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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/vectortrimpanel_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/edit/vectortrimpanel.cpp Source File

wxMessageDialog msgdlg(

, message,

(

) );

m_pParentWindow =

;

wxWindowID

,

wxPoint& pos,

wxSize&

,

style )

: m_TopSeqEntry(seh),

m_CmdProcessor(cmdProcessor),

m_pParentWindow(parent)

wxWindowID

,

wxPoint& pos,

wxSize&

,

style )

wxPanel::Create( parent,

, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemPanel1->SetSizer(itemBoxSizer2);

wxBoxSizer* sizerLabels =

wxBoxSizer(wxHORIZONTAL);

wxStaticText* matches =

wxStaticText(

,

,

(

),

wxDefaultPosition, wxDefaultSize, wxALIGN_CENTRE_VERTICAL );

wxStaticText* locations =

wxStaticText(

,

,

(

),

wxDefaultPosition, wxDefaultSize, wxALIGN_CENTRE_VERTICAL );

sizerLabels->Add(matches, 1, wxEXPAND|wxALL, 5);

sizerLabels->Add(locations, 1, wxEXPAND|wxALL, 5);

itemBoxSizer2->Add(sizerLabels, 0, wxEXPAND|wxALL, 5);

wxLC_REPORT | wxLC_SINGLE_SEL );

dwStyle |= LVS_EX_FULLROWSELECT;

::SendMessage((

)

->GetHandle(), LVM_SETEXTENDEDLISTVIEWSTYLE, 0, dwStyle);

wxLC_REPORT | wxLC_SINGLE_SEL );

wxBoxSizer* sizerSearchVector =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(sizerSearchVector, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* sizerFindText =

wxBoxSizer(wxHORIZONTAL);

wxStaticText* findtext =

wxStaticText(

,

,

(

), wxDefaultPosition, wxDefaultSize, wxALIGN_CENTRE_HORIZONTAL );

sizerFindText->Add(findtext, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

sizerFindText->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer2->Add(sizerFindText, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxArrayString buttons;

buttons.Add(

(

));

buttons.Add(

(

));

buttons.Add(

(

));

buttons.Add(

(

));

buttons, 0, wxRA_SPECIFY_COLS );

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxArrayString buttons2;

buttons2.Add(

(

));

buttons2.Add(

(

));

buttons2.Add(

(

));

(

),

wxDefaultPosition, wxDefaultSize,

buttons2, 0, wxRA_SPECIFY_COLS );

wxBoxSizer* sizerSelectResults =

wxBoxSizer(wxHORIZONTAL);

sizerSelectResults->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer2->Add(sizerSelectResults, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

=

wxCheckBox(

,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* sizerTrimSelected =

wxBoxSizer(wxHORIZONTAL);

sizerTrimSelected->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer2->Add(sizerTrimSelected, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

(!wxPanel::TransferDataToWindow())

(!wxPanel::TransferDataFromWindow())

vecscreenReport->Show();

& sorted_cuts)

(

& cut : sorted_cuts) {

(cut.m_range.GetTo() == right_pos) {

right_pos = cut.m_range.GetFrom() - 1;

(cut.m_range.GetFrom() == left_pos) {

left_pos = cut.m_range.GetTo() + 1;

1 + (right_pos - left_pos));

(; seqmap_ci; ++seqmap_ci) {

(seqmap_ci.

()) {

(pOriginalGapSeqLiteral) {

pNewGapLiteral->Assign(*pOriginalGapSeqLiteral);

(!bIsLengthKnown) {

pNewGapLiteral->SetLength(uGapLength);

pDeltaSeq->SetLiteral(*pNewGapLiteral);

pDeltaSeq->SetLiteral().SetLength(seqmap_ci.

());

pDeltaSeq->SetLiteral().SetSeq_data(*pSeqData);

inst->

(1 + (right_pos - left_pos));

(pDeltaExt->

().size() == 1) {

& seq_data = pDeltaSeq->SetLiteral().SetSeq_data();

inst->

().SetDelta(*pDeltaExt);

cut_size = cut_to - cut_from + 1;

(feat_to < cut_from)

(feat_from >= cut_from && feat_to <= cut_to)

bCompleteCut =

;

(feat_from > cut_to)

feat_from -= cut_size;

interval->

(feat_from);

interval->

(feat_to);

(feat_to > cut_to) {

feat_to = cut_from - 1;

(feat_from >= cut_from) {

feat_from = cut_to + 1;

feat_from -= cut_size;

interval->

(feat_from);

interval->

(feat_to);

