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mv gs pb files back to here due to RGLab/cytolib#45
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mikejiang
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Jan 21, 2021
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,10 @@ | ||
| 2.1.4 | ||
| ------------------------- | ||
| 1. build shared protobuf library instead of static | ||
| 2. load libprotobuf globally on .onLoad | ||
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| First release | ||
| ------------------------- | ||
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| bundle the protobuf c++ library and expose its headers and static libraries | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,258 @@ | ||
| syntax = "proto2"; | ||
| package pb; | ||
| message paramRange{ | ||
| required string name = 1; | ||
| required float min = 2; | ||
| required float max = 3; | ||
| } | ||
| message rangeGate{ | ||
| required paramRange param = 1; | ||
| } | ||
| message paramPoly{ | ||
| repeated string params = 1;//params.at(0) is x, params.at(1) is y axis | ||
| repeated coordinate vertices = 2; | ||
| } | ||
| message polygonGate{ | ||
| required paramPoly param = 1; | ||
| optional quadGate qg = 2; | ||
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| } | ||
| message coordinate{ | ||
| required float x = 1; | ||
| required float y = 2; | ||
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| } | ||
| message ellipseGate{ | ||
| required coordinate mu = 1;// center point | ||
| repeated coordinate cov = 2;//covariance matrix | ||
| repeated coordinate antipodal_vertices = 3; | ||
| optional float dist = 4; | ||
| } | ||
| message BOOL_GATE_OP{ | ||
| repeated string path = 1; | ||
| required uint32 op = 2; | ||
| required bool isNot =3; | ||
| } | ||
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| message boolGate{ | ||
| repeated BOOL_GATE_OP boolOpSpec = 1;//the gatePaths with the their logical operators | ||
| } | ||
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| message clusterGate{ | ||
| required string cluster_method = 1; | ||
| } | ||
| enum QUADRANT{ | ||
| Q1 = 1;//-+ | ||
| Q2 = 2;//++ | ||
| Q3 = 3;//+- | ||
| Q4 = 4;//-- | ||
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| }; | ||
| message quadGate{ | ||
| required string uid = 1; | ||
| required QUADRANT quadrant = 3; | ||
| } | ||
| enum GATE_TYPE{ | ||
| POLYGON_GATE = 1; | ||
| RANGE_GATE = 2; | ||
| BOOL_GATE = 3; | ||
| ELLIPSE_GATE = 4; | ||
| RECT_GATE = 5; | ||
| LOGICAL_GATE = 6; | ||
| ELLIPSOID_GATE = 7; | ||
| CLUSTER_GATE = 8; | ||
| QUAD_GATE = 9; | ||
| } | ||
| message gate{ | ||
| required bool neg =1; | ||
| required bool isTransformed =2; | ||
| required bool isGained = 3; | ||
| required GATE_TYPE type = 4; | ||
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| optional rangeGate rg = 5; | ||
| optional polygonGate pg = 6; | ||
| optional ellipseGate eg = 7; | ||
| optional boolGate bg = 8; | ||
| optional clusterGate cg = 9; | ||
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| } | ||
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| message POPSTATS{ | ||
| required string statType = 1; | ||
| required float statVal = 2; | ||
| } | ||
| enum ind_type { | ||
| BOOL = 0; | ||
| INT = 1; | ||
| ROOT = 2 ; | ||
| } | ||
| message calibrationTable{ | ||
| repeated float x = 1 [packed = true]; | ||
| repeated float y = 2 [packed = true]; | ||
| repeated float b = 3 [packed = true]; | ||
| repeated float c = 4 [packed = true]; | ||
| repeated float d = 5 [packed = true]; | ||
| optional uint32 spline_method = 6; | ||
| optional string caltype = 7; | ||
| optional bool flag = 8; | ||
| } | ||
| enum TRANS_TYPE { | ||
| PB_CALTBL = 0; | ||
| PB_LOG = 1 ; | ||
| PB_LIN = 2; | ||
| PB_FLIN = 3; | ||
| PB_FASIGNH = 4; | ||
| PB_BIEXP = 5; | ||
| PB_LOGICLE = 6; | ||
| PB_LOGGML2 = 7; | ||
| PB_SCALE = 8; | ||
| } | ||
| message biexpTrans{ | ||
| optional uint32 channelRange = 1; | ||
| optional float pos = 2; | ||
| optional float neg = 3; | ||
| optional float widthBasis = 4; | ||
| optional float maxValue = 5; | ||
| } | ||
| message fasinhTrans{ | ||
| optional float length = 1; | ||
| optional float maxRange= 2; | ||
| optional float T = 3; | ||
| optional float A = 4; | ||
| optional float M = 5;; | ||
| } | ||
| message scaleTrans{ | ||
| optional float scale_factor = 1; | ||
| optional float t_scale = 2; | ||
| optional float r_scale = 3; | ||
| } | ||
| message flinTrans{ | ||
