.10292079,((((4:0.09780566,3:0.07558274):0.17260496,10:0.35684935):0.11017788,((22:0.50524527,((28:0.10958918,29:0.09536010):0.26691263,25:0.49841657):0.03391956):0.05696541,(((32:0.03023503,31:0.05170754):0.49718552,((14:0.21218183,(15:0.08765387,16:0.25747977):0.07087899):0.16581063,(26:0.11473012,(12:0.11632502,11:0.07317669):0.21865315):0.06720179):0.09504242):0.00639096,((19:0.21159655,18:0.16062796):0.06147523,17:0.17146503):0.06865098):0.06735468):0.02290002):0.02864395,(((((27:0.12371550,13:0.26241311):0.09760657,33:0.17976275):0.15376519,(24:0.06420439,23:0.06113029):0.23022214):0.03430232,(6:0.31306236,(8:0.05328654,9:0.04046049):0.21189102):0.11170889):0.02112370,5:0.25643529):0.05138383):0.03807838):0.02579456):0.16665911,2:0.10958482);
tree 898topo212 = (1:0.16198847,((((20:0.26670432,7:0.22141509):0.05276667,21:0.52255443):0.08155109,((((4:0.09432053,3:0.05247520):0.16683187,10:0.36310306):0.05592855,(((25:0.38402025,(28:0.10044142,29:0.08872256):0.28362652):0.03888522,22:0.46054441):0.06647122,(((32:0.03010925,31:0.03149605):0.47312032,(((12:0.11790036,11:0.08874953):0.16495361,26:0.13870705):0.04269158,((16:0.19041063,15:0.11657282):0.03856503,14:0.21286280):0.16520670):0.06191210):0.02670160,((19:0.18325572,18:0.16495378):0.05088473,17:0.13629704):0.05781484):0.04884538):0.00534596):0.03356130,(((6:0.29267279,(8:0.04113496,9:0.03650958):0.11176421):0.09883280,(((27:0.19591516,13:0.32002223):0.04389872,33:0.19269516):0.18094088,(24:0.08522457,23:0.04779144):0.25657281):0.01681926):0.04264673,5:0.26109259):0.02740096):0.03792393):0.04607720,30:0.20333768):0.09994832,2:0.14568199);
tree 907topo212 = (1:0.20461837,((((7:0.23776249,20:0.25434065):0.02509091,21:0.90916260):0.17338878,((((6:0.38239503,(8:0.06381691,9:0.04168967):0.19944817):0.09643838,((24:0.04687438,23:0.07277379):0.41477468,((27:0.15245821,13:0.30907069):0.08394772,33:0.25676649):0.14788194):0.04833612):0.05490340,5:0.28519098):0.02167413,(((22:0.53790470,(25:0.47408819,(28:0.11004475,29:0.12790169):0.33528429):0.05567563):0.04519669,(((19:0.23449678,18:0.21631034):0.07767688,17:0.22290284):0.10064774,((((12:0.14072866,11:0.13139114):0.15031812,26:0.15025778):0.10488677,((16:0.20172241,15:0.10584334):0.04099575,14:0.24466104):0.20382049):0.06271032,(32:0.03650932,31:0.03375336):0.48832468):0.03467965):0.05204606):0.04022710,(10:0.44932193,(4:0.07760529,3:0.06515857):0.22255570):0.08206779):0.03658961):0.04350243):0.04258045,30:0.29612509):0.17567765,2:0.19394228);
tree 961topo212 = (1:0.17386767,(30:0.20096556,(((7:0.24838722,20:0.24967932):0.04924312,21:0.67176924):0.14161764,((5:0.31260921,((6:0.34205844,(8:0.04105908,9:0.03081368):0.15106287):0.10216270,(((27:0.12911654,13:0.32517888):0.12379905,33:0.24448261):0.22659492,(24:0.04748320,23:0.09031660):0.36680677):0.06703485):0.06555158):0.01726319,(((4:0.07427326,3:0.07296012):0.23644957,10:0.47937271):0.04292213,((((((15:0.14725263,16:0.23261244):0.04392687,14:0.16615839):0.22699258,(26:0.15460844,(12:0.15914763,11:0.09769891):0.19641188):0.02518916):0.05332953,(32:0.04194514,31:0.02829988):0.48827767):0.01147546,((19:0.28408934,18:0.14871767):0.06437906,17:0.12320983):0.06744618):0.10383004,(22:0.40866296,(25:0.41413100,(28:0.10463571,29:0.11786032):0.37944233):0.02072903):0.08122673):0.01002759):0.00599986):0.05123263):0.05585731):0.12454454,2:0.20340308);