(loc->

())

bCompleteCut, bTrimmed);

(intervals->CanGet()) {

CPacked_seqint::Tdata::iterator it;

(it = intervals->Set().begin();

it != intervals->Set().end(); )

(it == intervals->Set().begin()) {

bCompleteCut =

;

bDeleted =

;

it = intervals->Set().erase(it);

bCompleteCut =

;

mix->Assign(loc->

());

CSeq_loc_mix::Tdata::iterator it;

(it = mix->Set().begin();

it != mix->Set().end(); )

(it == mix->Set().begin()) {

bCompleteCut =

;

bDeleted =

;

it = mix->Set().erase(it);

bCompleteCut =

;

& sorted_cuts,

& bFeatureDeleted,

& bFeatureTrimmed,

(

ii = 0; ii < sorted_cuts.size(); ++ii)

bFeatureDeleted, bFeatureTrimmed);

(bFeatureDeleted) {

(new_product, from, to, seqid, bProdDeleted, bProdTrimmed);

(

ii = 0; ii < cuts.size(); ++ii)

(from != 0 && to != seq_length-1) {

(from - 0 < seq_length-1 - to) {

(it = sorted_cuts.begin(); it != sorted_cuts.end(); )

( it+1 != sorted_cuts.end() ) {

( next_from <= (to + 1) ) {

sorted_cuts.erase(it+1);

( !new_protein_bioseq ) {

->AddCommand(*chgInst);

prot_feat_ci(prot_bsh, sel);

( ; prot_feat_ci; ++prot_feat_ci ) {

->AddCommand(*chgFeat);

(seg = 0; seg < denseg.

(); ++seg) {

(pos >= start && pos < start +

) {

(pos == seg_start) {

first_len, second_len;

first_len = pos - seg_start;

second_len = denseg.

()[foundseg] - first_len;

second_len = pos - seg_start;

first_len = denseg.

()[foundseg] - second_len;

(denseg.

()[index] == -1) {

new_denseg->

().push_back(-1);

new_denseg->

().push_back(first_len);

(denseg.

()[index] == -1) {

new_denseg->

().push_back(-1);

new_denseg->

().push_back(second_len);

align->

().SetDenseg(*new_denseg);

& sorted_cuts)

(

ii = 0; ii < sorted_cuts.size(); ++ii)

cut_len = cut_to - cut_from + 1;

(cut_to < cut_from) {

cut_len = cut_from - cut_to + 1;

(seg_start < 0) {

(seg_start < cut_from) {

(seg_start >= cut_from &&

seg_start + denseg.

()[curseg] <= cut_from + cut_len) {

align->

().SetDenseg().SetStarts()[index] = -1;

align->

().SetDenseg().SetStarts()[index] -= cut_len;

num_cuts = sorted_cuts.size();

(num_cuts == 1 || num_cuts == 2);

& first_cut = sorted_cuts[0].m_range;

(num_cuts == 1) {

(first_cut.GetFrom() == 0) {

range.

(first_cut.GetTo() + 1);

range.

(seqLength - 1);

range.

(first_cut.GetFrom() - 1);

(first_cut.GetFrom() > 0);

range.

(first_cut.GetFrom() - 1);

range.

(sorted_cuts[1].m_range.GetTo() + 1);

->AddCommand(*chgInst);

copy_id->

(*seqid);

feat_ci(scope, *search_loc, feat_sel);

(; feat_ci; ++feat_ci)

bFeatureDeleted =

;

bFeatureTrimmed =

;

bProdDeleted =

;

bProdTrimmed =

;

bFeatureDeleted, bFeatureTrimmed,

bProdDeleted, bProdTrimmed);

(bFeatureDeleted) {

->AddCommand(*delFeat);

->AddCommand(*delProt);

(bFeatureTrimmed) {

new_frame = sequence::CFeatTrim::GetCdsFrame(feat_ci->

(), retainedRange);

new_feat->

().SetCdregion().SetFrame(new_frame);

->AddCommand(*chgFeat);

(changedORadded_citsub) {

(changedSeqdesc && seh_for_desc) {

->AddCommand(*change_cmd);

(!changedSeqdesc) {

->AddCommand(*cmdAddDesc);

(sorted_cuts.begin(), sorted_cuts.end(), asc);

(sorted_cuts.begin(), sorted_cuts.end(), descend);

(; align_ci; ++align_ci)

(cit = trimOnly.

