%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % This is the master file for the model_train graph % #include "commonParams.txt" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % DENSE PROBABILITY MASS FUNCTIONS % % none needed at this time ... DPMF_IN_FILE inline 0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % DIRICHLET TABLES % % none needed at this time ... DIRICHLET_TAB_IN_FILE inline 0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % DECISION TREEs % % % % a decision tree is needed whenever we use a DeterministicCPT or a mapping; % % here we list first those DTs that are paired with a DeterministicCPT of the % % same name (w/o the _DT ending), then those that are used as part of a % % mapping of some sort ... % DT_IN_FILE inline 20 % total number of decision trees to follow 0 % index setZero_DT % name 0 % no parents -1 0 % always return 0 1 % index setOne_DT % name 0 % no parents -1 1 % always return 1 2 % index badValue_DT % name 0 % no parents -1 999999 % always return a "bad" value % % here are the indexes and names of the states, with the emitClass and % lengthClass that they each map to -- the states are listed in an order % that loosely follows a path of a protein that starts with a short % cytoplasmic (inside) loop, then goes thru the membrane to the non- % cytoplasmic side (outside), then back thru the membrane ... % % the value "0" in all cases is being held back in case it comes in % handy as some sort of "special" value ... % % STATE NEXT EMIT LENGTH % # name STATE(s) CLASS CLASS % % 0 unknown state 0 0 0 % 1 loop_i 2 1 1 [1,20] % 2 cap_im 3 2 2 [4] % 3 helix_io 4 3 3 [5,25] % 4 cap_mo 5,8,9 4 2 [4] % 5 short_loop_obg 6 5 4 [10] % 6 short-outside-glob 7 6 5 [soExp] % 7 short_loop_oag 12 5 4 [10] % 8 loop_o 12 5 6 [1,20] % 9 long-loop_obg 10 7 4 [10] % 10 long-outside-glob 27 6 7 [loExp] % 27 long-outside-glob2 28 6 14 [loExp2] % 28 long-outside-glob3 11 6 15 [loExp3] % 11 long-loop_oag 12 7 4 [10] % 12 cap_om 13 4 2 [4] % 13 helix_oi 14 3 3 [5,25] % 14 cap_mi 1,15 2 2 [4] % 15 loop_ibg 16 1 4 [10] % 16 inside-glob 17 6 8 [iExp] % 17 loop_iag 2 1 4 [10] % % %%%%%%%% added states for SignalP model %%%%%%%%%%%%%%%%% % % 29 methionine 26 15 12 % 26 n-region-exp 18 8 13 [nExp] % 18 n-region 19 8 9 [1,10] % 19 h-region 20 9 10 [6,20] % 20 c-region 21 10 11 [1,15] % 21 c3 22 11 12 [1] % 22 c2 23 12 12 [1] % 23 c1 24 13 12 [1] % 24 cut 6,10,25 14 12 [1] % % %%%%%%%% added one new state to model globular-only proteins %% % % 25 globular 25 6 12 3 % index state2emitClass_DT % name 1 % one parent (the state) 0 30 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 default -1 0 -1 1 -1 2 -1 3 -1 4 -1 5 -1 6 -1 5 -1 5 -1 7 -1 6 -1 7 -1 4 -1 3 -1 2 -1 1 -1 6 -1 1 -1 8 -1 9 -1 10 -1 11 -1 12 -1 13 -1 14 -1 6 -1 8 -1 6 -1 6 -1 15 4 % index state2lengthClass_DT % name 1 % one parent (the state) 0 30 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 default -1 0 -1 1 -1 2 -1 3 -1 2 -1 4 -1 5 -1 4 -1 6 -1 4 -1 7 -1 4 -1 2 -1 3 -1 2 -1 4 -1 8 -1 4 -1 9 -1 10 -1 11 -1 12 -1 12 -1 12 -1 12 -1 12 -1 13 -1 14 -1 15 -1 12 % TOPOLOGY CLASSES % % there are currently 5 different topology classes: % 0 : unused % 1 : inside % 2 : membrane % 3 : outside % 4 : signal-peptide 5 % index state2topoClass_DT % name 1 % one parent (the state) 0 30 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 default -1 0 -1 1 -1 2 -1 2 -1 2 -1 3 -1 3 -1 3 -1 3 -1 3 -1 3 -1 3 -1 2 -1 2 -1 2 -1 1 -1 1 -1 1 -1 4 -1 4 -1 4 -1 4 -1 4 -1 4 -1 4 -1 3 -1 4 -1 3 -1 3 -1 4 % LABELS % % there are 10 different labels: % . : 0 wildcard % % i : 1 inside / cytoplasmic 1 % M : 2 membrane 2 % o : 3 outside / non-cytoplasmic *short* 3 % O : 4 outside / non-cytoplasmic *long* 4 % % n : 5 -- different regions of a signal peptide % h : 6 % c : 7 % C : 8 % s : 9 -- generic signal peptide label (n,h,c) % % a relationship needs to be defined between which labels correspond % to which states -- for example the label "i" corresponds to 4 different % allowable states: loop_i, loop_ibg, inside-glob, and loop_iag % % in addition, the the integer label *zero* will be interpreted as % placing no constraint whatsoever on the current state % % so the label to state relationships are such that we want this decision tree % to return TRUE (1) under