tree 143topo213 = (1:0.26112860,((5:0.31220582,((((25:0.51550560,(22:0.52353006,(28:0.14324520,29:0.14053730):0.34603630):0.02779240):0.03445346,((17:0.12387663,(19:0.22469310,18:0.15472169):0.04509815):0.11084823,((((15:0.11388810,16:0.22559712):0.06600357,14:0.25840723):0.20119355,((12:0.14685851,11:0.09607501):0.14959120,26:0.16966399):0.06829334):0.04224642,(32:0.04024682,31:0.03885332):0.40575374):0.02040799):0.09369484):0.05579514,(((6:0.41872582,(8:0.05164389,9:0.03771417):0.16775113):0.10410476,(((13:0.31823795,27:0.15018413):0.01891399,33:0.30915845):0.18292721,(24:0.08658377,23:0.06140332):0.32865726):0.05925033):0.03666646,(10:0.49113002,(4:0.08933284,3:0.06760523):0.22461695):0.08519352):0.00107753):0.00892563,(21:0.58770471,(20:0.26302490,7:0.26473277):0.05966628):0.15178740):0.10644283):0.02041923,30:0.24014992):0.21024026,2:0.18633689);
tree 741topo213 = (1:0.22171991,(30:0.25900641,((((20:0.30264240,7:0.24147233):0.07246882,21:0.56271716):0.16066237,(((((24:0.09299165,23:0.07584903):0.34500827,((13:0.22788123,27:0.16234166):0.14454174,33:0.26405592):0.12990463):0.03216220,(6:0.30613896,(8:0.05594103,9:0.03516623):0.23076364):0.08236131):0.06536683,(10:0.42464789,(4:0.10089239,3:0.07295535):0.19186868):0.09356935):0.02523984,(((22:0.59034781,(28:0.13156961,29:0.08483917):0.30973904):0.03177155,25:0.49933021):0.09034257,((((26:0.15910998,(12:0.16611627,11:0.10336010):0.21657205):0.08282432,((15:0.12929642,16:0.20443772):0.04498545,14:0.22750064):0.22144510):0.06868404,(32:0.05119722,31:0.02384305):0.45287767):0.01412821,(17:0.18654944,(19:0.18861905,18:0.15140115):0.06067833):0.08812682):0.07782974):0.05937663):0.02205317):0.02471975,5:0.28963780):0.04931392):0.17534565,2:0.15879502);
tree 78topo218 = (1:0.15522631,((((21:0.63937305,(7:0.29676164,20:0.26716385):0.01476052):0.22954033,((((4:0.11532201,3:0.07025891):0.21653955,10:0.44953101):0.14528780,((25:0.49466480,(22:0.58175930,(28:0.13780585,29:0.12603872):0.43663687):0.00844292):0.07533226,((17:0.17007284,(19:0.23223558,18:0.17873777):0.11473854):0.13444985,(((14:0.18674691,(15:0.16190401,16:0.20953263):0.07782970):0.25646314,((12:0.17044354,11:0.13048074):0.12871179,26:0.17921157):0.08045630):0.10115642,(32:0.03075485,31:0.04137420):0.50088434):0.02679635):0.06375535):0.03949351):0.04729054,((6:0.49065892,(8:0.07437414,9:0.01897836):0.25540707):0.08367898,((24:0.05263214,23:0.07925182):0.36175905,(33:0.23888496,(27:0.22637010,13:0.30307719):0.12722799):0.19726319):0.05587274):0.06519122):0.01583947):0.03829454,5:0.31514653):0.09045467,30:0.24889322):0.17176337,2:0.16431228);
tree 181topo218 = (1:0.21964821,(30:0.27363100,((((((33:0.24762730,(27:0.20385353,13:0.29958118):0.06762098):0.10210317,(24:0.06782967,23:0.06699537):0.28583354):0.06685218,(6:0.35643154,(8:0.06918355,9:0.02062018):0.19556919):0.06974259):0.07027374,(((4:0.12631969,3:0.06463356):0.17474300,10:0.33499744):0.06093443,((25:0.43545684,(22:0.40373512,(28:0.09904870,29:0.12819919):0.27599699):0.04636438):0.03631356,(((((12:0.11493983,11:0.07465273):0.16300252,26:0.17871081):0.05881028,(14:0.19629105,(16:0.20683871,15:0.14839281):0.06470277):0.16790528):0.06855440,(32:0.03751764,31:0.04360540):0.44400476):0.00648923,(17:0.13897113,(19:0.22368314,18:0.17822496):0.09479475):0.07382450):0.09096026):0.02086107):0.01598582):0.04150429,(21:0.61629981,(20:0.26123912,7:0.26226663):0.05685599):0.12688860):0.01280565,5:0.25337869):0.02665355):0.12477771,2:0.17934048);