(); cit != trimOnly.

(); ++cit)

* seqid = cit->first;

(

ii = 0; ii < ids.size(); ++ii) {

( ids[ii]->Match(*seqid) ) {

->AddCommand(*chgAlign);

->AddCommand(*delAlign);

& sorted_cuts,

(

ii = 0; ii < sorted_cuts.size(); ++ii)

new_loc->Assign(new_graph->

());

bDeleted =

;

bTrimmed =

;

new_graph->

(*new_loc);

(

ii = 0; ii < sorted_cuts.size(); ++ii)

( trim_start <= to ) {

trim_start = to + 1;

( trim_stop >= from ) {

trim_stop = from - 1;

& sorted_cuts,

copy_start = graph_start;

(trim_start > graph_start) {

copy_start = trim_start;

copy_stop = graph_stop;

(trim_stop < graph_stop) {

copy_stop = trim_stop;

( src_data.

() ) {

copy_start -= graph_start;

copy_stop -= graph_start;

new_graph->

(copy_stop - copy_start + 1);

(; graph_ci; ++graph_ci)

(cit = trimOnly.

(); cit != trimOnly.

(); ++cit)

* seqid = cit->first;

( graph.

().GetId()->Match(*seqid) ) {

->AddCommand(*chgGraph);

(sorted_cuts.empty()) {

(sorted_cuts.size() == 1) {

(from == 0 && to == seq_length - 1) {

(

ii = 0; ii < sorted_cuts.size(); ++ii)

(from > max_to + 1) {

min_from =

(min_from, from);

max_to =

(max_to, to);

(min_from == 0 && max_to == seq_length - 1) {

(cit = seqidSummary.

(); cit != seqidSummary.

(); ++cit)

* seqid = cit->first;

(sorted_cuts.begin(), sorted_cuts.end(), asc);

->AddCommand(*delSet);

->AddCommand(*delSeq);

( !completeDeletions.

() ) {

header <<

<< completeDeletions.

()

<<

<<

;

(cit = completeDeletions.

(); cit != completeDeletions.

(); ++cit)

* seqid = cit->first;

footer <<

;

( listReport->ShowModal() == wxID_CANCEL ) {

(cit = completeDeletions.

(); cit != completeDeletions.

(); ++cit)

* seqid = cit->first;

(cit = trimOnly.

(); cit != trimOnly.

(); ++cit)

* seqid = cit->first;

(!report.IsEmpty()) {

(

),

vecscreenReport->Show();

wxWindowID

,

wxSize&

,

wxSize &

,

InsertColumn( 0,

(

), wxLIST_FORMAT_LEFT);

InsertColumn( 1,

(

), wxLIST_FORMAT_LEFT);

InsertColumn( 2,

(

), wxLIST_FORMAT_LEFT );

InsertColumn( 3,

(

), wxLIST_FORMAT_LEFT );

(

);

(

);

ss <<

(

) << start <<

(

)

<< hitloc.

- stop <<

(

);

( ss.str() );

(

);

(

);

stringstream ssMatchType;

(

ii = 0; ii < hitloc.

.size(); ++ii)

ssMatchType <<

;

ssMatchType << hitloc.

[ii].m_match_type;

( ssMatchType.str() );

SetItem(

, col,

(

));

GetColumn(col, objcol);

objcol.SetWidth(450);

SetColumn(col, objcol);

GetColumn(col, objcol);

objcol.SetWidth(50);

SetColumn(col, objcol);

seqidSummaryBySeqid.

();

TVecscreenSummaryByLocation::const_iterator cit;

(cit = seqidSummaryByLocation.begin(); cit != seqidSummaryByLocation.end(); ++cit) {

pair<TVecscreenSummaryBySeqid::iterator, bool> ins_res =

(!ins_res.second) {

vector<SRangeMatch>& sorted_matches,

(sorted_matches.empty()) {

kTerminalLenFromEnd = 50;

loc_start = sorted_matches[0].m_range.GetFrom();

loc_stop = sorted_matches[sorted_matches.size()-1].m_range.GetTo();

(loc_start < kTerminalLenFromEnd) {

(vecres.

- loc_stop < kTerminalLenFromEnd) {

selected =

;

seqidSummaryByLocation.push_back(hits);

seqidSummaryByLocation.clear();

(cit = vecscreen_summary.

(); cit != vecscreen_summary.

