File: hscore.dy

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%{
#include "wisebase.h"
#include "histogram.h"

#define HscoreLISTLENGTH 256
#define DATAENTRYSTDPOINTS 8

#define DATASCORESTORAGE_LENGTH 1024

typedef long BytePosition;
%}


struct DataEntry
char * name // name of the entry
int  data[DATAENTRYSTDPOINTS] // space for algorithms to use 
boolean is_reversed !def="FALSE" // for sequences. handy
BytePosition byte_position !hidden // useful for indexers - hopefully long enough!
char * filename !hidden !link  // useful for indexers etc.
%info
A lightweight structure to represent the information
a db search algorithm will want to store and *nothing*
more about a single entry

This object will be stored twice (once for the target
and once for the query) for each comparison: they probably
will be on different databases and different objects. 

The data field is just a number (8 at the moment) of int's available
for databases to store useful information (eg, length) of the 
object.

A number of extra fields are provided for convience sake for indexers, 
including byte_position and filename.
%%

struct DataScore
DataEntry * query
DataEntry * target
int score
double evalue
int is_stored !hidden
%info
The basic one entry vs one entry structure. Each
of the DataEntry datastructures actually store the 
information about the indexing etc.
%%

struct DataScoreStorage
DataScore score_array[DATASCORESTORAGE_LENGTH]
DataEntry query_array[DATASCORESTORAGE_LENGTH]
DataEntry target_array[DATASCORESTORAGE_LENGTH]
int curr_pos !def="0"
%info
This object was needed because for very large searches
the memory usage of allocation DataScore and DataEntry's
on the heap was becoming prohibative.

This datastructure holds pre-allocated DataScore and DataEntry
objects read for use. A complicated constructor/deconstructor
pair for DataScore objects ensures that these can be used
cleanly.
%%

struct Hscore
DataScore ** ds !list !hidden
DataScoreStorage ** store !list !len="st_" !hidden
Histogram * his
double  score_level    // passed into should_store function
boolean (*should_store)(int given_score,double internal_score_level) !func
float   (*score_to_his)(int given_score) !func
int     report_level  // number of sequences to report on
long    total         // total number of scores (duplicated info in histogram) 
%info
Holds the information about a db search.
Meant to be very lightweight

The histogram is carried for on-the-fly histogram storage outside
of the database. The idea is that the function should_store will
tell whether the datascore structure should be stored (if it is
NULL, it is always stored). The score_to_his function maps the
score in datascore to the float in Histogram, allowing the scoring
system of the search method to be on a different basis to the 
scoring system of the histogram. For most times, this is going to
be Score2Bits

To prevent too much dependency, the 'standard' way of making a 
histogram that has a bits cut off level is done using functions
in the dynlibcross module (cross code), as it needs both Hscore and
Probability. You should read dynlibcross module for the constructors
for Hscore
%%



api
object Hscore
des free_Hscore
func minimum_score_Hscore
func maximum_score_Hscore
func sort_Hscore_by_score
func length_datascore_Hscore
func get_datascore_Hscore
func get_score_Hscore
func get_evalue_Hscore
func basic_show_Hscore
endobject
object DataScore
des free_DataScore
endobject
object DataEntry
des free_DataEntry
endobject
func std_score_Hscore
endapi

%{
#include "hscore.h"

%func
This gives you a standard Hscore
module with a cutoff in score
%%
Hscore * std_score_Hscore(int cut_off,int report_stagger)
{
  Hscore * out;

  out = Hscore_alloc_std();
  out->his = new_Histogram(-1000,1000,100);
  out->score_level = cut_off;
  out->should_store = raw_should_store_Hscore;
  out->score_to_his = raw_score_to_his;
  out->report_level = report_stagger;

  return out;
}

%func
This function is for the Hscore std constructor,
%type internal
%%
boolean raw_should_store_Hscore(int score,double cutoff)
{
  if( score > cutoff ) {
    return TRUE;
  }
  return FALSE;
}

%func
This function is for the Hscore std constructor,
%type internal
%%
float raw_score_to_his(int score)
{
  return score;
}