tree 770topo218 = (1:0.24683995,(30:0.23499262,(5:0.29182290,(((20:0.28526547,7:0.20545052):0.11577018,21:0.55003228):0.14414435,(((6:0.31471083,(8:0.06555849,9:0.04108222):0.12079612):0.10432817,((24:0.06852803,23:0.07649896):0.30656467,(33:0.21687230,(27:0.15343279,13:0.34449458):0.09761427):0.15844681):0.02787049):0.05700115,(((25:0.47865528,((28:0.12203615,29:0.11872703):0.37324123,22:0.51644453):0.01738390):0.01553634,((17:0.12362208,(19:0.23597518,18:0.22705861):0.05786148):0.11534667,(((14:0.19408493,(15:0.13251694,16:0.23517370):0.06014407):0.19660936,(26:0.19105958,(12:0.12787843,11:0.11116912):0.13330968):0.01395272):0.08336366,(32:0.04532188,31:0.02779489):0.45442555):0.01338702):0.07440054):0.02111174,(10:0.41687095,(4:0.08593922,3:0.06383540):0.18327578):0.06307708):0.01822460):0.03213461):0.02492279):0.05835069):0.16422981,2:0.13747389);
tree 816topo218 = (1:0.19037066,(30:0.27962058,(5:0.34820923,(((20:0.33568596,7:0.12588165):0.02689698,21:0.61142091):0.19723424,(((((22:0.40512882,(28:0.14881953,29:0.11329904):0.29764565):0.01775492,25:0.42212569):0.04609111,((((26:0.19713142,(12:0.10971368,11:0.10479760):0.14713900):0.02758304,(14:0.25032452,(15:0.15117264,16:0.16866836):0.07906727):0.19041807):0.04732945,(32:0.05177143,31:0.04051608):0.37330425):0.01624963,((19:0.22631626,18:0.16409233):0.06442115,17:0.12726306):0.07221645):0.06752339):0.02170407,((4:0.07773644,3:0.06579250):0.13552964,10:0.39817844):0.11136795):0.03268384,((((13:0.23728602,27:0.14842231):0.11460138,33:0.23859964):0.15758011,(24:0.04437028,23:0.07482049):0.26098719):0.10172317,(6:0.37061080,(8:0.05306116,9:0.05018997):0.18335257):0.06972578):0.03051827):0.01956732):0.00497875):0.04248373):0.12778280,2:0.16254617);
end;
Modify the main function
Modify the main.cpp file to look like this:
#include <iostream>
#include "tree_summary.hpp"
using namespace strom;
const double Node::_smallest_edge_length = 1.0e-12;
int main(int argc, const char * argv[]) {
std::cout << "Starting..." << std::endl;
TreeSummary sumt;
try {
sumt.readTreefile("test.tre", 1);
}
catch(NxsException x) {
std::cerr << "Program aborting due to errors encountered reading tree file." << std::endl;
std::cerr << x.what() << std::endl;
std::exit(0);
}
sumt.showSummary();
std::cout << "\nFinished!" << std::endl;
return 0;
}
Note that a try...catch combination is used to catch and report any exceptions raised by the Nexus Class Library when it attempts to read and interpret the tree file. For example, if the file test.tre is missing, the program will say
"test.tre" does not refer to a valid file.
Program aborted due to errors encountered reading tree file.
Exceptions are small objects that are “thrown” when something unexpected happens within the try block. The catch block specifies what particular exceptions it is prepared to handle (in this case an object of type NxsException). The NxsException object is stored in the variable x, and the what() member function of x returns the message string stored when the exception was generated. Because exceptions normally represent situations from which recovery is impossible, the catch block calls the std::exit function in order to terminate the program after the message is output on the standard error stream.
Installing the Nexus Class Library
When you compile strom, you will receive the following error:
Unknown type name 'NxsException'
The readTreefile function in our TreeSummary class makes use of the Nexus Class Library’s MultiFormatReader class, and the compiler is simply telling us that we haven’t yet told it where to find the code for NCL’s NxsException class used in the main.cpp file. Before we can compile strom again, we must install the Nexus Class Library and tell Xcode where to find it.
Download the NCL gzipped tar file ncl-2.1.18.tar.gz or zip file ncl-2.1.18.zip from the SourceForge web site.
Navigate into your ~/Documents/libraries directory and unpack the file you downloaded there.
