// Generate an estimated breakpoint from mapping positions of discordant reads. New breakpoint is
// added to MEI_bps. This function assumes that objects in cluster are already ordered by position.
// Another assumption is that there are at least 2 reads in the cluster (i.e.
// user setting MIN_DD_CLUSTER_SIZE > 1).
void get_breakpoint_estimation(std::vector<simple_read*>& cluster, int insert_size, int cluster_tid,
char cluster_strand, std::vector<MEI_breakpoint>& MEI_bps) {
// Compute average distance between read mapping positions.
float dist_mean = 0;
for (unsigned int i = 0; i < (cluster.size() - 1); i++) {
dist_mean += (1.0 / (i+1)) * ((cluster.at(i+1)->pos - cluster.at(i)->pos) - dist_mean);
}
// Compute mean read lenght in cluster.
float read_len_mean = 0;
for (unsigned int i = 0; i < cluster.size(); i++) {
read_len_mean += (1.0 / (i+1)) * (cluster.at(i)->sequence.length() - read_len_mean);
}
int outer_pos_high = cluster.at(cluster.size()-1)->pos + cluster.at(cluster.size()-1)->sequence.length();
int outer_pos_low = cluster.at(0)->pos;
int estimation = (cluster_strand == Plus)? outer_pos_high + dist_mean : outer_pos_low - dist_mean;
MEI_breakpoint new_bp(cluster_tid, estimation, cluster_strand);
// Link associated discordant reads (all reads from cluster) and split reads.
std::vector<simple_read*>::iterator read_iter;
for (read_iter = cluster.begin(); read_iter != cluster.end(); ++read_iter) {
new_bp.associated_reads.push_back(*(*read_iter));
}
MEI_bps.push_back(new_bp);
}
/*设置断点*/
void set_b(unsigned x)
{
BP* newb = new_bp();//从free中找到一个新的可使用的断点
if(newb == NULL) { assert(0);}//free为空
newb -> b_or_w = true;
newb -> addr = x;//储存内存地址
newb -> sav_istr = swaddr_read(x,1);//储存原指令
swaddr_write(x,1,INT3_CODE);
newb -> enb = true;//enable
newb -> isUsed = true;
printf("Breakpoint %d at 0x%x\n",(newb -> NO)+1,x);
}
void CodeLiteLLDBApp::NotifyBreakpointsUpdated()
{
LLDBBreakpoint::Vec_t breakpoints;
int num = m_target.GetNumBreakpoints();
wxPrintf("codelite-lldb: Calling NotifyBreakpointsUpdated(). Got %d breakpoints\n", num);
for(int i=0; i<num; ++i) {
lldb::SBBreakpoint bp = m_target.GetBreakpointAtIndex(i);
if ( bp.IsValid() && bp.GetNumResolvedLocations() ) {
// Add the parent breakpoint
LLDBBreakpoint::Ptr_t mainBreakpoint( new LLDBBreakpoint() );
mainBreakpoint->SetId( bp.GetID() );
if ( bp.GetNumLocations() > 1 ) {
// add all the children locations to the main breakpoint
for(size_t i=0; i<bp.GetNumLocations(); ++i) {
lldb::SBBreakpointLocation loc = bp.GetLocationAtIndex(i);
lldb::SBFileSpec fileLoc = loc.GetAddress().GetLineEntry().GetFileSpec();
wxFileName bpFile( fileLoc.GetDirectory(), fileLoc.GetFilename() );
// Create a breakpoint for this location
LLDBBreakpoint::Ptr_t new_bp(new LLDBBreakpoint());
new_bp->SetType( LLDBBreakpoint::kLocation );
new_bp->SetFilename( bpFile.GetFullPath() );
new_bp->SetLineNumber( loc.GetAddress().GetLineEntry().GetLine() );
new_bp->SetName( loc.GetAddress().GetFunction().GetName() );
mainBreakpoint->GetChildren().push_back( new_bp );
}
} else {
lldb::SBBreakpointLocation loc = bp.GetLocationAtIndex(0);
lldb::SBFileSpec fileLoc = loc.GetAddress().GetLineEntry().GetFileSpec();
wxFileName bpFile( fileLoc.GetDirectory(), fileLoc.GetFilename() );
mainBreakpoint->SetType( LLDBBreakpoint::kFileLine );
mainBreakpoint->SetName( loc.GetAddress().GetFunction().GetName() );
mainBreakpoint->SetFilename( bpFile.GetFullPath() );
mainBreakpoint->SetLineNumber( loc.GetAddress().GetLineEntry().GetLine() );
}
breakpoints.push_back( mainBreakpoint );
}
}
LLDBReply reply;
reply.SetReplyType( kReplyTypeBreakpointsUpdated );
reply.SetBreakpoints( breakpoints );
SendReply( reply );
}
void set_w(char *e)
{
BP* neww = new_bp();
if(neww == NULL) {assert(0);}
neww -> b_or_w = false;
strcpy(neww -> e,e);
bool success = true;
neww -> last_value = expr(e,&success);
if(success)
{
neww -> enb = true;
neww -> isUsed = true;