the following conditions: % p1=0 p0=anything (*) % p1=1 p0=1,15,16,17 (i) % p1=2 p0=2,3,4,12,13,14 (m) % p1=3 p0=5,6,7,8 (o) % p1=4 p0=9,10,11,25,27,28 (O) % % p1=5 p0=18,26,29 (n-region) % p1=6 p0=19 (h-region) % p1=7 p0=20,21,22,23 (c-region,c3,c2,c1) % p1=8 p0=24 (cut) % p1=9 p0=18,19,20,21,22,23,26,29 6 % index stateANDlabel_DT % name 2 % two parents (state, label) 1 10 0 1 2 3 4 5 6 7 8 default % split on p1(label); 9 splits -1 1 % if p1=0, always return TRUE 0 3 1 15:17 default % if p1=1, split on p0(state); 3 splits -1 1 % if p0=1, return TRUE -1 1 % if p0 in [15,17], return TRUE -1 0 % otherwise, return FALSE 0 3 2:4 12:14 default % if p1=2, split on p0(state); 3 splits -1 1 % if p0 in [2,4], return TRUE -1 1 % if p0 in [12,14], return TRUE -1 0 % otherwise, return FALSE 0 2 5:8 default % if p1=3, split on p0(state); 2 splits -1 1 % if p0 in [5,8], return TRUE -1 0 % otherwise, return FALSE 0 4 9:11 25 27:28 default % if p1=4, split on p0(state); 2 splits -1 1 % if p0 in [9,11], return TRUE -1 1 % if p0=25, return TRUE -1 1 % if p0 in [27,28], return TRUE -1 0 % otherwise, return FALSE 0 4 18 26 29 default % if p1=5, split on p0(state); 2 splits -1 1 % if p0=18, return TRUE -1 1 % if p0=26, return TRUE -1 1 % if p0=29, return TRUE -1 0 % otherwise, return FALSE 0 2 19 default % if p1=6, split on p0(state); 2 splits -1 1 % if p0=19, return TRUE -1 0 % otherwise, return FALSE 0 2 20:23 default % if p1=7, split on p0(state); 2 splits -1 1 % if p0 in [20,23], return TRUE -1 0 % otherwise, return FALSE 0 2 24 default % if p1=8, split on p0(state); 2 splits -1 1 % if p0=24, return TRUE -1 0 % otherwise, return FALSE 0 4 18:23 26 29 default % if p1=9, split on p0(state); 4 splits -1 1 -1 1 -1 1 -1 0 7 copyParent_DT % name 1 % one parent -1 {p0} % just return parent value 8 % index incParent_DT % name 1 % one parent -1 {p0+1} % return parent+1 9 % index decParent_DT % name 1 % one parent 0 2 0 default % split on p0; 2 splits -1 0 % if p0=0, return 0 -1 {p0-1} % if p0>0, return p0-1 % % this decision tree is used to constrain the final state (which is the parent % in this case), and the value returned is 1 if the final state is a valid % final state, and is 0 if the final state is NOT valid ... % % --> the following states are INVALID end states : % 2,3,4,7,11,12,13,14,17,18,19,20,21,22,23,24,26,29 % % --> VALID end states : 1, 5, 6, 8, 9, 10, 15, 16, 25, 27, 28 % 10 % index finalState_DT % name 1 % one parent (state) 0 7 2:4 7 11:14 17:24 26 29 default % split on p0; 7 splits -1 0 -1 0 -1 0 -1 0 -1 0 -1 0 -1 1 % otherwise, return TRUE % % this mapping is used for switching parents when we just want the mapping % to imitate the parent value (typically binary) ... % 11 % index oneD_map % name 1 % one parent -1 { p0 } % return copy of parent % % this mapping is used to map the stateCountDown variable from [0,N] % down to just 3 classes: 0 --> 0, 1 --> 1, and >1 --> 2 % 12 % index counter_map % name 1 % one parent 0 3 0 1 default % split on p0; 3 splits -1 0 % if counter=0, return 0 -1 1 % if counter=1, return 1 -1 2 % if counter>1, return 2 13 % index forceEqual_DT % name 2 % two parents -1 { (p0==p1) } 14 % index isSP_DT % name 1 % one parent (topoClass) 0 2 4 default -1 1 % if topoClass==4, return 1 -1 0 % else, return 0 15 % index isTM_DT % name 1 % one parent (topoClass) 0 2 2 default -1 1 % if topoClass==2, return 1 -1 0 % else, return 0 % this used to be set based on two binary variables which only required a % simple leaf computation to determine the protein type: % -1 { p0 + 2*p1 } % but now p0=spBit and p1=iNumTM and the output pType is defined as: % G:0 SP+G:1 TM:2 SP+TM:3 16 % index setPtype_DT % name 2 % two parents (spBit, iNumTM) 1 2 0 default % split on p1=iNumTM: 2 splits: 0 vs >0 -1 { p0 } % if iNumTM=0, return spBit -1 { p0+2 } % if iNumTM>0, return spBit+2 17 % index areDiff_map % name 2 % two parents -1 { p0 != p1 } % return TRUE if different % we only want to increment the number of TMs if the previous % state is either 4 or 14 ... % iNumTM : 0 --> 1 --> 2 --> 3 --> 2 --> 3 --> etc 18 % index incNumTM_DT % name 2 % two parents: p0=prevState, p1=prevNumTM 0 3 4 14 default % split on p0 1 2 3 default % if p0= 4, split on p1 -1 { 2 } % if p1=3, return 2 -1 { p1+1 } % otherwise, return p1+1 1 2 3 