(); ++cit) {

* seqid = cit->first;

previous_to = -99;

vector<SRangeMatch> previous_matches;

(

.m_range.GetFrom() <= previous_to+1) {

previous_matches.push_back(

);

vector<SRangeMatch> current_matches;

current_matches.push_back(

);

(seqidSummaryByLocation, previous_matches, seqid, vecres);

previous_matches.swap(current_matches);

previous_to =

.m_range.GetTo();

(seqidSummaryByLocation, previous_matches, seqid, vecres);

report <<

(

);

TVecscreenSummaryByLocation::const_iterator cit;

(seqidSummaryByLocation.begin(), seqidSummaryByLocation.end(),

);

TVecscreenSummaryByLocation::const_iterator cit;

(cit = seqidSummaryByLocation.begin(); cit != seqidSummaryByLocation.end(); ++cit)

(cit->m_Selected && !cit->m_matches.empty()) {

report << cit->m_FastaSeqid <<

(

);

& firstrange = cit->m_matches[0];

& lastrange = cit->m_matches[cit->m_matches.size()-1];

seq_length = cit->m_SeqLen;

(from != 0 && to != seq_length-1) {

(from - 0 < seq_length-1 - to) {

report << from + 1 <<

<< to + 1 <<

(

);

(searchstr.empty()) {

(s.Find(searchstr) != wxNOT_FOUND) {

(s.Find(searchstr) != wxNOT_FOUND) {

(s.Find(searchstr) != wxNOT_FOUND) {

SetItemState(

, wxLIST_STATE_SELECTED, wxLIST_STATE_SELECTED);

wxMessageDialog

(

,

(

),

(

) );

bFound =

;

initialSearchRow =

;

bFound =

(hitloc, searchstr);

initialSearchRow =

;

bFound =

;

initialSearchRow =

;

bFound =

(hitloc, searchstr);

initialSearchRow =

;

TVecscreenSummaryByLocation::const_iterator cit;

(!cit->m_Selected) {

(

ii = 0; ii < matches.size(); ++ii) {

matchstr = matches[ii].m_match_type;

(matchstr ==

) {

(matchstr ==

) {

(matchstr ==

) {

(matchstr ==

) {

(current < matchtype) {

matchtype = current;

vector<SRangeMatch>& y)

x_FindStrongestMatchType(x, xMatchType);

x_FindStrongestMatchType(y, yMatchType);

xMatchType - yMatchType;

TVecscreenSummaryByLocation::const_iterator cit;

SetItem(

, 0, wxEmptyString );

SetColumnWidth(0, wxLIST_AUTOSIZE_USEHEADER);

SetColumnWidth(1, wxLIST_AUTOSIZE_USEHEADER);

SetColumnWidth(2, wxLIST_AUTOSIZE);

SetColumnWidth(3, wxLIST_AUTOSIZE);

TVecscreenSummaryByLocation::iterator it;

TVecscreenSummaryByLocation::iterator it;

(

ii = 0; ii < hitloc.

.size(); ++ii)

TVecscreenSummaryByLocation::iterator it;

TVecscreenSummaryByLocation::iterator it;

col =

.GetColumn();

( GetWindowStyle() & wxLC_REPORT )

selected_row =

.GetIndex();

TVecscreenSummaryByLocation::const_iterator cit;

(

== selected_row)

selected_row =

.GetIndex();

wxWindowID

,

wxSize&

,

wxSize &

,

wxListCtrl::Create(parent,

, pos,

, style);

col0.SetText(

(

) );

InsertColumn( 0, col0 );

.SetText(

(

) );

.SetWidth(220);

InsertColumn( 1,

);

vector<SRangeMatch>& matches)

(

ii = 0; ii < matches.size(); ++ii)

SetItem( ii, 0,

( fastaseqid ) );

stringstream ssRange;

SetItem( ii, 1,

( ssRange.str() ) );

( GetWindowStyle() & wxLC_REPORT )

.m_itemId =

.GetIndex();