printf("Hardware watchpoint %d:%s\n",(neww->NO)+1,e);
}
else
printf("Invalid expression!\n");
}
void watchpoint_start(swaddr_t n){
int m;
BP* temp;
BP* p;
m=swaddr_read(n,1);
new_bp();
temp=head;
p=head;
assert(head!=NULL);
while(temp->next!=NULL)
temp=temp->next;
temp->instr=m;
temp->address=n;
temp->type=false;
head=p;
watchpoint_continue(n);
}
/* add new breakpoint in the rear position */
void add_bp(swaddr_t addr) {
BP* temp = new_bp();
/* add to the rear */
if (head == NULL) {
head = temp;
} else {
/* travel to the rear */
BP* rear = head;
while (rear->next != NULL)
rear = rear->next;
rear->next = temp;
}
/* init */
temp->next = NULL;
temp->addr = addr;
temp->value = swaddr_read(addr, 1);
swaddr_write(addr, 1, INT3_CODE);
assert(temp->expr[0] == '\0');
}
/* add new watchpoint in the rear position */
void add_watchpoint(char* expr) {
BP* new_wp = new_bp();
/* add to the rear */
if (head == NULL) {
head = new_wp;
} else {
/* travel to rear */
BP* rear = head;
while (rear->next != NULL) {
rear = rear->next;
}
rear->next = new_wp;
}
/* init */
new_wp->next = NULL;
new_wp->value = calculate(expr);
strncpy(new_wp->expr, expr, 32);
assert(new_wp->addr == 0);
}
// Update breakpoint information
bool BreakPoint::update(string& info_output,
std::ostream& undo_commands,
bool& need_total_undo)
{
string file = file_name();
BreakPoint new_bp(info_output, arg(), number(), file);
bool changed = false;
myenabled_changed = false;
myposition_changed = false;
myfile_changed = false;
myaddress_changed = false;
need_total_undo = false;
const string num = "@" + itostring(number()) + "@";
if (new_bp.number() != number())
{
mynumber = new_bp.number();
need_total_undo = changed = true;
}
if (new_bp.type() != type())
{
mytype = new_bp.type();
need_total_undo = changed = myenabled_changed = true;
}
if (new_bp.dispo() != dispo())
{
need_total_undo = changed = myenabled_changed = true;
mydispo = new_bp.dispo();
}
if (new_bp.watch_mode() != watch_mode())
{
need_total_undo = changed = myenabled_changed = true;
mywatch_mode = new_bp.watch_mode();
}
if (new_bp.myenabled != myenabled)
{
changed = myenabled_changed = true;
myenabled = new_bp.myenabled;
if (myenabled)
{
if (gdb->has_disable_command())
undo_commands << gdb->disable_command(num) << "\n";
else
need_total_undo = true;
}
else
{
if (gdb->has_enable_command())
undo_commands << gdb->enable_command(num) << "\n";
else
need_total_undo = true;
}
}
if (type() == BREAKPOINT)
{
if (new_bp.address() != address())
{
changed = myaddress_changed = true;
myaddress = new_bp.address();
}
if (new_bp.func() != func())
{
changed = myposition_changed = true;
myfunc = new_bp.func();
}
if (new_bp.file_name() != file_name())
{
changed = myposition_changed = myfile_changed = true;
myfile_name = new_bp.file_name();
}
if (new_bp.line_nr() != line_nr())
{
changed = myposition_changed = true;
myline_nr = new_bp.line_nr();
}
}
else if (type() == WATCHPOINT)
{
if (new_bp.expr() != expr())
{
changed = true;
myexpr = new_bp.expr();
}
}
if (new_bp.infos() != infos())
{
changed = true;
myinfos = new_bp.infos();
}
if (new_bp.ignore_count() != ignore_count())
{
if (gdb->has_ignore_command())
undo_commands << gdb->ignore_command(num, myignore_count) << "\n";
else
need_total_undo = true;
changed = myenabled_changed = true;
myignore_count = new_bp.ignore_count();
}
if (new_bp.mycondition != mycondition)
{
if (gdb->has_condition_command())
undo_commands << gdb->condition_command(num, condition()) << "\n";
else
need_total_undo = true;
changed = myenabled_changed = true;
mycondition = new_bp.mycondition;
}
if (!equal(new_bp.commands(), commands()))
{
if (gdb->type() == GDB || gdb->type() == PYDB || gdb->type() == BASH)
{
undo_commands << "commands " << num << '\n';
for (int i = 0; i < commands().size(); i++)
undo_commands << commands()[i] << '\n';
undo_commands << "end\n";
}
changed = myenabled_changed = true;
mycommands = new_bp.commands();
}
return changed;
}