/* hgGeneRing - Gene Network Browser. */
/* Copyright (C) 2013 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "cheapcgi.h"
#include "htmshell.h"
#include "obscure.h"
#include "web.h"
#include "cart.h"
#include "hdb.h"
#include "dbDb.h"
#include "hgFind.h"
#include "hCommon.h"
#include "hui.h"
#include "interaction.h"
#include "bdgpGeneInfo.h"
#include "portable.h"
char *errMsg = NULL;
char *geneList = NULL;
struct slName *geneNames = NULL;
struct hash *aliasHash = NULL;
struct interaction *interactions = NULL;
struct node {
char *name; /* name or id - use also as hash key */
char *alias; /* if used */
struct nodelist *xrays; /* out-going rays in directed graph */
struct nodelist *nrays; /* in-coming rays in directed graph */
boolean ring; /* member of gene-ring? */
int ringRank; /* number of ring members connected to by x or n rays */
int xpos; /* x position */
int ypos; /* y position */
};
struct nodelist {
struct nodelist *next; /* next in list */
struct node *node;
};
struct nodelist* allNodes = NULL;
struct hash *nodeHash = NULL;
int ringCount = 0;
int insideCount = 0;
int outsideCount = 0;
struct cart *cart = NULL;
struct hash *oldVars = NULL;
char *clade = NULL;
char *organism = NULL;
char *db = NULL;
/* ------ old junk cloned from hgGateway --------- */
void hgGateway()
/* hgGateway - Human Genome Browser Gateway. */
{
char *defaultPosition = hDefaultPos(db);
char *position = cloneString(cartUsualString(cart, "position", defaultPosition));
boolean gotClade = hGotClade();
/* JavaScript to copy input data on the change genome button to a hidden form
This was done in order to be able to flexibly arrange the UI HTML
*/
char *onChangeDB = "onchange=\"document.orgForm.db.value = document.mainForm.db.options[document.mainForm.db.selectedIndex].value; document.orgForm.submit();\"";
char *onChangeOrg = "onchange=\"document.orgForm.org.value = document.mainForm.org.options[document.mainForm.org.selectedIndex].value; document.orgForm.db.value = 0; document.orgForm.submit();\"";
char *onChangeClade = "onchange=\"document.orgForm.clade.value = document.mainForm.clade.options[document.mainForm.clade.selectedIndex].value; document.orgForm.org.value = 0; document.orgForm.db.value = 0; document.orgForm.submit();\"";
if (sameString(position, "genome") || sameString(position, "hgBatch"))
position = defaultPosition;
puts("\n"
);
puts(" ");
}
/* end of hgGateway junk that this code was cloned from */
/* ----------------------------------------------------------------------- */
boolean getGenesAsList()
/* create name-list from geneString,
so that we don't have to keep re-parsing
the cart string in different places
*/
{
char* ss = cloneString(geneList);
char* s = ss;
char* w = NULL;
int c=0;
char emsg[256];
/* clean up unwanted characters if any */
subChar(ss, ',' ,' ');
subChar(ss, '\t',' ');
subChar(ss, '\n',' ');
subChar(ss, '\r',' ');
while (1)
{
if (!(w = nextWord(&s))) break;
if (slNameInList(geneNames, w))
/* could be optimized, but not expecting large lists for ring */
{
safef(emsg,sizeof(emsg), "Duplicate gene id (%s) found in list.",w);
errMsg = cloneString(emsg);
freez(&ss);
return FALSE;
}
slNameAddHead(&geneNames, w);
c++;
}
slReverse(&geneNames);
if (c==0)
{
errMsg = "No genes in list. Please specify genes for ring.";
return FALSE;
}
freez(&ss);
return TRUE;
}
void updateGeneList()
/* update the cart list of genes */
{
char *sep = "";
struct slName *sn = geneNames;
struct dyString *geneList=dyStringNew(512);
while(sn)
{
dyStringPrintf(geneList,"%s%s",sep,sn->name);
sep=" ";
sn=sn->next;
}
cartSetString(cart, "ring_geneList", geneList->string);
dyStringFree(&geneList);
}
struct bdgpGeneInfo *bdgpGeneInfoLoadByQuery(struct sqlConnection *conn, char *query)
/* Load all interaction from table that satisfy the query given.