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

wxDialog::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* dialogSizer =

wxBoxSizer(wxVERTICAL);

this->SetSizer(dialogSizer);

m_textHeader =

wxStaticText(

,

dialogSizer->Add(m_textHeader, 0, wxEXPAND|wxALL, 5);

m_textList =

wxTextCtrl(

,

wxTE_MULTILINE|wxTE_READONLY );

dialogSizer->Add(m_textList, 1, wxEXPAND|wxALL, 5);

m_textFooter =

wxStaticText(

,

dialogSizer->Add(m_textFooter, 0, wxEXPAND|wxALL, 5);

wxBoxSizer* buttonSizer =

wxBoxSizer(wxHORIZONTAL);

wxButton* okButton =

wxButton(

, wxID_OK,

(

), wxDefaultPosition, wxDefaultSize, 0 );

wxButton* cancelButton =

wxButton(

, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0 );

buttonSizer->Add(okButton, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

buttonSizer->Add(cancelButton, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

dialogSizer->Add(buttonSizer, 0, wxEXPAND|wxALL, 5);

m_textHeader->SetLabel(header);

m_textList->SetValue(list);

m_textFooter->SetLabel(footer);

wxPanel::Create( parent,

, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* panelSizer =

wxBoxSizer(wxVERTICAL);

this->SetSizer(panelSizer);

m_textReport =

wxTextCtrl(

,

panelSizer->Add(m_textReport, 1, wxEXPAND|wxALL, 5);

m_textReport->SetValue(report);

(parent,

, caption, pos,

, style);

wxDialog::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* dialogSizer =

wxBoxSizer(wxVERTICAL);

this->SetSizer(dialogSizer);

dialogSizer->Add(m_panel, 1, wxEXPAND|wxALL, 5);

m_panel->SetReport(report);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

void Set(T *object)

Initialize with an existing object.

TSeqPos GetLength(void) const

static CRef< objects::CSeqdesc > s_GetCitSubForTrimmedSequence(const objects::CBioseq_Handle &bsh, string &message, CConstRef< objects::CSeqdesc > &changedSeqdesc, objects::CSeq_entry_Handle &seh)

void SetHeader(const wxString &header)

~CListReportDlg()

Destructor.

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxString &caption=_("Report Dialog"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

CListReportDlg()

Constructors.

void CreateControls()

Creates the controls and sizers.

void Init()

Initialises member variables.

void SetList(const wxString &list)

void SetFooter(const wxString &footer)

bool Create(wxWindow *parent, wxWindowID id, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxLC_ICON)

void OnSelected(wxListEvent &event)

bool UpdateData(const string &fastaseqid, const vector< SRangeMatch > &matches)

int x_Compare(const CUVHitLoc &x, const CUVHitLoc &y) const

void x_FindStrongestMatchType(const vector< SRangeMatch > &matches, SRangeMatch::EMatchType &matchtype) const

int x_CompareMatches(const vector< SRangeMatch > &x, const vector< SRangeMatch > &y) const

bool operator()(const CUVHitLoc &x, const CUVHitLoc &y) const

vector< SRangeMatch > m_matches

@ eSortInternal5Prime3Prime

bool x_Find(const CUVHitLoc &hitloc, const wxString &searchstr)

void x_DisplaySearchResult(bool bFound, long row)

void x_InsertMatches(TVecscreenSummaryByLocation &seqidSummaryByLocation, const vector< SRangeMatch > &sorted_matches, const CSeq_id *seqid, const SVecscreenResult &vecres) const

vector< CUVHitLoc > TVecscreenSummaryByLocation

bool UpdateData(const TVecscreenSummaryBySeqid &vecscreen_summary)

TVecscreenSummaryBySeqid m_seqidSummaryBySeqid

void Sort(ESortOption eSortOption, bool bAscending)

const TVecscreenSummaryBySeqid & GetSelectedVecscreenSummaryBySeqid()

void x_ConvertSelectedToBySeqid(const TVecscreenSummaryByLocation &seqidSummaryByLocation, TVecscreenSummaryBySeqid &seqidSummaryBySeqid) const

bool Create(wxWindow *parent, wxWindowID id, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxLC_ICON)

void OnSelected(wxListEvent &event)

void SetAlignGraphicView(wxHtmlWindow *view)

void OnColClick(wxListEvent &event)

void SetRangeView(CLocationsListCtrl *view)

CLocationsListCtrl * m_RangeView

wxString x_GetSeqid(const CUVHitLoc &hitloc)

void OnChecked(wxListEvent &event)

void GetSelectedLocations(wxString &report, CVectorTrimPanel::EInternalTrimType eInternalTrimType)

wxListItemAttr m_listItemAttr

void SelectStrongModerate()

wxString x_GetHitLocation(const CUVHitLoc &hitloc)

wxHtmlWindow * m_AlignView

bool x_GetSelected(const CUVHitLoc &hitloc)

void FindReverse(wxString searchstr)