| optional float min = 1; | ||
| optional float max = 2; | ||
| } | ||
| message logTrans{ | ||
| optional float offset = 1; | ||
| optional float decade = 2; | ||
| optional float T = 3; | ||
| optional float scale = 4; | ||
| } | ||
| message logGML2Trans{ | ||
| optional float T = 1; | ||
| optional float M = 2; | ||
| } | ||
| message logicleTrans{ | ||
| optional float T = 1; | ||
| optional float W= 2; | ||
| optional float M = 3; | ||
| optional float A = 4; | ||
| optional float bins = 5; | ||
| optional bool isGml2 = 6; | ||
| optional bool isInverse = 7; | ||
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| } | ||
| message transformation{ | ||
| optional calibrationTable calTbl = 1; | ||
| optional bool isGateOnly = 2; | ||
| optional string name = 4; | ||
| optional string channel = 5; | ||
| optional bool isComputed = 6; | ||
| optional uint32 type = 12; | ||
| optional TRANS_TYPE trans_type = 3; //used to handle polymorphism | ||
| optional biexpTrans bt = 7; | ||
| optional logTrans lt = 8; | ||
| optional flinTrans flt = 9; | ||
| optional scaleTrans st = 10; | ||
| optional fasinhTrans ft = 11; | ||
| optional logicleTrans lgt = 13; | ||
| optional logGML2Trans lgml2t = 14; | ||
| } | ||
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| message trans_pair{ | ||
| required string name = 1; | ||
| optional uint64 trans_address = 2;//legacy | ||
| optional transformation trans = 3; | ||
| } | ||
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| message trans_local{ | ||
| repeated trans_pair tp = 1; | ||
| optional string groupName = 2; | ||
| repeated uint32 sampleIDs = 3 [packed = true]; | ||
| } | ||
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| message POPINDICES{ | ||
| required uint32 nEvents = 1; | ||
| required ind_type indtype = 2; | ||
| repeated uint32 iInd = 3 [packed = true]; | ||
| optional bytes bInd = 4;//bits packaged into bytes | ||
| } | ||
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| message nodeProperties{ | ||
| required string thisName = 1; | ||
| repeated POPSTATS fjStats = 2; | ||
| repeated POPSTATS fcStats = 3; | ||
| required bool hidden = 4; | ||
| optional POPINDICES indices = 5; | ||
| optional gate thisGate = 6; | ||
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| } | ||
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| message treeNodes { | ||
| required nodeProperties node = 1; | ||
| optional uint32 parent = 2; | ||
| } | ||
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| message populationTree{ | ||
| repeated treeNodes node = 1; | ||
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| } | ||
| message COMP{ | ||
| optional string cid = 1; | ||
| optional string prefix = 2; | ||
| optional string suffix = 3; | ||
| optional string name = 4; | ||
| optional string comment = 5; | ||
| repeated string marker = 6; | ||
| repeated float spillOver = 7; | ||
| } | ||
| message PARAM{ | ||
| optional string param = 1; | ||
| optional bool log = 2; | ||
| optional uint32 range = 3; | ||
| optional uint32 highValue = 4; | ||
| optional uint32 calibrationIndex = 5; | ||
| //optional float timestep = 6; | ||
| } | ||
| message GatingHierarchy { | ||
| required populationTree tree = 2; | ||
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| optional COMP comp = 1; | ||
| optional bool isLoaded = 3; | ||
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| repeated PARAM transFlag = 4; | ||
| optional trans_local trans = 5; | ||
| optional CytoFrame frame = 6; | ||
| } | ||
| message CytoFrame { | ||
| required bool is_h5 = 1; | ||
| } | ||
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| //legacy | ||
| message TRANS_TBL{ | ||
| optional uint64 trans_address = 1; | ||
| optional transformation trans = 2; | ||
| } | ||
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| message GatingSet { | ||
| repeated TRANS_TBL trans_tbl = 2;//legacy | ||
| repeated string sampleName = 1; //a view of ghs | ||
| optional uint64 globalBiExpTrans = 3;//address of globalBiExpTrans, the actual object stored in trans_tbl | ||
| optional uint64 globalLinTrans = 4;//address of globalLinTrans, the actual object stored in trans_tbl | ||
| repeated trans_local gTrans = 5; | ||
| optional string guid = 6; | ||
| optional string cytolib_verion = 7; | ||
| optional string pb_verion = 8; | ||
| optional string h5_verion = 9; | ||
| // repeated gh_tbl ghs = 7;//gh is separately stored due to the size limit of pb message | ||
| } | ||
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