ReadsInRect Class Reference

#include <readsinrect.h>

Collaboration diagram for ReadsInRect:

[legend]List of all members.

Public Member Functions
	ReadsInRect (TrapperDoc *doc)
	~ReadsInRect ()
void	setWindowCoord (TR_DNA x_dna_, TR_DNA y_dna_, TR_DNA w_dna_, TR_DNA h_dna_)
ReadData *	first ()
ReadData *	next ()
Private Member Functions
ReadData *	find ()
bool	hasAnythingInsideWindow (ReadData *d)
bool	hasRightEndInsideWindow (ReadData *d)
Private Attributes
bool	cursor_positioned
bool	need_to_call_first
TR_DNA	x_dna
TR_DNA	y_dna
TR_DNA	w_dna
TR_DNA	h_dna
TR_DNA	x_iter
TR_DNA	y_iter
Database::SecondaryIterator< ReadData > *	readIt

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Detailed Description

Definition at line 10 of file readsinrect.h.

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Constructor & Destructor Documentation

ReadsInRect::ReadsInRect

(

TrapperDoc *

doc

)

[inline]

Definition at line 13 of file readsinrect.h.

References cursor_positioned, h_dna, need_to_call_first, readIt, w_dna, x_dna, and y_dna.

                                {
    cursor_positioned = false;
    need_to_call_first = true;
    readIt  = new Database::SecondaryIterator<ReadData>( "pos", doc, "ReadData" );
    x_dna = 0;
    y_dna = 0;
    w_dna = 0;
    h_dna = 0;
  }

ReadsInRect::~ReadsInRect

(

)

[inline]

Definition at line 22 of file readsinrect.h.

References readIt.

                 {
    delete readIt;
  }

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Member Function Documentation

void ReadsInRect::setWindowCoord	(	TR_DNA	x_dna_,
		TR_DNA	y_dna_,
		TR_DNA	w_dna_,
		TR_DNA	h_dna_
	)			[inline]

Definition at line 25 of file readsinrect.h.

References h_dna, w_dna, x_dna, and y_dna.

Referenced by TrapperView::contentsMouseReleaseEvent(), and TrapperView::drawContents_helper().

                                                                                 {
    x_dna = x_dna_;
    y_dna = y_dna_;
    w_dna = w_dna_;
    h_dna = h_dna_;
    return;
  }

ReadData* ReadsInRect::first

(

)

[inline]

Definition at line 32 of file readsinrect.h.

References cursor_positioned, find(), need_to_call_first, x_dna, x_iter, y_dna, and y_iter.

Referenced by TrapperView::contentsMouseReleaseEvent(), and TrapperView::drawContents_helper().

  { 
    y_iter = y_dna; 
    x_iter = x_dna; 
    cursor_positioned = false;  
    need_to_call_first = false;
    return find(); 
  }

ReadData* ReadsInRect::next

(

)

[inline]

Definition at line 40 of file readsinrect.h.

References find().

Referenced by TrapperView::contentsMouseReleaseEvent(), and TrapperView::drawContents_helper().

  {  
     return find(); 
  }

ReadData* ReadsInRect::find

(

)

[inline, private]

Definition at line 45 of file readsinrect.h.

References Database::SecondaryIterator< T >::answer(), cursor_positioned, ReadData::endPos(), h_dna, hasAnythingInsideWindow(), hasRightEndInsideWindow(), Database::SecondaryIterator< T >::key(), need_to_call_first, Database::SecondaryIterator< T >::next(), readIt, ReadData::row(), ReadData::setEndPos(), Database::SecondaryIterator< T >::setRange(), ReadData::setRow(), w_dna, x_dna, x_iter, y_dna, and y_iter.

Referenced by first(), and next().

