panman.proto

syntax = "proto3";

package panman;

message nucMut
{
    int32 nucPosition = 1; 
    int32 nucGapPosition = 2;  
    bool  nucGapExist = 3;
    uint32 mutInfo = 4; 
}

message mutation
{
    int64 blockId = 1;
    bool  blockGapExist = 2;
    bool  blockMutExist = 3;
    bool  blockMutInfo = 4;
    bool  blockInversion = 5;
    repeated nucMut nucMutation = 6;
}

message node
{
    repeated mutation mutations = 1;
    repeated string   annotations = 2;
}

message consensusSeqToBlockIds
{
    repeated    int64   blockId = 1;
    repeated    uint32  consensusSeq = 2;
    repeated    bool    blockGapExist = 3;
    repeated    string  chromosomeName = 4;
}

message gapList
{
    int64          blockId = 1;
    bool           blockGapExist = 2;
    repeated int32 nucGapLength = 3;
    repeated int32 nucPosition = 4;
}

message blockGapList
{
    repeated int32  blockPosition = 1;
    repeated int32  blockGapLength = 2;
}

message circularOffset
{
    string          sequenceId = 1;
    int32           offset = 2;
}

message rotationIndex
{
    string          sequenceId = 1;
    int32           blockOffset = 2;
}

message sequenceInverted
{
    string          sequenceId = 1;
    bool            inverted = 2;
}

message tree
{
    string           newick = 1;
    repeated node    nodes = 2;
    repeated consensusSeqToBlockIds consensusSeqMap = 4;
    repeated gapList gaps = 5;
    blockGapList     blockGaps = 6;
    repeated circularOffset circularSequences = 7;
    repeated rotationIndex rotationIndexes = 8;
    repeated sequenceInverted sequencesInverted = 9;
}

message complexMutation {
    bool            mutationType = 1;
    int32           treeIndex1 = 2;
    int32           treeIndex2 = 3;
    int32           treeIndex3 = 4;
    string          sequenceId1 = 5;
    string          sequenceId2 = 6;

    int64           blockIdStart1 = 7;
    bool            blockGapExistStart1 = 8;
    int32           nucPositionStart1 = 9;
    int32           nucGapPositionStart1 = 10;
    bool            nucGapExistStart1 = 11;

    int64           blockIdEnd1 = 12;
    bool            blockGapExistEnd1 = 13;
    int32           nucPositionEnd1 = 14;
    int32           nucGapPositionEnd1 = 15;
    bool            nucGapExistEnd1 = 16;

    int64           blockIdStart2 = 17;
    bool            blockGapExistStart2 = 18;
    int32           nucPositionStart2 = 19;
    int32           nucGapPositionStart2 = 20;
    bool            nucGapExistStart2 = 21;

    int64           blockIdEnd2 = 22;
    bool            blockGapExistEnd2 = 23;
    int32           nucPositionEnd2 = 24;
    int32           nucGapPositionEnd2 = 25;
    bool            nucGapExistEnd2 = 26;

    string          sequenceId3 = 27;
}

message treeGroup
{
    repeated tree   trees = 1;
    repeated complexMutation complexMutations = 2;
}