001    package calhoun.analysis.crf.test;
002    
003    import calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree;
004    
005    public class ExampleTrees {
006            public static RootedBinaryPhylogeneticTree bigTree() {
007                    String ss = "(((tetraodon:0.0524461,fugu:0.0524461):0.297194,zebrafish:0.34964):0.524462,(chicken:0.699282,((echidna:0.0838436,platypus:0.0600156):0.310795,((opossum:0.192285,(wallaby:0.092812,dromiciops:0.141167):0.0387401):0.360601,((((sloth:0.100183,anteater:0.108382):0.0161167,armadillo:0.0996493):0.0566051,((((hedgehog:0.241741,shrew:0.218368):0.0207599,mole:0.152703):0.0210518,(((phyllostomid_microbat:0.163881,free_tailed_bat:0.0820922):0.0203543,(false_vampire_bat:0.110086,(flying_fox:0.0326739,(rousette_fruit_bat:0,rfbat:0):0.0333085):0.0646344):0.00844204):0.0288873,((((((whale:0.0242546,dolphin:0.0386667):0.0344168,hippo:0.0701869):0.00860814,(ruminant:0,cow:0):0.128778):0.0148405,pig:0.118656):0.0103651,llama:0.108768):0.0488151,((horse:0.0768631,(rhino:0.0508046,tapir:0.0503865):0.00901022):0.0362157,((cat:0.0815971,(caniform:0,dog:0):0.0982242):0.0406107,pangolin:0.133636):0.00683199):0.00299292):0.0020419):0.00428834):0.0194505,(((sciurid:0.147831,((mouse:0.0740066,rat:0.0800222):0.21466,(hystricid:0.13118,caviomorph:0.152469):0.10924):0.00958887):0.020891,(rabbit:0.101787,pika:0.191106):0.0769716):0.0101291,(((tree_shrew_tupaia:0.0167268,tree_shrew_urogale:0.0139996):0.163411,(flying_lemur_variegatus:0.0207529,flying_lemur_volans:0.0224679):0.0904572):0.00288803,((((((ring_tailed_lemur:0,lemur:0):0.026223,mouse_lemur:0.026223):0.026223,galago:0.0524461):0.0314239,bushbaby:0.136447):0.02355,(tarsier_bancanus:0.0192389,tarsier_syrichta:0.0155887):0.161919):0.0114769,(((spider_monkey:0.021342,goeldi_monkey:0.0349867):0.017482,marmoset:0.034964):0.0159383,((((rhesus_macaque:0,macaque:0):0.00874098,baboon:0.00874098):0.00524462,vervet:0.0139856):0.00955917,((((human:0.00484776,chimpanzee:0.00385478):0.0017482,gorilla:0.00559422):0.00524462,orangutan:0.0108388):0.0032499,gibbon:0.020884):0.0119752):0.0202878):0.0589005):0.0114664):0.00300341):0.0135573):0.0161569):0.0105294,((((tenrec:0.251035,golden_mole:0.118346):0.0165607,(short_eared_elephant_shrew:0.0687235,long_eared_elephant_shrew:0.0634442):0.156287):0.00395443,aardvark:0.120713):0.00574457,((sirenian:0.0671414,hyrax:0.157511):0.0051467,elephant:0.0895361):0.0260569):0.0457241):0.231147):0.0699282):0.17482):0.17482):0;";
008                    return new RootedBinaryPhylogeneticTree(ss);
009            }
010            public static RootedBinaryPhylogeneticTree bigTreeForEncode() {
011                    String ss = "(((tetraodon:0.0524461,fugu:0.0524461):0.297194,zebrafish:0.34964):0.699282,(xenopus:0.874102,(chicken:0.699282,((echidna:0.0838436,platypus:0.0600156):0.310795,(((monodelphis:0.0,opossum:0.0):0.192285,(wallaby:0.092812,dromiciops:0.141167):0.0387401):0.360601,((((sloth:0.100183,anteater:0.108382):0.0161167,armadillo:0.0996493):0.0566051,((((hedgehog:0.241741,shrew:0.218368):0.0207599,mole:0.152703):0.0210518,(((phyllostomid_microbat:0.163881,free_tailed_bat:0.0820922):0.0203543,(false_vampire_bat:0.110086,(flying_fox:0.0326739,(rousette_fruit_bat:0,rfbat:0):0.0333085):0.0646344):0.00844204):0.0288873,((((((whale:0.0242546,dolphin:0.0386667):0.0344168,hippo:0.0701869):0.00860814,(ruminant:0,cow:0):0.128778):0.0148405,pig:0.118656):0.0103651,llama:0.108768):0.0488151,((horse:0.0768631,(rhino:0.0508046,tapir:0.0503865):0.00901022):0.0362157,((cat:0.0815971,(caniform:0,dog:0):0.0982242):0.0406107,pangolin:0.133636):0.00683199):0.00299292):0.0020419):0.00428834):0.0194505,(((sciurid:0.147831,((mouse:0.0740066,rat:0.0800222):0.21466,(hystricid:0.13118,caviomorph:0.152469):0.10924):0.00958887):0.020891,(rabbit:0.101787,pika:0.191106):0.0769716):0.0101291,(((tree_shrew_tupaia:0.0167268,tree_shrew_urogale:0.0139996):0.163411,(flying_lemur_variegatus:0.0207529,flying_lemur_volans:0.0224679):0.0904572):0.00288803,((((((ring_tailed_lemur:0,lemur:0):0.026223,mouse_lemur:0.026223):0.026223,galago:0.0524461):0.0314239,bushbaby:0.136447):0.02355,(tarsier_bancanus:0.0192389,tarsier_syrichta:0.0155887):0.161919):0.0114769,(((((spider_monkey:0.021342,goeldi_monkey:0.0349867):0.017482,marmoset:0.034964):0.0,owl_monkey:0.034964):0.0,dusky_titi:0.034964):0.0159383,(((((rhesus_macaque:0,macaque:0):0.00874098,baboon:0.00874098):0.00524462,vervet:0.0139856):0.0,colobus_monkey:0.0139856):0.00955917,(((((human:0.0,hg17:0.0):0.00484776,(chimp:0.0,chimpanzee:0.0):0.00385478):0.0017482,gorilla:0.00559422):0.00524462,orangutan:0.0108388):0.0032499,gibbon:0.020884):0.0119752):0.0202878):0.0589005):0.0114664):0.00300341):0.0135573):0.0161569):0.0105294,((((tenrec:0.251035,golden_mole:0.118346):0.0165607,(short_eared_elephant_shrew:0.0687235,long_eared_elephant_shrew:0.0634442):0.156287):0.00395443,aardvark:0.120713):0.00574457,((sirenian:0.0671414,hyrax:0.157511):0.0051467,elephant:0.0895361):0.0260569):0.0457241):0.231147):0.0699282):0.17482):0.17482):0.172482):0;";
012                    return new RootedBinaryPhylogeneticTree(ss);
013            }
014            public static RootedBinaryPhylogeneticTree crypto4dan() {
015                    String ss = "((cnBB: 0.034084, cnBV: 0.034065): 0.186256, cnA: 0.081165, cnDT: 0.071992):0.0;";
016                    return new RootedBinaryPhylogeneticTree(ss);
017            }       
018            public static RootedBinaryPhylogeneticTree crypto5() {
019                    String ss = "(((cnDT:0.0025,cnDS:0.0025):0.0475,cnAB:0.05):0.02,(cnBB:0.02,cnBV:0.02):0.05):0;";
020                    return new RootedBinaryPhylogeneticTree(ss);
021            }
022    }