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NCBI C++ ToolKit: src/gui/widgets/phylo_tree/phylo_tree_node.cpp Source File

&

)

: m_ExtendedParms(

)

remainder =

;

marker_size = 2.0f;

(marker_size_str !=

) {

(marker_size <= 0.0f) marker_size = 2.0f;

string::size_type idx = remainder.find_first_of(

);

(idx != string::npos) {

= remainder.substr(0, idx + 1);

start_idx = remainder.find_first_of(

);

(start_idx == string::npos)

remainder = remainder.substr(idx + 1, remainder.size() - (idx + 1));

idx = remainder.find_first_of(

);

&

)

= dict.

(name);

);

= dict.

(name);

(std::exception&) {}

(!

.empty()) {

(std::exception&) {}

(!marker.empty()) {

(std::exception&){}

(sel_id || errno == 0)

(!sel_clusters.empty()) {

vector<CTempString>

;

(

=0;

<

.size(); ++

) {

(!sel_id && errno != 0)

(!bounded.empty()) {

color_idx = -1;

(!node_color.empty()) {

(!

->FindColor(c, color_idx)) {

color_idx =

->AddColor(c);

(!node_color.empty()) {

(!

->FindColor(c, color_idx)) {

color_idx =

->AddColor(c);

(node_color !=

) {

(!node_color.empty()) {

(!

->FindColor(c, color_idx)) {

color_idx =

->AddColor(c);

(!node_color.empty()) {

(!

->FindColor(c, color_idx)) {

color_idx =

->AddColor(c);

(

objects::CSeq_id(sid));

(!gi_str.empty()) {

(

objects::CSeq_id(gi_str));

lcl_sid =

;

(

objects::CSeq_id(lcl_sid));

(std::exception&)

(std::exception&)

parm_lower = parm;

features_lower = features;

idx = features_lower.find(parm_lower);

(idx != string::npos) {

end_idx = features.find_first_of(

, idx);

(end_idx == string::npos)

end_idx = features.size();

features.substr(idx + parm_lower.length(), end_idx-(idx+parm_lower.length()));

cos_a = cosf(

) / scale.

();

sin_a = sinf(

) / scale.

();

= atan2f(sin_a, cos_a);

(for_label && cos_a < 0.0f) {

size_scaler)

p.

() += cosf(

) * node_size * size_scaler * scale.

();

p.

() += sinf(

) * node_size * size_scaler * scale.

();

p.

() += node_size * size_scaler * scale.

();

truncate_labels,

pos_xmin = (

)(

() + (

.Left() * scale.

()));

pos_xmax = (

)(

() + (

.Right() * scale.

()));

pos_y = (

)(

() + (

.Bottom() * scale.

()));

text_out =

;

(truncate_labels) {

text_len =

(tw, vp_width - screen_minx);

text_len =

(tw, screen_maxx);

text_len =

(text_len, max_len);

(text_len > 0.0 && text_len < tw) {

std::reverse(text_out.begin(), text_out.end());

text_out = font.

(text_out.c_str(), text_len);

std::reverse(text_out.begin(), text_out.end());

pos_xmin += (tw - new_width)*scale.

();

(text_out ==

)

gl.

(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

gl.

(GL_TRIANGLE_STRIP);

font.

(pos_xmin, pos_y, text_out.c_str());

truncate_labels)

angle_degrees = angle * (360.0f / (2.0f*float(M_PI)));

gl.

(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

gl.

(GL_TRIANGLE_STRIP);

gl.

(corners[3].

(), corners[3].

());

gl.

(corners[0].

(), corners[0].

());

gl.

(corners[2].

(), corners[2].

());

gl.

(corners[1].

(), corners[1].