default % if p0=14, split on p1 -1 { 2 } % if p1=3, return 2 -1 { p1+1 } % otherwise, return p1+1 -1 { p1 } % otherwise, return p1 19 % index two2one_DT % name 2 % two parents -1 { p0*cp1 + p1 } %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % DETERMINISTIC CPTs % % % DETERMINISTIC_CPT_IN_FILE inline 18 % total number of Det CPTs to follow 0 % index setBinaryFALSE % name 0 % no parents BINARY_CARD % self-cardinality setZero_DT % DT name 1 % index setBinaryTRUE % name 0 % no parents BINARY_CARD % self-cardinality setOne_DT % DT name 2 % index badLength % name 0 % no parents MAX_STATE_LENGTH_CARD % self-cardinality badValue_DT % DT name 3 % index state2emitClass % name 1 % one parent (state) STATE_CARD EMIT_CLASS_CARD % parent, self cardinalities state2emitClass_DT % DT name 4 % index state2lengthClass % name 1 % one parent (state) STATE_CARD LENGTH_CLASS_CARD % parent, self cardinalities state2lengthClass_DT % DT name 5 % index state2topoClass % name 1 % one parent (state) STATE_CARD TOPO_CLASS_CARD % parent, self cardinalities state2topoClass_DT % DT name 6 % index stateANDlabel % name 2 % two parents STATE_CARD LABEL_CARD BINARY_CARD % parents, then self cardinalities stateANDlabel_DT % DT name 7 % index copyState % name 1 % one parent (state) STATE_CARD STATE_CARD % parent, then self cardinalities copyParent_DT % DT name 8 % index decLength % name 1 % one parent (length) MAX_STATE_LENGTH_CARD MAX_STATE_LENGTH_CARD decParent_DT % DT name 9 % index finalState % name 1 % one parent(state) STATE_CARD BINARY_CARD % parent, then self cardinalities finalState_DT % DT name 10 % index forceEqual % name 2 % two parents TOPO_CLASS_CARD TOPO_CLASS_CARD BINARY_CARD forceEqual_DT % DT name 11 % index isSP % name 1 % one parent TOPO_CLASS_CARD BINARY_CARD % cardinalities isSP_DT % DT name 12 % index isTM % name 1 % one parent TOPO_CLASS_CARD BINARY_CARD % cardinalities isTM_DT % DT name 13 % index setPtype % name 2 % one parent BINARY_CARD NUM_TM_CARD PROTEIN_TYPE_CARD setPtype_DT % DT name 14 % index incNumTM % name 2 % two parents STATE_CARD NUM_TM_CARD NUM_TM_CARD % cardinalities incNumTM_DT % DT name 15 % index copyNumTM % name 1 % one parent NUM_TM_CARD NUM_TM_CARD % cardinalities copyParent_DT % DT name 16 % index setNumTMZero % name 0 % no parents NUM_TM_CARD % self cardinality setZero_DT % DT name 17 % index two2oneMap % name 2 % two parents BINARY_CARD TOPO_CLASS_CARD TOPO_10_CARD two2one_DT % DT name %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % MEANs and COVARs for GAUSSIAN COMPONENTS % % none needed at this time ... MEAN_IN_FILE inline 0 COVAR_IN_FILE inline 0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % GAUSSIAN COMPONENTS % % none needed at this time ... MC_IN_FILE inline 0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % MIXTURES OF GAUSSIAN COMPONENTS % % none needed at this time ... MX_IN_FILE inline 0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % NAME COLLECTIONs % % none needed at this time ... NAME_COLLECTION_IN_FILE inline 0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % DENSE CPTs % % % DENSE_CPT_IN_FILE inline 5 % total number of dense CPTs to follow % the startState_CPT will be initialized to have equal-probability for any % "allowed" starting-state, and *zero* probability for all the rest ... % % the currently allowed start-states are: % 1 : short-inside-loop % 6 : short-outside-globular % 8 : short-outside-loop % 10 : long-outside-globular % 16 : inside-globular % 25 : globular-only % 29 : methionine start before SP % 0 % index startState_CPT % name 0 % no parents STATE_CARD % cardinality 0. 0.1429 0. 0. 0. 0. 0.1429 0. 0.1429 0. 0.1429 0. 0. 0. 0. 0. 0.1429 0. 0. 0. 0. 0. 0. 0. 0. 0.1429 0. 0. 0. 0.1429 % the length_CPT specifies the allowed lengths for each of the length "classes" % note that a length of *zero* has the special meaning that the current % state is actually an exponential state % % of the 15 lengthClasses (indexed 1-15, skipping 0), three are fixed length, six % are a range of finite lengths, and six are exponential (but will have % different rates, so they need to be handled separately) % % the exponential states are those with prob=1 for length=0 % 1 % index length_CPT % name 1 % one parent LENGTH_CLASS_CARD MAX_STATE_LENGTH_CARD 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.03846 0.0385 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.0666 0.0666 0.0666 0.0666 0.0666 0.0666 0.0666 0.0666 0.0666 0.0666 0.0666 0.0666 0.0666 0.0666 0.0676 0. 