* Where query is of the form 'select * from example where something=something'
* or 'select example.* from example, anotherTable where example.something =
* anotherTable.something'.
* Dispose of this with bdgpGeneInfoFreeList(). */
{
struct bdgpGeneInfo *list = NULL, *el;
struct sqlResult *sr;
char **row;
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
el = bdgpGeneInfoLoad(row);
slAddHead(&list, el);
}
slReverse(&list);
sqlFreeResult(&sr);
return list;
}
void getGeneAliasesFromTable(char* table)
/* read all the gene aliases from database, return bdgpGeneInfo-list */
{
struct bdgpGeneInfo *result = NULL, *this=NULL;
struct dyString *query=dyStringNew(512);
char *sep = "where";
struct slName *sn = geneNames;
sqlDyStringPrintf(query,"select * from %s",table);
while(sn)
{
char * nm = sn->name;
if (startsWith("CG",nm))
{
sqlDyStringPrintf(query," %s bdgpName='%s'",sep,nm);
sep = "or";
}
else if (!startsWith("FBgn",nm))
{
sqlDyStringPrintf(query," %s symbol='%s'",sep,nm);
sep = "or";
}
sn = sn->next;
}
//uglyf(" SQL=%s
\n",query->string);
struct sqlConnection* conn = hAllocConn();
result = bdgpGeneInfoLoadByQuery(conn, query->string);
for(this=result;this;this=this->next)
{
//uglyf(" adding %s=%s \n",this->bdgpName,this->flyBaseId); // debug
hashAdd(aliasHash,this->bdgpName,cloneString(this->flyBaseId));
//uglyf(" adding %s=%s \n",this->symbol,this->flyBaseId); // debug
hashAdd(aliasHash,this->symbol,cloneString(this->flyBaseId));
}
// Mysterious crashes if I free this list:
//bdgpGeneInfoFreeList(&result);
hFreeConn(&conn);
dyStringFree(&query);
}
struct interaction *getGenesFromTable(char* table)
/* read all the gene interactions from database, returns interaction-list */
{
struct interaction *result = NULL;
struct dyString *query=dyStringNew(512);
char *sep = "where";
struct slName *sn = geneNames;
getGeneAliasesFromTable("bdgpGeneInfo"); /* load aliases into hash */
sqlDyStringPrintf(query,"select * from %s",table);
while(sn)
{
struct hashEl *hel = NULL, *hf=NULL;
char * nm = sn->name;
char * alias = NULL;
if (!startsWith("FBgn",nm))
{
if (hf = hashLookup(aliasHash,nm))
{
alias = sn->name;
//uglyf(" aliasing %s with %s \n",nm,(char *)hf->val); // debug
nm = (char *)hf->val;
}
}
hel = hashStore(nodeHash,nm);
if (!hel->val) /* add geneList elements to the hash */
{
struct node *n;
struct nodelist *nl;
AllocVar(n);
AllocVar(nl);
n->name = cloneString(nm);
n->alias = cloneString(alias);
n->ring = TRUE; /* this is a special ring member */
nl->node = n;
slAddHead(&allNodes,nl); /* all nodes going in hash are added to all-nodes list */
hel->val = n;
}
sqlDyStringPrintf(query," %s fromX='%s' or toY='%s'",sep,nm,nm);
sep = "or";
sn = sn->next;
}
//uglyf(" SQL=%s
\n",query->string);
struct sqlConnection* conn = hAllocConn();
result = interactionLoadByQuery(conn, query->string);
hFreeConn(&conn);
dyStringFree(&query);
return result;
}
void getGeneList()
/* hgGeneRing - Gene Network Browser. */
{
/* not much point in this, though called old it's the same as current
at this point. It is not the old value from before the last submit.
char *oldGeneList = hashFindVal(oldVars, "ring_geneList");
*/
if (!sameString(errMsg,""))
{
printf("
%s
\n",errMsg);
}
puts("\n");
cartSetString(cart, "ring_action", "saveGeneList");
cartSetString(cart, "ring_errMsg", "");
}
int compareNodes(const void *va, const void *vb)
{
const struct nodelist *a = *((struct nodelist **)va);
const struct nodelist *b = *((struct nodelist **)vb);
if (a->node->ring && !b->node->ring) return -1;
if (!a->node->ring && b->node->ring) return 1;
if (a->node->ring && b->node->ring)
{
return differentWord(a->node->name,b->node->name)*-1;
}
if (a->node->ringRank == b->node->ringRank)
{
return differentWord(a->node->name,b->node->name)*-1;
}
else
{
return (b->node->ringRank - a->node->ringRank);
}
}
boolean saveGeneList(boolean showAll)
/* Check for valid gene-list: parse and save.