Open Terminal or iTerm, navigate into the ncl-2.1.18 directory and build the NCL using the traditional configure script followed by make install. The --prefix option passed to the configure script results in the NCL being installed in your home directory. Leaving off the --prefix option would result in NCL being installed for all users in your system, which is arguably preferable as long as you have the necessary privileges to install libraries systemwide, but this tutorial assumes you do not have superuser powers and thus shows you how to do everything locally.
cd ~/Documents/libraries/ncl-2.1.18
./configure --prefix=$HOME
make install
Create a directory for static library files
The make install step above creates a directory lib inside your home directory. Navigate to the ~/lib directory and create a directory named static there, and copy the libncl.a file to that directory:
cd ~/lib
mkdir static
cd static
cp ~/lib/ncl/libncl.a .
Why not simply use libncl.a where it was created? Compilers in unix-based operating systems prefer to create dynamic link (a.k.a. shared object) libraries. These are separate files (with the filename extension .so or .dylib) that are linked to your program at run time. In order to force the libraries to be linked at compile time so that our program is not split up over several files, it is necessary to separate the static libraries (e.g. libncl.a) from the shared object files (e.g. libncl-2.1.18.so) so that the compiler can’t even find the shared object version when linking is carried out.
Inform Xcode of the existence of NCL
You now need to tell Xcode where the installed NCL header files are located (~/include) and where to find the compiled library.
Choose Xcode > Preferences… from the main menu, then choose the “Locations” tab, then click the “Custom Paths” subtab.
Click the + button and add a new custom path item named NCL_ROOT with display name NCL_ROOT. On my computer, I entered the path /Users/plewis/include/ncl (but you should of course modify this for your case).
Click the red button at the top left to close the preferences dialog box.
In the Xcode main menu, choose View > Navigators > Show Project Navigator, then click on the blue project icon 
labeled strom at the top of the Project Navigator. Click on the Build Phases tab. Click the + sign in Link Binary With Libraries and (after clicking the Add Other… button) navigate to the directory ~/lib/static and select the libncl.a file. This informs Xcode where to find the compiled library code for purposes of linking the library into your program’s executable file. Linking means to establish pointers from function calls in your program to the start of the that function in the library, so that when strom calls, for example, nexusReader.ReadFilepath in TreeSummary::readTreeFile, the code for the ReadFilepath function will be executed.
Click on Build Settings, All (not Basic or Customized), Levels (not Combined), and then type “Header Search Paths” into the Search box to filter out all build settings except the one we are interested in at the moment. In the “Header Search Paths” row, double-click on the column with the blue project icon (this is the column for the project settings, the other column labeled strom contains target-specific settings). Click the + symbol and add $(NCL_ROOT), pressing the enter key when finished. This tells Xcode where to find NCL-specific header files, such as the nxsmultiformat.h header included near the top of the tree_summary.hpp file.
Now search for “Library Search Paths” in Build Settings. In the “Library Search Paths” row, double-click on the column with the blue project icon (this is the column for the project settings, the other column labeled strom contains target-specific settings). Click the + symbol and add $(HOME)/lib/static, pressing the enter key when finished. This tells Xcode where to find the libncl.a file when it reaches the linking step.
Expected output
The expected output is shown below. Keep in mind that tree topologies are ordered arbitrarily; the important thing to note is whether 7 of the trees in the file have one topology, 4 have a distinctly different topology, and the final 2 trees have a third topology distinct from the first two.
Starting...
storing read block: TAXA
storing read block: TREES
Read 13 trees from file
Topology 1 seen in these 4 trees:
9 10 11 12
Topology 2 seen in these 2 trees:
7 8
Topology 3 seen in these 7 trees:
0 1 2 3 4 5 6
Topologies sorted by sample frequency:
topology frequency
3 7
1 4
2 2
Finished!
“test.tre” does not refer to a valid file
If you get the error message above, it means that you have tried to run strom from a directory other than the directory containing the tree file (test.tre). The test.tre file should have been installed in the same directory as the strom executable when you issued the command meson install. If you used a command like this to run strom:
../../distr/strom
then you will get the error because strom will look for the test.tre file in the current working directory, which differs from the directory where test.tre resides.
Lost at sea
Important! The lines of output above will be lost in a sea of constructor and destructor notifications unless you comment those out. Visit the Node, Tree, Split, TreeManip, and TreeSummary classes and use // to comment out the std::cout << "Constructing a XXXX" << std::endl; statement inside the constructor and the std::cout << "Destroying a XXXX" << std::endl; statement inside the destructor. In future steps, these “reporter” output lines will be created already commented out so that they can be easily turned on if needed during debugging but not clutter the output during normal operation.