());

text_out =

;

(truncate_labels) {

(

= 0;

< 4; ++

) {

(cos(orig_angle) >= 0.0) {

(screen_minx < vp_width && screen_maxx > vp_width) {

pct = (vp_width - screen_minx) / (screen_maxx - screen_minx);

(screen_miny < vp_height && screen_maxy > vp_height) {

pct =

(pct, (vp_height - screen_miny) / (screen_maxy - screen_miny));

(screen_maxy > 0.0 && screen_miny < 0.0) {

pct =

(pct, (screen_maxy) / (screen_maxy - screen_miny));

(screen_minx < 0.0 && screen_maxx > 0.0) {

pct = (screen_maxx) / (screen_maxx - screen_minx);

(screen_miny < vp_height && screen_maxy > vp_height) {

pct =

(pct, (vp_height - screen_miny) / (screen_maxy - screen_miny));

(screen_maxy > 0.0 && screen_miny < 0.0) {

pct =

(pct, (screen_maxy) / (screen_maxy - screen_miny));

std::reverse(text_out.begin(), text_out.end());

text_out = font.

(text_out.c_str(), text_box_len*pct);

std::reverse(text_out.begin(), text_out.end());

= float((tw-new_width)/tw);

corners[0] = corners[0] + text_dir *

;

(text_out ==

)

& angle,

orig_angle)

cos_a = cosf(angle);

sin_a = sinf(angle);

(overhang > 0.0f) {

(orig_angle < 0.0f)

dir.

(cosf(orig_angle)*overhang*scale.

(), sinf(orig_angle)*overhang*scale.

());

(

corner=0; corner<4; ++corner) {

rpos((pos.

())*cos_a-pos.

()*sin_a, (pos.

())*sin_a + pos.

()*cos_a);

rpos.

() =

() + scale.

()*rpos.

() + dir.

();

rpos.

() =

() + scale.

()*rpos.

() + dir.

();

cos_a = cosf(angle);

sin_a = sinf(angle);

tpr(tp.

()*cos_a-tp.

()*sin_a, tp.

()*sin_a + tp.

()*cos_a);

() + tpr.

()*scale.

());

truncate_labels,

pos.

() = (float)(

() +

(

.Left() * scale.

()));

pos.

() = (float)(

() +

(

.Bottom() * scale.

()));

(truncate_labels) {

screen_x = (float)(pane.

(pos.

()));

(screen_x > 0.0f) {

std::reverse(text_out.begin(), text_out.end());

text_out = font.

(text_out.c_str(),

.Width()+screen_x);

std::reverse(text_out.begin(), text_out.end());

(!rotated ||

.Width() == 0.0f ||

.Height() == 0.0f) {

lower_left.

() =

() +

.Left()*scale.

();

lower_left.

() =

() +

.Bottom()*scale.

();

upper_right.

() =

() +

.Right()*scale.

();

upper_right.

() =

() +

.Top()*scale.

();

(

corner=0; corner<4; ++corner) {

lower_left.

() =

(lower_left.

(), corners[corner].

());

lower_left.

() =

(lower_left.

(), corners[corner].

());

upper_right.

() =

(upper_right.

(), corners[corner].

());

upper_right.

() =

(upper_right.

(), corners[corner].

());

pt.

() *= 1.0f/scale.

();

pt.

() *= 1.0f/scale.

();

cos_a = cosf(

);

sin_a = sinf(

);

rpos(pt.

()*cos_a-pt.

()*sin_a, pt.

()*sin_a + pt.

()*cos_a);

(

.PtInRect(pt.

(), pt.

()))

cos_a = cosf(

)*1.0f/scale.

();

sin_a = sinf(

)*1.0f/scale.

();

= atan2f(sin_a, cos_a);

(

corner=0; corner<4; ++corner) {

rpos(pos.

()*cos_a-pos.

()*sin_a, pos.

()*sin_a + pos.

()*cos_a);

(scale, lower_left, upper_right, rotated);

lower_left.

() =

(lower_left.

(),

()-deltax);

lower_left.

() =

(lower_left.

(),

()-deltay);

upper_right.

() =

(upper_right.

(),

()+deltax);

upper_right.

() =

(upper_right.

