#include <dnpsort.h>
Inheritance diagram for DnpSortAlgo:
Public Member Functions | |
| DnpSortAlgo (TrapperDoc *pDoc_, std::set< db_recno_t > &recnoList, AlgoParam *param) | |
| void | start () |
| void | init () |
| bool | dnpDone (int dnp_id) |
Private Types | |
| typedef std::map< int, std::set< size_t > > | MapSet |
| typedef std::vector< std::set< int > > | VectorSet |
Private Attributes | |
| MapSet | dnpID_to_readID |
| VectorSet | readID_to_dnpID |
| vector< bool > | used_reads |
Definition at line 9 of file dnpsort.h.
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Definition at line 12 of file dnpsort.h. 00012 : 00013 RWAlgo(pDoc_, recnoList, param) {}
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Definition at line 126 of file dnpsort.cc. References dnpID_to_readID. Referenced by start(). 00127 { 00128 return dnpID_to_readID.find( dnp_id ) == dnpID_to_readID.end(); 00129 }
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Definition at line 107 of file dnpsort.cc. References dnpID_to_readID, MAl_Readonly::get_DNP_ID(), MAl_Readonly::get_num_seq(), MAl_Readonly::get_seq_end(), RWAlgo::getMAl(), readID_to_dnpID, and used_reads. Referenced by start(). 00108 { 00109 for( size_t i = 0; i < getMAl()->get_num_seq(); i++ ) { 00110 set<int> tmpset; 00111 readID_to_dnpID.push_back(tmpset); 00112 used_reads.push_back(false); 00113 00114 for( size_t j = 0; j < getMAl()->get_seq_end( i ); j++ ) { 00115 00116 if ( getMAl()->is_DNP(i, j) ) { 00117 dnpID_to_readID[ getMAl()->get_DNP_ID(i, j) ].insert( i ); 00118 readID_to_dnpID[ i ].insert( getMAl()->get_DNP_ID(i, j) ); 00119 used_reads[i] = true; 00120 } 00121 00122 } 00123 } 00124 }
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Implements RWAlgo. Definition at line 7 of file dnpsort.cc. References dnpDone(), dnpID_to_readID, RWAlgo::getMAl(), init(), readID_to_dnpID, Algo::selectedReads, MAl::set_seq_row(), and used_reads. 00008 { 00009 if ( selectedReads.empty() ) { 00010 return; 00011 } 00012 00013 bool ok; 00014 int res = QInputDialog::getInteger( 00015 "DNP sort", "Enter start row for selected reads:", 0, 1, numeric_limits<int>::max(), 1, 00016 &ok, 0 ); 00017 00018 size_t row(1); 00019 if ( ok ) { 00020 // user entered something and pressed OK 00021 row = res; 00022 } else { 00023 // user pressed Cancel 00024 return; 00025 } 00026 00027 00028 //Fill structures for bookkeeping 00029 init(); 00030 00031 if ( dnpID_to_readID.empty() ) { 00032 return; 00033 } 00034 00035 vector<vector<size_t> > groups; 00036 00037 while ( !dnpID_to_readID.empty() ) { 00038 00039 //Pick dnp with ID dnp_id 00040 MapSet::iterator firstIt = dnpID_to_readID.begin(); 00041 00042 int dnp_id = firstIt->first; 00043 00044 //Put into working set 00045 set<int> working_set; 00046 working_set.insert( dnp_id ); 00047 00048 //create new group 00049 groups.push_back( vector<size_t>() ); 00050 00051 while ( !working_set.empty() ) { 00052 00053 int curr_dnp_id = *(working_set.begin()); 00054 working_set.erase( working_set.begin() ); 00055 assert( !dnpDone( curr_dnp_id ) ); 00056 00057 //Pull out all reads with dnp curr_dnp_id and add to current group and register new dnps 00058 for( set<size_t>::iterator it = dnpID_to_readID[ curr_dnp_id ].begin(); 00059 it != dnpID_to_readID[ curr_dnp_id ].end(); ++it ) { 00060 00061 if ( readID_to_dnpID[ *it ].empty() ) continue; 00062 00063 assert( used_reads[ *it ] ); 00064 groups[ groups.size() - 1 ].push_back( *it ); 00065 00066 for( set<int>::iterator it2 = readID_to_dnpID[ *it ].begin(); 00067 it2 != readID_to_dnpID[ *it ].end(); ++it2 ) { 00068 if ( *it2 != curr_dnp_id ) { 00069 working_set.insert( *it2 ); 00070 } 00071 00072 } 00073 readID_to_dnpID[ *it ].clear(); 00074 } 00075 00076 dnpID_to_readID.erase( curr_dnp_id ); 00077 assert( dnpDone( curr_dnp_id ) ); 00078 00079 } 00080 00081 } 00082 00083 //Assign new rows to groups 00084 // size_t row(1); 00085 for( size_t i = 0; i < groups.size(); i++ ) { 00086 00087 for( size_t j = 0; j < groups[ i ].size(); j++ ) { 00088 assert( used_reads[ groups[i][j] ] ); 00089 getMAl()->set_seq_row( groups[i][j], row ); 00090 row++; 00091 } 00092 row += 5; 00093 } 00094 00095 //put remaining reads at the bottom 00096 for( size_t i = 0; i < used_reads.size(); i++ ) { 00097 if ( !used_reads[ i ] ) { 00098 getMAl()->set_seq_row( i, row ); 00099 row++; 00100 00101 } 00102 00103 } 00104 00105 }
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1.4.4