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Macros | Functions | Variables
graph_aligner_gui.cxx File Reference
#include "graph_aligner_gui.hxx"
#include "ed4_defs.hxx"
#include <fast_aligner.hxx>
#include <aw_awars.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <awt_sel_boxes.hxx>
#include <awt_config_manager.hxx>
#include <servercntrl.h>
#include <PT_com.h>
#include <client.h>
#include <arbdbt.h>
#include <arb_strbuf.h>
#include <arb_misc.h>
#include <sys/types.h>
#include <sys/wait.h>
#include <unistd.h>
#include <string>
#include <sstream>
#include <iostream>
#include <vector>
Include dependency graph for graph_aligner_gui.cxx:

Go to the source code of this file.

Macros

#define GA_AWAR_ROOT   "sina/"
 
#define GA_AWAR_CMD   GA_AWAR_ROOT "command"
 
#define GA_AWAR_TGT   GA_AWAR_ROOT "target"
 
#define GA_AWAR_SAI   GA_AWAR_ROOT "sai"
 
#define GA_AWAR_ALIGNMENT   GA_AWAR_ROOT "alignment"
 
#define GA_AWAR_PROTECTION   GA_AWAR_ROOT "protection"
 
#define GA_AWAR_TURN_CHECK   GA_AWAR_ROOT "turncheck"
 
#define GA_AWAR_REALIGN   GA_AWAR_ROOT "realign"
 
#define GA_AWAR_COPYMARKREF   GA_AWAR_ROOT "copymarkref"
 
#define GA_AWAR_MATCH_SCORE   GA_AWAR_ROOT "match_score"
 
#define GA_AWAR_MISMATCH_SCORE   GA_AWAR_ROOT "mismatch_score"
 
#define GA_AWAR_GAP_PEN   GA_AWAR_ROOT "gap_pen"
 
#define GA_AWAR_GAP_EXT   GA_AWAR_ROOT "gap_ext"
 
#define GA_AWAR_ADVANCED   GA_AWAR_ROOT "advanced"
 
#define GA_AWAR_FS_MIN   GA_AWAR_ROOT "fs_min"
 
#define GA_AWAR_FS_MAX   GA_AWAR_ROOT "fs_max"
 
#define GA_AWAR_FS_MSC   GA_AWAR_ROOT "fs_msc"
 
#define GA_AWAR_MIN_FULL   GA_AWAR_ROOT "min_full"
 
#define GA_AWAR_FULL_MINLEN   GA_AWAR_ROOT "full_minlen"
 
#define GA_AWAR_OVERHANG   GA_AWAR_ROOT "overhang"
 
#define GA_AWAR_THREADS   GA_AWAR_ROOT "threads"
 
#define GA_AWAR_QSIZE   GA_AWAR_ROOT "qsize"
 
#define GA_AWAR_KMER_LEN   GA_AWAR_ROOT "kmer_len"
 
#define GA_AWAR_KMER_MM   GA_AWAR_ROOT "kmer_mm"
 
#define GA_AWAR_MIN_LEN   GA_AWAR_ROOT "min_len"
 
#define GA_AWAR_WEIGHT   GA_AWAR_ROOT "weight"
 
#define GA_AWAR_INSERT   GA_AWAR_ROOT "insert"
 
#define GA_AWAR_LOWERCASE   GA_AWAR_ROOT "lowercase"
 
#define GA_AWAR_AUTOFILTER   GA_AWAR_ROOT "autofilter"
 
#define GA_AWAR_KMER_NOREL   GA_AWAR_ROOT "kmer_norel"
 
#define GA_AWAR_KMER_NOFAST   GA_AWAR_ROOT "kmer_nofast"
 
#define GA_AWAR_SHOW_DIST   GA_AWAR_ROOT "show_dist"
 
#define GA_AWAR_SHOW_DIFF   GA_AWAR_ROOT "show_diff"
 
#define GA_AWAR_COLOR   GA_AWAR_ROOT "color"
 
#define GA_AWAR_GENE_START   GA_AWAR_ROOT "gene_start"
 
#define GA_AWAR_GENE_END   GA_AWAR_ROOT "gene_end"
 
#define GA_AWAR_FS_COVER_GENE   GA_AWAR_ROOT "fs_cover_gene"
 

Functions

void create_sina_variables (AW_root *root, AW_default db1)
 
AW_active sina_mask (AW_root *root)
 
const charstream2static (const std::stringstream &str)
 
const charempty_as_none (const char *sainame)
 
static void sina_start (AW_window *window, const AlignDataAccess *data_access)
 
static charfilter_posvar_SAI_for_ali (GBDATA *gb_extended, const char *ali_name)
 
static AW_window_simple * new_sina_simple (AW_root *root, const AlignDataAccess *alignData, bool adv)
 
void show_sina_window (UNFIXED, const AlignDataAccess *alignData)
 

Variables

static AWT_config_mapping_def sina_config_mapping []
 

Macro Definition Documentation

#define GA_AWAR_ROOT   "sina/"

Definition at line 45 of file graph_aligner_gui.cxx.