(),

()+deltay);

def_node_size = 0;

(forced_size < 0.0f) {

def_node_size = (float)(min_node_size + (max_node_size - min_node_size) *

(

(this_childs_size) -

(min_child_size)) /

(

(max_child_size) -

(min_child_size)));

def_node_size = (float)scheme->

()*1.5;

def_node_size = (float)forced_size;

def_node_size;

max_branch_dist > 1e-04f) {

scaled_max_child_dist = (

/ max_branch_dist)*(max_dist - min_dist) + min_dist;

= 4.0f*((float)(min_width + (max_width - min_width) *

(

(scaled_max_child_dist) -

(min_dist)) /

(

(max_dist) -

(min_dist))));

total_extension > 0.0f ? total_extension : 0.0f;

Features storage for the bio tree node.

CSubtreeBoundary * GetSubtreeBoundary()

Gets current boundary or creates a new one if m_Boundary is NULL.

bool PointInTextBox(const CVect2< float > &scale, CVect2< float > pt, bool rotated=false)

Return true if pt is inside of this nodes text box.

const TLabel & GetLabel() const

void SetClusterID(TClusterID x_id)

void DeleteSubtreeBoundary()

Deletes current boundary (if not NULL).

TSelectedState m_Selected

CVect2< float > m_NodeOffset

void SetLabelBgColorIdx(short idx)

float m_NodeWidth

This is computed by GetNodeWidthScaler(..) for collapsed nodes and we need to hang onto it for node l...

float GetNodeOverhang(const CVect2< float > &scale) const

Get extenstion of node beyond end of edge in pixels.

TSelClusterIDs & GetSelClusters()

CRef< objects::CSeq_id > m_SeqID

void Init(const CBioTreeFeatureDictionary &dict, CRgbaGradColorTable *t)

TBoundingState GetBoundedDisplay() const

CGlRect< float > m_LabelRect

TLabel m_Label

Full label.

void SetVisible(bool b)

Flag to renderer to determine whether to draw label.

void SetNodeFgColorIdx(short idx)

bool m_AlreadyDrawn

Text is alpha-blended so we add a flag to prevent drawing multiple times.

bool x_HasExtendedParms() const

void Sync(CBioTreeFeatureDictionary &dict)

void RenderRotated(const CGlPane &pane, const CGlTextureFont &font, CRgbaGradColorTable *color_table, const CVect3< float > &scale, float orig_angle, bool truncate_labels)

Draw the label and rotate it to match m_Angle (radial text) This form does not support label truncati...

void SetDistance(TDistance x_dist)

static const TColor TNoColor

SExtendedNodeParms * m_ExtendedParms

CRgbaColor m_FgColor

Current text color.

int GetNumLeavesEx() const

short m_NodeEdColorIdx

Node colors defined by scheme.

void SetSeqID(objects::CSeq_id *sid)

void SetBioTreeFeatureList(const CBioTreeFeatureList &btcfl)

CVect2< float > GetNodePosEx(const CVect3< float > &scale, CPhyloTreeScheme *scheme, float &node_size, float size_scaler=1.0f) const

Get modified center of node position - this works for collapsed nodes in rotated layouts and with off...

CVect2< float > GetTextOut(CGlPane &pane, const CGlTextureFont &font, const CVect3< float > &scale, bool truncate_labels, string &text_out)

Return the drawing position and (possibly truncated) text.

void RemoveFeature(CBioTreeFeatureDictionary &dict, const string &name)

void SetLabelColorIdx(short idx)

bool HasNodeMarker() const

int GetPrimaryCluster() const

With selection clusters a node may have multiple cluster ids.

size_t GetNumClusters() const

Return total # of applicable clusters - selection + m_ClusterID.

float GetNodeSize() const

float GetMarkerSize() const

void SetDrawAngle(float angle)

void SetSelClusters(const TSelClusterIDs &sc)

float GetNodeWidthScaler(const CPhyloTreeScheme *scheme) const

Get modified node width (length) for collapsed nodes. Default is 1.