TVecscreenSummaryByLocation m_seqidSummaryByLocation

void GetReport(wxString &report)

bool x_IsValidRow(long row)

wxString x_GetMatchType(const CUVHitLoc &hitloc)

void x_ConvertAllToByLocation(const TVecscreenSummaryBySeqid &vecscreen_summary, TVecscreenSummaryByLocation &seqidSummaryByLocation) const

void FindForward(wxString searchstr)

Helper functor to compare cuts during sorting.

bool operator()(const SRangeMatch &a1, const SRangeMatch &a2)

CRangeCmp(ESortOrder sortorder=eAscending)

namespace ncbi::objects::

static TSeqPos Pack(CSeq_data *in_seq, TSeqPos uLength=ncbi::numeric_limits< TSeqPos >::max())

void SetReport(const wxString &report)

void Init()

Initialises member variables.

void CreateControls()

Creates the controls and sizers.

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxBORDER_SIMPLE)

Creation.

~CVecscreenReportPanel()

Destructor.

CVecscreenReportPanel()

Constructors.

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxString &title=_("VecScreen Report"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxDEFAULT_DIALOG_STYLE|wxRESIZE_BORDER)

Creation.

void CreateControls()

Creates the controls and sizers.

void SetReport(const wxString &report)

void Init()

Initialises member variables.

~CVecscreenReport()

Destructor.

CVecscreenReport()

Constructors.

void Run(objects::CSeq_entry_Handle seh, wxGauge &progress)

static bool IsDbAvailable()

const TVecscreenSummaryBySeqid & GetVecscreenSummaryBySeqid() const

void OnTrimSelected(wxCommandEvent &event)

bool Create(wxWindow *parent, wxWindowID id=ID_CVECTORTRIMPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxTAB_TRAVERSAL)

Creation.

void OnDismiss(wxCommandEvent &event)

CLocationsListCtrl * m_listLocations

wxButton * m_buttonSelectStrongModerate

void x_RetranslateCDS(CScope &scope, CRef< CCmdComposite > command, CRef< CSeq_feat > cds)

wxHtmlWindow * m_viewAlignGraphic

void x_SeqLocDelete(CRef< CSeq_loc > loc, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, bool &bTrimmed)

void OnUnselectInternal(wxCommandEvent &event)

objects::CSeq_entry_Handle m_TopSeqEntry

void OnFindReverse(wxCommandEvent &event)

CRange< TSeqPos > x_GetRetainedRange(const TCuts &sorted_cuts, TSeqPos seqLength)

void x_TrimSeqGraphs(CRef< CCmdComposite > command, const TVecscreenSummaryBySeqid &trimOnly)

void OnSort(wxCommandEvent &event)

void Init()

Initialises member variables.

bool x_FindSegment(const CDense_seg &denseg, CDense_seg::TDim row, TSeqPos pos, CDense_seg::TNumseg &seg, TSeqPos &seg_start) const

wxGauge * m_gaugeProgressBar

void x_TrimSeqGraphData(CRef< CSeq_graph > new_graph, const CMappedGraph &orig_graph, const TCuts &sorted_cuts, const CSeq_id *seqid)

void x_TrimFeatureLocations(CRef< CSeq_feat > feat, const TCuts &sorted_cuts, const CSeq_id *seqid, bool &bFeatureDeleted, bool &bFeatureTrimmed, bool &bProdDeleted, bool &bProdTrimmed)

~CVectorTrimPanel()

Destructor.

void x_CutDensegSegment(CRef< CSeq_align > align, CDense_seg::TDim row, TSeqPos pos)

void x_AdjustDensegAlignment(CRef< CSeq_align > align, CDense_seg::TDim row, const TCuts &sorted_cuts)

wxButton * m_buttonUnselectInternal

wxButton * m_buttonUnselectAll

void x_GetSortedCuts(TCuts &sorted_cuts, const CSeq_id *seqid)

wxButton * m_buttonMakeReport

void CreateControls()

Creates the controls and sizers.

wxButton * m_buttonFindForward

static bool ShowToolTips()

Should we show tooltips?

wxRadioBox * m_radioBoxInternalTrimOptions

void OnSelectStrongModerate(wxCommandEvent &event)

void x_AdjustInternalCutLocations(TCuts &cuts, TSeqPos seq_length)

void OnUnselectAll(wxCommandEvent &event)

wxButton * m_buttonSelectAll

void x_MergeCuts(TCuts &sorted_cuts)