#define GA_AWAR_CMD   GA_AWAR_ROOT "command"
#define GA_AWAR_TGT   GA_AWAR_ROOT "target"

Definition at line 48 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_SAI   GA_AWAR_ROOT "sai"

Definition at line 49 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_ALIGNMENT   GA_AWAR_ROOT "alignment"

Definition at line 50 of file graph_aligner_gui.cxx.

#define GA_AWAR_PROTECTION   GA_AWAR_ROOT "protection"

Definition at line 51 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_TURN_CHECK   GA_AWAR_ROOT "turncheck"

Definition at line 52 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_REALIGN   GA_AWAR_ROOT "realign"

Definition at line 53 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_COPYMARKREF   GA_AWAR_ROOT "copymarkref"

Definition at line 54 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables().

#define GA_AWAR_MATCH_SCORE   GA_AWAR_ROOT "match_score"

Definition at line 55 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_MISMATCH_SCORE   GA_AWAR_ROOT "mismatch_score"

Definition at line 56 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_GAP_PEN   GA_AWAR_ROOT "gap_pen"

Definition at line 57 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_GAP_EXT   GA_AWAR_ROOT "gap_ext"

Definition at line 58 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_ADVANCED   GA_AWAR_ROOT "advanced"

Definition at line 59 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and show_sina_window().

#define GA_AWAR_FS_MIN   GA_AWAR_ROOT "fs_min"

Definition at line 60 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_FS_MAX   GA_AWAR_ROOT "fs_max"

Definition at line 61 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_FS_MSC   GA_AWAR_ROOT "fs_msc"

Definition at line 62 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_MIN_FULL   GA_AWAR_ROOT "min_full"

Definition at line 63 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_FULL_MINLEN   GA_AWAR_ROOT "full_minlen"

Definition at line 64 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_OVERHANG   GA_AWAR_ROOT "overhang"

Definition at line 65 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_THREADS   GA_AWAR_ROOT "threads"

Definition at line 66 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables().

#define GA_AWAR_QSIZE   GA_AWAR_ROOT "qsize"

Definition at line 67 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables().

#define GA_AWAR_KMER_LEN   GA_AWAR_ROOT "kmer_len"

Definition at line 68 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_KMER_MM   GA_AWAR_ROOT "kmer_mm"

Definition at line 69 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_MIN_LEN   GA_AWAR_ROOT "min_len"

Definition at line 70 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_WEIGHT   GA_AWAR_ROOT "weight"

Definition at line 71 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_INSERT   GA_AWAR_ROOT "insert"

Definition at line 72 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_LOWERCASE   GA_AWAR_ROOT "lowercase"

Definition at line 73 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_AUTOFILTER   GA_AWAR_ROOT "autofilter"

Definition at line 74 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_KMER_NOREL   GA_AWAR_ROOT "kmer_norel"

Definition at line 75 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_KMER_NOFAST   GA_AWAR_ROOT "kmer_nofast"

Definition at line 76 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_SHOW_DIST   GA_AWAR_ROOT "show_dist"

Definition at line 77 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_SHOW_DIFF   GA_AWAR_ROOT "show_diff"

Definition at line 78 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_COLOR   GA_AWAR_ROOT "color"

Definition at line 79 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_GENE_START   GA_AWAR_ROOT "gene_start"

Definition at line 80 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_GENE_END   GA_AWAR_ROOT "gene_end"

Definition at line 81 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

#define GA_AWAR_FS_COVER_GENE   GA_AWAR_ROOT "fs_cover_gene"

Definition at line 82 of file graph_aligner_gui.cxx.

Referenced by create_sina_variables(), new_sina_simple(), and sina_start().

Function Documentation

void create_sina_variables ( AW_root root,
AW_default  db1 
)
AW_active sina_mask ( AW_root root)
const char* stream2static ( const std::stringstream &  str)
inline

Definition at line 161 of file graph_aligner_gui.cxx.

References GBS_static_string().

Referenced by sina_start().

const char* empty_as_none ( const char sainame)
inline

Definition at line 165 of file graph_aligner_gui.cxx.

Referenced by sina_start().

static void sina_start ( AW_window window,
const AlignDataAccess data_access 
)
static
static char* filter_posvar_SAI_for_ali ( GBDATA gb_extended,
const char ali_name 
)
static
static AW_window_simple* new_sina_simple ( AW_root root,
const AlignDataAccess alignData,
bool  adv 
)
static
void show_sina_window ( UNFIXED  ,
const AlignDataAccess alignData 
)

Variable Documentation

AWT_config_mapping_def sina_config_mapping[]
static

Definition at line 340 of file graph_aligner_gui.cxx.