bool HasSelClusters() const

void SetMarkerColors(const string &str)

float GetNodeLayoutSize(const CPhyloTreeScheme *scheme) const

Get modified node size - use this instead of GetDefaultNodeSize when doing layout (doesn't go to 0 if...

string GetMarkerColorsAsString()

void SetMarkerSize(float f)

short m_LabelFgColorIdx

Label color.

float GetScaledAngle(const CVect3< float > &scale, float a, bool for_label=true) const

Utility to get screen rotation angle after scaling.

vector< CRgbaColor > & GetMarkerColors()

void InitFeatures(const CBioTreeFeatureDictionary &dict, CRgbaGradColorTable *t)

TDistance m_MaxChildDistance

void SetNodeEdgeColorIdx(short idx)

TClusterID GetClusterID(void) const

string x_GetParameter(const string &features, const string &parm)

void GetBoundingRect(const CVect2< float > &scale, CVect2< float > &lower_left, CVect2< float > &upper_right, bool rotated=false)

Find the rectangle for the node and label combined given the current zoom level (scale)

void SetNodeSize(float x_sz)

float GetAngle(void) const

void Render(const CGlPane &pane, const CGlTextureFont &font, CRgbaGradColorTable *color_table, const CVect3< float > &scale, bool truncate_labels, TModelUnit max_len=-1.0f)

Draw the label using scale to compute its offset from m_BasePos.

CVect2< float > GetRotatedTextPos(const CVect3< float > &scale, float &angle) const

Return the text starting point rotated to align with radial edges.

void Set(TID x_id, TDistance x_dist, const TLabel &x_label)

CGlRect< float > GetLabelRect() const

float GetDefaultNodeSize(const CPhyloTreeScheme *scheme) const

Get modified node size - includes scaled (BOA) size.

CPhyloNodeData & operator=(const CPhyloNodeData &rhs)

void SetLabel(const TLabel &x_label)

TDisplayChildren GetDisplayChildren() const

TDistance m_DistanceFromRoot

bool m_Children

expand-collapse state (expanded==true)

float GetMinX(const CVect2< float > &scale)

Return labels minimal X coordinate.

void SetDisplayChildren(TDisplayChildren show)

CVect4< CVect2< float > > GetRotatedTextBox(const CVect3< float > &scale, float &angle, float orig_angle=0.0f) const

Return text box (m_LabelRect) rotated to align with radial edges.

vector< int > TSelClusterIDs

string m_Text

Text to render.

CBioTreeFeatureList & GetBioTreeFeatureList()

CRgbaColor m_NodeColor

Current node color.

bool m_EdgeColorGradient

Controls use of gradient coloring for edges - if false, edges will be a single color,...

bool m_Visible

True if node is visible.

CPhyloTreeScheme::TPhyloTreeColors m_ColorType

float m_NodeSize

Scaled node size.

TDistance GetDistance() const

CBioTreeFeatureList m_Features

CVect2< float > m_NodePixelOffset

Pixel offset to apply the node.

void SetFeature(CBioTreeFeatureDictionary &dict, const string &name, const string &value)

bool Expanded() const

Return true if node is currently not collapsed.

void ExpandCollapse(CBioTreeFeatureDictionary &dict, CPhyloNodeData::TDisplayChildren chds)

Set this node to be expanded/collapsed.

bool CanExpandCollapse(CPhyloNodeData::TDisplayChildren chds)

Return true if node can have its expand/collapsed state changed to chds.

void SetLabel(CBioTreeFeatureDictionary &dict, const string &label)

Set label string and synch value to the feature list for this ndoe.

bool IsLeafEx() const

Return true if node is a leaf or is collapsed.

GLdouble GetMaxNumChildren() const

GLdouble GetMaxNodeSize() const

size range for variable-sized collapsed nodes (so min node size here may be greater than node size)

GLdouble GetMaxBranchDist() const

And we scale the length of the collapsed node marker based on the max.