%func
Tells whether this score should be stored
or not. Also updates Histogram if needed
%%
boolean should_store_Hscore(Hscore * hs,int score)
{
  hs->total++;

  if( hs->report_level != -1 && (hs->total % hs->report_level == 0)) {
    if( hs->len > 0) {
      info("Done %d comparisons: last stored comparison was %s to %s",hs->total,hs->ds[hs->len-1]->query->name,hs->ds[hs->len-1]->target->name);
    } else {
      info("Done %d comparisons: No stored comparisons",hs->total);
    }
  }

  if( hs->his != NULL && hs->score_to_his != NULL ) {
    AddToHistogram(hs->his,(*hs->score_to_his)(score));
  }
  if( hs->should_store == NULL ) {
    return TRUE;
  }
  return (*hs->should_store)(score,hs->score_level);
}

 
%func
Returns the number of datascores in the hscore
structure
%simple length
%arg
obj r Hscore object
%%
int length_datascore_Hscore(Hscore * obj)
{
  return obj->len;
}


%func
Returns the specific datascore held at this
position.

This requires a considerable amount of memory
duplication, so please dont process all your
results by looping through this.
%simple datascore
%arg
hs r Hscore object
i position to be read
return o New datascore object
%%
DataScore * get_datascore_Hscore(Hscore * hs,int i)
{
  DataScore * out;

  out = new_DataScore();
  copy_DataEntry(hs->ds[i]->query,out->query);
  copy_DataEntry(hs->ds[i]->target,out->target);
  out->score = hs->ds[i]->score;
  out->evalue = hs->ds[i]->evalue;
  return out;
}

%func 
Copies the info from one DataEntry to another
%type internal
%%
void copy_DataEntry(DataEntry * from,DataEntry * to)
{
  int i;

  to->name = stringalloc(from->name);
  for(i=0;i<DATAENTRYSTDPOINTS;i++) 
    to->data[i] = from->data[i];
  to->is_reversed = from->is_reversed;
  to->byte_position = from->byte_position;
  to->filename = from->filename; /* linked! */
}

%func 

Returns the score of the specific datascore held at this position.

%simple score
%arg
hs r Hscore object
i position to be read
return score 
%%
int get_score_Hscore(Hscore * hs,int i)
{
  return hs->ds[i]->score;
}


%func 
Returns the evalue of the specific datascore held at this position.

%simple evalue
%arg
hs r Hscore object
i position to be read
return evalue 
%%
double get_evalue_Hscore(Hscore * hs,int i)
{
  return hs->ds[i]->evalue;
}

%func
If a histogram is present, tries to fit the histogram and
then gives evalues to all the scores in the Hscore model
%%
boolean fit_Hscore_to_EVD(Hscore * hs,float guess_of_outliers)
{
  int i;


  if( hs->his == NULL ) {
    warn("Your Hscore has no histogram structure, and so no EVD can be fitted");
    return FALSE;
  }
  
  if( ExtremeValueFitHistogram(hs->his,TRUE,guess_of_outliers) == 0 ) {
    warn("Extreme Value distribution is unable to be fitted. Sorry!");
    return FALSE;
  }


  for(i=0;i<hs->len;i++) {
    hs->ds[i]->evalue  = ExtremeValueE((*hs->score_to_his)(hs->ds[i]->score),hs->his->param[EVD_MU],hs->his->param[EVD_LAMBDA],hs->his->total);
  }

  return TRUE;
}

  
%func
gets the minimum score from Hscore
%%
int minimum_score_Hscore(Hscore * hs)
{
  int i;
  int min;

  if( hs->len == 0) {
    warn("Can't get a minimum score with no entries");
    return 0;
  }

  for(i=1,min=hs->ds[0]->score;i<hs->len;i++) {
    if( min > hs->ds[i]->score ) {
      min = hs->ds[i]->score;
    }
  }

  return min;
}

%func
gets the maximum score from Hscore
%%
int maximum_score_Hscore(Hscore * hs)
{
  int i;
  int max;

  if( hs->len == 0) {
    warn("Can't get a minimum score with no entries");
    return 0;
  }

  for(i=1,max=hs->ds[0]->score;i<hs->len;i++) {
    if( max < hs->ds[i]->score ) {
      max = hs->ds[i]->score;
    }
  }

  return max;
}
 

%func
The most baby-talk showing of Hscore
%simple show
%arg
%%
void basic_show_Hscore(Hscore * hs,FILE * ofp)
{
  int i;