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void DisplaySummaryBySeqid(const TVecscreenSummaryBySeqid &vecscreen_summary)

wxButton * m_buttonDismiss

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void x_FindCompleteDeletions(const TVecscreenSummaryBySeqid &seqidSummary, TVecscreenSummaryBySeqid &completeDeletions, TVecscreenSummaryBySeqid &trimOnly)

CVectorScreen m_vectorscreen

void OnSelectAll(wxCommandEvent &event)

void x_SetSeqData(const CBioseq_Handle &bsh, CRef< objects::CSeq_inst > inst, const TCuts &sorted_cuts)

void x_DeleteSelected(CRef< CCmdComposite > command, const CSeq_id *seqid)

void OnFindForward(wxCommandEvent &event)

void x_TrimAlignments(CRef< CCmdComposite > command, const TVecscreenSummaryBySeqid &trimOnly)

wxButton * m_buttonRunVecscreen

void OnRunVecscreen(wxCommandEvent &event)

void x_SeqIntervalDelete(CRef< CSeq_interval > interval, TSeqPos cut_from, TSeqPos cut_to, const CSeq_id *seqid, bool &bCompleteCut, bool &bTrimmed)

ICommandProccessor * m_CmdProcessor

void x_UpdateSeqGraphLoc(CRef< CSeq_graph > new_graph, const TCuts &sorted_cuts, const CSeq_id *seqid)

void OnMakeReport(wxCommandEvent &event)

bool x_IsCompleteCut(const TCuts &sorted_cuts, TSeqPos seq_length)

vector< SRangeMatch > TCuts

wxWindow * m_pParentWindow

CMatchesListCtrl * m_listMatches

void x_GetTrimCoordinates(const TCuts &sorted_cuts, const CSeq_id *seqid, TSeqPos &trim_start, TSeqPos &trim_stop)

wxRadioBox * m_radioBoxSort

CVectorTrimPanel()

Constructors.

virtual bool TransferDataToWindow()

wxButton * m_buttonTrimSelected

virtual bool TransferDataFromWindow()

wxBoxSizer * m_sizerVectorResults

wxButton * m_buttonFindReverse

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

container_type::const_iterator const_iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

bool Create(wxWindow *parent, wxWindowID winid=wxID_ANY, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxLC_REPORT, const wxValidator &validator=wxDefaultValidator, const wxString &name=wxListCtrlNameStr)

bool IsChecked(long item) const

void SetChecked(long item, bool checked)

static const char si[8][64]

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

const TPrim & Get(void) const

const string AsFastaString(void) const

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

void SetPacked_int(TPacked_int &v)

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

TSeqPos GetStop(ESeqLocExtremes ext) const

static CRef< CBioseq > TranslateToProtein(const CSeq_feat &cds, CScope &scope)

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

void RemoveBioseq(const CBioseq_Handle &seq)

Revoke Bioseq previously added using AddBioseq().

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool IsNucleotide(void) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TClass GetClass(void) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

bool CanGetClass(void) const

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

bool IsSetProduct(void) const

void SetInst(TInst &v) const

bool IsProtein(void) const

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

const CSeqMap & GetSeqMap(void) const

Get sequence map.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

bool IsSetData(void) const

const TInst & GetInst(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

const string & GetTitle(void) const

bool IsSetTitle(void) const

const CSeq_align & GetOriginalSeq_align(void) const

Get original alignment.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_loc & GetProduct(void) const

CSeqMap::ESegmentType GetType(void) const

bool IsUnknownLength(void) const

return true if current segment is a gap of unknown length

const CSeq_graph & GetOriginalGraph(void) const

Get original graph with unmapped location/product.

const CSeq_loc & GetLoc(void) const

CSeq_align_Handle GetSeq_align_Handle(void) const

Get original alignment handle.

TSeqPos GetPosition(void) const

return position of current segment in sequence

TSeqPos GetLength(void) const

return length of current segment

CConstRef< CSeq_literal > GetRefGapLiteral(void) const

return CSeq_literal with gap data, or null if either the segment is not a gap, or an unspecified gap

const CSeq_graph::C_Graph & GetGraph(void) const

CSeq_graph_Handle GetSeq_graph_Handle(void) const

Get original graph handle.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

CSeqMap_CI ResolvedRangeIterator(CScope *scope, TSeqPos from, TSeqPos length, ENa_strand strand=eNa_strand_plus, size_t maxResolve=size_t(-1), TFlags flags=fDefaultFlags) const

Iterate segments in the range with specified strand coordinates.