GLdouble GetLeafNodeSize() const

GLdouble GetMinNumChildren() const

collapsed node sizes are scaled from min to max values based on number of children so we need to have...

GLdouble GetMinNodeSize() const

GLdouble GetNodeSize() const

class CRgbaColor provides a simple abstraction for managing colors.

CRgbaGradColorTable Provides a storage for colors (to eliminate color creation overhead) and Function...

void CreateShapes(const std::string &features)

Parse the features to create the shapes and set their options.

CPhyloNodeData & GetValue()

Return the value object for the node.

bool HasParent() const

Check if the node has a parent.

static vector< string > arr

static const char * str(char *buf, int n)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

static bool GetGIString(const string &sid, string *gi_str)

ad-hoc GI extraction (for misformed seq-id strings like: "gi|55823257|ref|YP_141698....

void Color4fv(const GLfloat *v)

virtual void Enable(GLenum glstate)=0

virtual void Begin(GLenum mode)=0

Start rendering.

virtual void BlendFunc(GLenum sfactor, GLenum dfactor)=0

Options to be used when GL_BLEND is enabled.

TVPUnit ProjectX(TModelUnit m_x) const

IRender & GetGl()

convenience function for getting current render manager

void WriteText(TModelUnit x, TModelUnit y, const char *text, TModelUnit rotate_degrees=0.0) const

Write text at specified model coords.

void Vertex2d(GLdouble x, GLdouble y)

TVPRect & GetViewport(void)

TVPUnit ProjectY(TModelUnit m_y) const

TModelUnit UnProjectX(TVPUnit m_x) const

void BeginText() const

WriteText interface The WriteText functions produce the same results as TextOut but they are more eff...

virtual void End()=0

Finish rendering (create buffer and send to renderer)

virtual void PolygonMode(GLenum face, GLenum mode)=0

Set the polygon rasterization mode.

void EndText() const

Pops matrices and attributes after writing text.

virtual TModelUnit GetMetric(EMetric metric, const char *text=NULL, int len=-1) const

virtual TModelUnit TextWidth(const char *text) const

Compute and return font metrics.

virtual void TextOut(const char *text) const

TextOut interface Write the specified text and set up state and transformation as needed.

void Vertex2f(GLfloat x, GLfloat y)

TModelUnit GetScaleX(void) const

TModelUnit GetScaleY(void) const

string Truncate(const char *text, TModelUnit w, ETruncate trunc=eTruncate_Ellipsis) const

Truncate text to the secified width.

TVPPoint Project(TModelUnit m_x, TModelUnit m_y) const

CRgbaColor & GetColor(size_t i)

const float * GetColorArray(void) const

Access the color array directly.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ fConvErr_NoThrow

Do not throw an exception on error.

unsigned int TBioTreeFeatureId

Feature Id.

void SetFeature(TBioTreeFeatureId id, const string &value)

Set feature value, feature if exists replaced, if not added.

TBioTreeFeatureId GetId(const string &feature_name) const

If feature is already registered returns its id by name.

TBioTreeFeatureId Register(const string &feature_name)

Register new feature, return its id.

const string & GetFeatureValue(TBioTreeFeatureId id) const

Get feature value by id.

bool HasFeature(const string &feature_name) const

Check if feature is listed in the dictionary.

void RemoveFeature(TBioTreeFeatureId id)

Remove feature from the list.

static const char label[]

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

const GenericPointer< typename T::ValueType > T2 value

Int4 delta(size_t dimension_, const Int4 *score_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

#define PHYLO_NODE_MARKER

#define PHYLO_LABEL_BGCOLOR

#define PHYLO_NODE_COLLAPSED

#define PHYLO_FEAT_CLUSTERID

#define PHYLO_LABEL_COLOR

#define PHYLO_NODE_BOUNDED

#define PHYLO_SELECT_CLUSTERS

vector< CRgbaColor > m_MarkerColors

CSubtreeBoundary * m_Boundary

SExtendedNodeParms & operator=(const SExtendedNodeParms &rhs)

vector< int > m_SelClusters

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