  if( hs == NULL ) {
    warn("parsing in a NULL Hscore object - cannot show!");
    fprintf(ofp,"parsing in a NULL Hscore object - cannot show!");
  }

  for(i=0;i<hs->len;i++) {
    fprintf(ofp,"%3d Query: %12s Target: %12s Score %d\n",i,
	    hs->ds[i]->query->name == NULL ? "NoName" : hs->ds[i]->query->name,
	    hs->ds[i]->target->name == NULL ? "NoName" : hs->ds[i]->target->name,
	    hs->ds[i]->score);
  }
}

%func
As it says, sorts the high score by its score
%arg
hs Hscore to be sorted
%%
void sort_Hscore_by_score(Hscore * hs)
{
  sort_Hscore(hs,compare_DataScore_by_score);
}


%func
Used to compare two datascores for
/sort_Hscore_by_score
%type internal
%arg
%%
int compare_DataScore_by_score(DataScore * one,DataScore * two)
{
  if( one->score == two->score ) {
    if( one->query != NULL && one->query->name != NULL && two->query != NULL && two->query->name != NULL )
      return strcmp(one->query->name,two->query->name);
    else return 1;
  }

  return two->score - one->score;
}


%func
The best way to make a new DataScore.
Allocates the query and target DataEntry structures
as well as the DataScore structure.
%type internal
%arg
%%
DataScore * new_DataScore(void)
{
  DataScore * ds;

  ds = DataScore_alloc();
  ds->query = DataEntry_alloc();
  ds->target = DataEntry_alloc();

  return ds;
}

%func 
Gets a new DataScore from Storage
%type internal
%%
DataScore * new_DataScore_from_storage(Hscore * hs)
{
  DataScoreStorage * new;
  DataScoreStorage * curr;

  if( hs->st_len == 0 ) {
    new = new_DataScoreStorage();
    if( new == NULL ) {
      warn("could not make initial data score storage!");
      return NULL;
    }
    add_st_Hscore(hs,new);
    curr = new;
  } else {
    curr = hs->store[hs->st_len-1];
    if( curr->curr_pos == DATASCORESTORAGE_LENGTH ) {
      new = new_DataScoreStorage();
      if( new == NULL ) {
	warn("could not make data score storage block %d!",hs->st_len-1);
	return NULL;
      }
      add_st_Hscore(hs,new);
      curr = new;
    }
  }

  return &curr->score_array[curr->curr_pos++];
}

      
  
%func
Correctly handles destruction of a datascore
%%
!deconstructor
DataScore * free_DataScore(DataScore * obj)
{
  if( obj->is_stored == 1 ) {
    return NULL; /* don't free! */
  }
  if( obj->dynamite_hard_link > 1 ) {
    obj->dynamite_hard_link--;
    return NULL;
  }

  if( obj->query != NULL )
    free_DataEntry(obj->query);

  if( obj->target != NULL )
    free_DataEntry(obj->target);

  return NULL;
}

%func
Correctly handles destruction of DataScoreStorage, by
freeing members in data storage
%%
!deconstructor
DataScoreStorage * free_DataScoreStorage(DataScoreStorage * obj)
{
  int i;

  for(i=0;i<obj->curr_pos;i++) {
    if( obj->query_array[i].name != NULL ) {
      ckfree(obj->query_array[i].name);
    }
    if( obj->target_array[i].name != NULL ) {
      ckfree(obj->target_array[i].name);
    }
  }

  ckfree(obj);

  return NULL;
}
    


%func
Makes a new DataScoreStorage with all the pointers connected correctly
%%
DataScoreStorage * new_DataScoreStorage(void)
{
  DataScoreStorage * out;
  int i;

  out = DataScoreStorage_alloc();
  if( out == NULL ) {
    warn("Unable to make a new DataScoreStorage block with blocksize %d",DATASCORESTORAGE_LENGTH);
    return NULL;
  }

  for(i=0;i<DATASCORESTORAGE_LENGTH;i++) {
    out->score_array[i].query = &out->query_array[i];
    out->score_array[i].target = &out->target_array[i];
    out->score_array[i].is_stored = 1;
  }
    
  return out;
}

%}