0. 0. 0. 0. 0. 0.14286 0.14286 0.14286 0.14286 0.14286 0.14286 0.14286 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. % now we have the emission CPT, with one row of length 21 (20 amino acids plus % one wild-card at 0), for each of the emitClasses (of which there are 15) 2 % index aaEmitByClass_CPT % name 1 % one parent EMIT_CLASS_CARD AA_CARD % parent, self cardinalities DirichletConst 1 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.020 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 0.049 % this CPT contains the probability of leaving a particular state ... % we need one row for each 'length class', although in reality this will only % be used for exponential states % % as a sanity-check, any length-class that is *not* exponential (and therefore % should never query this CPT), we will set the probability of "leaving" to 0. 3 % index leaveExpState_CPT % name 1 % one parent LENGTH_CLASS_CARD BINARY_CARD 1. 0. 1. 0. 1. 0. 1. 0. 1. 0. 0.96 0.04 % short outside globular 1. 0. 0.96 0.04 % long outside glob #1 0.96 0.04 % inside glob 1. 0. 1. 0. 1. 0. 1. 0. 0.96 0.04 % SP-n-exp 0.96 0.04 % long outside glob #2 0.96 0.04 % long outside glob #3 % this CPT defines the allowed state-transitions ... most states can only % transition to one state, although a few of the transitions are random % ( state-0, which is not currently used, will stay in state-0 forever ) % % note that state-25, the "globular-only" state is a sink: once a path comes % into this state, it may never leave ... 4 % index stateTrans_CPT % name 1 % one parent STATE_CARD STATE_CARD 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% ( unused ) 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-1 --> state-2 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-2 --> state-3 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-3 --> state-4 0. 0. 0. 0. 0. 0.3 0. 0. 0.3 0.4 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-4 --> state-5,8,9 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-5 --> state-6 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-6 --> state-7 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-7 --> state-12 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-8 --> state-12 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-9 --> state-10 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. %% state-10 --> state-27 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-11 --> state-12 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-12 --> state-13 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-13 --> state-14 0. 0.5 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.5 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-14 --> state-1,15 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-15 --> state-16 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-16 --> state-17 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-17 --> state-2 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-18 --> state-19 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.8 0.2 0. 0. 0. 0. 0. 0. 0. 0. %% state-19 --> state-20,21 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. %% state-20 --> state-21 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. %% state-21 --> state-22 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. %% state-22 --> state-23 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. %% state-23 --> state-24 0. 0. 0. 0. 0. 0. 0.1 0. 0. 0. 0.2 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.7 0. 0. 0. 0. %% state-24 --> state-6,10,25 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. %% state-25 --> state-25 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-26 --> state-18 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. %% state-27 --> state-28 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. %% state-28 --> state-11 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. %% state-29 --> state-26 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % END % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%