@ eSeqData

real sequence data

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static string & ToLower(string &str)

Convert string to lower case – string& version.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

bool CanGetDim(void) const

Check if it is safe to call GetDim method.

const TDenseg & GetDenseg(void) const

Get the variant data.

TLens & SetLens(void)

Assign a value to Lens data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetStrands(void) const

Check if a value has been assigned to Strands data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

const TLens & GetLens(void) const

Get the Lens member data.

bool CanGetNumseg(void) const

Check if it is safe to call GetNumseg method.

void SetDim(TDim value)

Assign a value to Dim data member.

bool CanGetIds(void) const

Check if it is safe to call GetIds method.

vector< CRef< CSeq_id > > TIds

bool CanGetSegs(void) const

Check if it is safe to call GetSegs method.

TDim GetDim(void) const

Get the Dim member data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TIds & GetIds(void) const

Get the Ids member data.

bool CanGetStarts(void) const

Check if it is safe to call GetStarts method.

TNumseg GetNumseg(void) const

Get the Numseg member data.

TIds & SetIds(void)

Assign a value to Ids data member.

const TStrands & GetStrands(void) const

Get the Strands member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool CanGetLens(void) const

Check if it is safe to call GetLens method.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

E_Choice Which(void) const

Which variant is currently selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

bool CanGetLocation(void) const

Check if it is safe to call GetLocation method.

const TProduct & GetProduct(void) const

Get the Product member data.

bool CanGetProduct(void) const

Check if it is safe to call GetProduct method.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

void SetTo(TTo value)

Assign a value to To data member.

TFrom GetFrom(void) const

Get the From member data.

bool CanGetTo(void) const

Check if it is safe to call GetTo method.

E_Choice Which(void) const

Which variant is currently selected.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

const TMix & GetMix(void) const

Get the variant data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

bool CanGetFrom(void) const

Check if it is safe to call GetFrom method.

void SetMin(TMin value)

Assign a value to Min data member.

TByte & SetByte(void)

Select the variant.

void SetNumval(TNumval value)

Assign a value to Numval data member.

TAxis GetAxis(void) const

Get the Axis member data.

TValues & SetValues(void)

Assign a value to Values data member.

TMax GetMax(void) const

Get the Max member data.

const TByte & GetByte(void) const

Get the variant data.

void SetGraph(TGraph &value)

Assign a value to Graph data member.

bool CanGetLoc(void) const

Check if it is safe to call GetLoc method.

void SetMax(TMax value)

Assign a value to Max data member.

TMin GetMin(void) const

Get the Min member data.

const TValues & GetValues(void) const

Get the Values member data.

E_Choice Which(void) const

Which variant is currently selected.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TLoc & GetLoc(void) const

Get the Loc member data.

void SetAxis(TAxis value)

Assign a value to Axis data member.

void Reset(void)

Reset the whole object.

@ eClass_nuc_prot

nuc acid and coded proteins

const TIupacaa & GetIupacaa(void) const

Get the variant data.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

bool IsNcbieaa(void) const

Check if variant Ncbieaa is selected.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

void SetExt(TExt &value)

Assign a value to Ext data member.

TIupacna & SetIupacna(void)

Select the variant.

TLength GetLength(void) const

Get the Length member data.

const TNcbieaa & GetNcbieaa(void) const

Get the variant data.

void SetRepr(TRepr value)

Assign a value to Repr data member.

void SetLength(TLength value)

Assign a value to Length data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

void ResetExt(void)

Reset Ext data member.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

void ResetSeq_data(void)

Reset Seq_data data member.

@ eRepr_raw

continuous sequence

constexpr auto sort(_Init &&init)

const struct ncbi::grid::netcache::search::fields::SIZE size

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

CRange< TSeqPos > m_range

vector< SRangeMatch > m_arrRangeMatch

@ MYID_BUTTON_RUN_VECSCREEN

@ MYID_CHECKBOX_VIEWGRAPHIC

@ MYID_BUTTON_SELECT_STRONG_MODERATE

@ MYID_BUTTON_FIND_REVERSE

@ MYID_RADIOBOX_INTERNAL_TRIM_OPTIONS

@ MYID_BUTTON_UNSELECT_INTERNAL

@ MYID_BUTTON_UNSELECT_ALL

@ MYID_BUTTON_MAKE_REPORT

@ MYID_BUTTON_TRIM_SELECTED

@ MYID_BUTTON_FIND_FORWARD

@ MYID_LISTCTRL_LOCATIONS

void ShowDebugMessage(const wxString &message)

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