                    {
    if ( need_to_call_first ) {
      return NULL;
    }
    
    if ( w_dna <= 0 ) { 
      //Bug fix
      return NULL;
    }
    
    while ( y_iter < y_dna + h_dna ) {
      
      while ( x_iter < x_dna + w_dna ) {
        int ret;
        /* 
           It is faster to get the next data item by invoking next() on the cursor,
           than doing a new search ( i.e. setRange() ).
           Because the data item are sorted in the berkeley db first y-wise and
           then x-wise we use next() when we want to get the next Read to the right 
           in the same row. If we change rows we have to do a new search ( i.e. setRange() ).
           We use the boolean cursor_positioned to indicate which of them to use.
        */
        if ( cursor_positioned ) {
          ret = readIt->next();
        }
        else {
          readIt->key()->setRow( y_iter );
          readIt->key()->setEndPos( x_iter );
          ret = readIt->setRange();
          
        }
        if ( ret != 0 ) {
          
          // no records left in the sorted index
          need_to_call_first = true;
          return NULL;
        }
        ReadData * d = readIt->answer();
        assert( d );
        if ( hasRightEndInsideWindow( d ) ) {
          cursor_positioned = true;
          
        } 
        else {
          
          cursor_positioned = false;
          x_iter = x_dna;
          y_iter = d->row();
          if ( d->endPos() >= x_dna + w_dna ) { // we won't find any more reads on this row
            ++y_iter;
            
          }
        }
        if ( hasAnythingInsideWindow( d ) ) {   
          
          return d;               
        } 
        
      }
    }
    need_to_call_first = true;
    cursor_positioned = false;
    return NULL;
  }

bool ReadsInRect::hasAnythingInsideWindow

(

ReadData *

d

)

[inline, private]

Definition at line 109 of file readsinrect.h.

References ReadData::endPos(), h_dna, ReadData::row(), ReadData::startPos(), w_dna, x_dna, and y_dna.

Referenced by find().

                                               {
    if ( d->endPos() < x_dna )
      return false;
    if (( d->startPos() < x_dna + w_dna ) && ( d->row() < y_dna + h_dna ))
      return true;
    //default
    return false;
  }

bool ReadsInRect::hasRightEndInsideWindow

(

ReadData *

d

)

[inline, private]

Definition at line 118 of file readsinrect.h.

References ReadData::endPos(), w_dna, and x_dna.

Referenced by find().

                                               {
    return (( d->endPos() < x_dna + w_dna )
            && ( d->endPos() >= x_dna ) );
  }

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Member Data Documentation

bool ReadsInRect::cursor_positioned [private]

Definition at line 125 of file readsinrect.h.

Referenced by find(), first(), and ReadsInRect().

bool ReadsInRect::need_to_call_first [private]

Definition at line 126 of file readsinrect.h.

Referenced by find(), first(), and ReadsInRect().

TR_DNA ReadsInRect::x_dna [private]

Definition at line 127 of file readsinrect.h.

Referenced by find(), first(), hasAnythingInsideWindow(), hasRightEndInsideWindow(), ReadsInRect(), and setWindowCoord().

TR_DNA ReadsInRect::y_dna [private]

Definition at line 128 of file readsinrect.h.

Referenced by find(), first(), hasAnythingInsideWindow(), ReadsInRect(), and setWindowCoord().

TR_DNA ReadsInRect::w_dna [private]

Definition at line 129 of file readsinrect.h.

Referenced by find(), hasAnythingInsideWindow(), hasRightEndInsideWindow(), ReadsInRect(), and setWindowCoord().

TR_DNA ReadsInRect::h_dna [private]

Definition at line 130 of file readsinrect.h.

Referenced by find(), hasAnythingInsideWindow(), ReadsInRect(), and setWindowCoord().

TR_DNA ReadsInRect::x_iter [private]

Definition at line 131 of file readsinrect.h.

Referenced by find(), and first().

TR_DNA ReadsInRect::y_iter [private]

Definition at line 132 of file readsinrect.h.

Referenced by find(), and first().

Database::SecondaryIterator<ReadData>* ReadsInRect::readIt [private]

Definition at line 133 of file readsinrect.h.

Referenced by find(), ReadsInRect(), and ~ReadsInRect().

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The documentation for this class was generated from the following file:

• readsinrect.h

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