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ReadsInRect Class Reference

#include <readsinrect.h>

Collaboration diagram for ReadsInRect:

Collaboration graph
[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

Detailed Description

Definition at line 10 of file readsinrect.h.

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.

00013                                 {
00014     cursor_positioned = false;
00015     need_to_call_first = true;
00016     readIt  = new Database::SecondaryIterator<ReadData>( "pos", doc, "ReadData" );
00017     x_dna = 0;
00018     y_dna = 0;
00019     w_dna = 0;
00020     h_dna = 0;
00021   }

ReadsInRect::~ReadsInRect (   )  [inline]
 

Definition at line 22 of file readsinrect.h.

References readIt.

00022                  {
00023     delete readIt;
00024   }

Member Function Documentation

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().

00045                     {
00046     if ( need_to_call_first ) {
00047       return NULL;
00048     }
00049     
00050     if ( w_dna <= 0 ) { 
00051       //Bug fix
00052       return NULL;
00053     }
00054     
00055     while ( y_iter < y_dna + h_dna ) {
00056       
00057       while ( x_iter < x_dna + w_dna ) {
00058         int ret;
00059         /* 
00060            It is faster to get the next data item by invoking next() on the cursor,
00061            than doing a new search ( i.e. setRange() ).
00062            Because the data item are sorted in the berkeley db first y-wise and
00063            then x-wise we use next() when we want to get the next Read to the right 
00064            in the same row. If we change rows we have to do a new search ( i.e. setRange() ).
00065            We use the boolean cursor_positioned to indicate which of them to use.
00066         */
00067         if ( cursor_positioned ) {
00068           ret = readIt->next();
00069         }
00070         else {
00071           readIt->key()->setRow( y_iter );
00072           readIt->key()->setEndPos( x_iter );
00073           ret = readIt->setRange();
00074           
00075         }
00076         if ( ret != 0 ) {
00077           
00078           // no records left in the sorted index
00079           need_to_call_first = true;
00080           return NULL;
00081         }
00082         ReadData * d = readIt->answer();
00083         assert( d );
00084         if ( hasRightEndInsideWindow( d ) ) {
00085           cursor_positioned = true;
00086           
00087         } 
00088         else {
00089           
00090           cursor_positioned = false;
00091           x_iter = x_dna;
00092           y_iter = d->row();
00093           if ( d->endPos() >= x_dna + w_dna ) { // we won't find any more reads on this row
00094             ++y_iter;
00095             
00096           }
00097         }
00098         if ( hasAnythingInsideWindow( d ) ) {   
00099           
00100           return d;               
00101         } 
00102         
00103       }
00104     }
00105     need_to_call_first = true;
00106     cursor_positioned = false;
00107     return NULL;
00108   }

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::contentsMousePressEvent(), TrapperView::contentsMouseReleaseEvent(), TrapperView::drawContents_helper(), TrapperView::getInfo(), and MoveAlgo::start().

00033   { 
00034     y_iter = y_dna; 
00035     x_iter = x_dna; 
00036     cursor_positioned = false;  
00037     need_to_call_first = false;
00038     return find(); 
00039   }

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().

00109                                                {
00110     if ( d->endPos() < x_dna )
00111       return false;
00112     if (( d->startPos() < x_dna + w_dna ) && ( d->row() < y_dna + h_dna ))
00113       return true;
00114     //default
00115     return false;
00116   }

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().

00118                                                {
00119     return (( d->endPos() < x_dna + w_dna )
00120             && ( d->endPos() >= x_dna ) );
00121   }

ReadData* ReadsInRect::next (   )  [inline]
 

Definition at line 40 of file readsinrect.h.

References find().

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

00041   {  
00042      return find(); 
00043   }

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::contentsMousePressEvent(), TrapperView::contentsMouseReleaseEvent(), TrapperView::drawContents_helper(), TrapperView::getInfo(), and MoveAlgo::start().

00025                                                                                  {
00026     x_dna = x_dna_;
00027     y_dna = y_dna_;
00028     w_dna = w_dna_;
00029     h_dna = h_dna_;
00030     return;
00031   }

Member Data Documentation

bool ReadsInRect::cursor_positioned [private]
 

Definition at line 125 of file readsinrect.h.

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

TR_DNA ReadsInRect::h_dna [private]
 

Definition at line 130 of file readsinrect.h.

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

bool ReadsInRect::need_to_call_first [private]
 

Definition at line 126 of file readsinrect.h.

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

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

Definition at line 133 of file readsinrect.h.

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

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::x_dna [private]
 

Definition at line 127 of file readsinrect.h.

Referenced by find(), first(), hasAnythingInsideWindow(), hasRightEndInsideWindow(), 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_dna [private]
 

Definition at line 128 of file readsinrect.h.

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

TR_DNA ReadsInRect::y_iter [private]
 

Definition at line 132 of file readsinrect.h.

Referenced by find(), and first().

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