If list not ok, return to getGeneList page.
Otherwise, show user's list and offer some links.
*/
{
struct interaction* intr;
struct nodelist *nl;
if (!getGenesAsList())
{
getGeneList();
return FALSE;
}
if (showAll)
{
puts("
\n");
}
interactions = getGenesFromTable("intrP2P"); /* adds geneList elements to hash */
if (showAll)
{
uglyf("slCount = %d for result list for %s.
\n",slCount(interactions),geneList);
}
/* this might get moved later */
/* add to hash the remaining interactions members */
for(intr=interactions;intr;intr=intr->next)
{
//uglyf("%s %s %f. \n",intr->fromX,intr->toY,intr->score);
struct hashEl *helX = hashStore(nodeHash,intr->fromX);
struct hashEl *helY = hashStore(nodeHash,intr->toY);
struct node *x, *y;
struct nodelist *nl;
if (!helX->val) /* add X to hash for 1st time */
{
AllocVar(x);
AllocVar(nl);
x->name = cloneString(intr->fromX);
nl->node = x;
slAddHead(&allNodes,nl); /* add X to list of all nodes */
helX->val = x;
}
if (!helY->val) /* do same stuff for Y */
{
AllocVar(y);
AllocVar(nl);
y->name = cloneString(intr->toY);
nl->node = y;
slAddHead(&allNodes,nl);
helY->val = y;
}
x = helX->val; /* get X,Y from hash */
y = helY->val;
if (x->ring) y->ringRank++; /* increment ringRank counts */
if (y->ring) x->ringRank++;
AllocVar(nl);
nl->node = y;
slAddHead(&x->xrays,nl); /* add Y to X's list of x-rays */
AllocVar(nl);
nl->node = x;
slAddHead(&y->nrays,nl); /* likewise */
}
interactionFreeList(&interactions);
slReverse(&allNodes);
slSort(&allNodes, compareNodes);
/* sum counts and if showAll, display our structure */
if (showAll)
{
uglyf("
\n");
}
// TODO: add some real code for freeing these things properly
// e.g. for xrays and nrays lists, free up the nodelist list itself,
// but not the *node values themselves, which are allocated
// in the main nodelist/hash. If the nodelist is freed up
// properly then hash freeing should be easy enough.
// Do we use valgrind or some other util to verify mem-release?
return TRUE;
}
/* Count up elements in list that are outside ring. */
int slCountOutside(void *list)
{
struct slList *pt = (struct slList *)list;
int len = 0;
while (pt != NULL)
{
struct node *n = ((struct nodelist *)pt)->node;
if ((!n->ring) && (n->ringRank==1))
len += 1;
pt = pt->next;
}
return len;
}
#define NODE_SIZE 10
void addMap(struct nodelist *nl)
{
struct node *node = nl->node;
int x=node->xpos;
int y=node->ypos;
int r=NODE_SIZE;
char *name = node->name;
if (node->alias)
{
name = node->alias;
}
printf(
"",
x,y,r,
name,
node->name,
name,
name
);
}
void drawScreen()
/*
Draw Gene Ring using given genes and interactions
and display it in a page as a .gif
*/
{
#define SCREEN_SIZE 800
#define RING_SIZE 200
#define INRING_SIZE 140
#define OUTRING_SIZE 340
struct tempName filename;
int width,height;
char *mapName="ring_map";
ZeroVar(&filename);
makeTempName(&filename, "hgGeneRing_screen", ".gif");
printf("\n");
mgSaveGif(mg, filename.forCgi, FALSE);
width=height=SCREEN_SIZE;
printf("