/* Handle details pages for rna fold (evofold) tracks. */

/* 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 "jksql.h"
#include "hgMaf.h"
#include "maf.h"
#include "cart.h"
#include "hgc.h"
#include "hCommon.h"
#include "hgColors.h"
#include "obscure.h"
#include "customTrack.h"
#include "htmshell.h"
#include "rnautil.h"
#include "rnaSecStr.h"
#include "memalloc.h"
#include "hgConfig.h"
#include "pipeline.h"


/* Taken from hgc.c (should probably be in hgc.h)*/
#define RED 0xFF0000
#define GREEN 0x00FF00
#define BLUE 0x0000FF
#define BLACK 0x000000
#define CYAN 0x00FFFF
#define GRAY 0xcccccc
#define LTGRAY 0x999999
#define ORANGE 0xDD6600
#define MAGENTA 0xFF00FF

#define LTPURPLE 0x9966CC
#define SCORE_SHADES_COUNT 10

void printRfamUrl(char *itemName)
/* Print a link to the Rfam entry corresponding to the item. */
{
char *query = cloneString(itemName);
char *end   = strchr(query, '.');
if (!end)
    return;
else
    *end = 0;
printf("<p><A HREF=\"");
printf("http://www.sanger.ac.uk/cgi-bin/Rfam/seqget.pl?name=%s", query);
printf("\" TARGET=_blank>%s</A></p>", itemName);
freeMem(query);
}

void doubleArray2binArray(double *scores, int size, double minScore, double maxScore, int *binArray, int binCount)
/* Will assign a bin to each score in 'scores' and store it in 'binArray' */
{
int i;
for (i = 0; i < size; i++)
    binArray[i] = assignBin(scores[i], minScore, maxScore, binCount);
}

void htmlColorPrintString(FILE *f, char *s, int *colorFormat, int *colors, int L)
/* Prints s to f wrapping characters in html tags for coloring
 * according to colorFormat and colors. colorFormat must be of same
 * length as s. Each position of colorFormat defines which of the
 * colors to use. Use 0 for default color. If L is non-NULL it
 * defines a mximum length to print.*/
{
int i;

if (!L || (L && strlen(s)<L) )
    L = strlen(s);

fprintf(f, "<span style='color:#%06X;'>", colors[0]); /* default color */
for (i = 0; i < L; i++)
    {
    if (colorFormat[i] == 0)
	fprintf(f, "%c", s[i]);
    else
	fprintf(f, "<span style='color:#%06X;'>%c</span>", colors[ colorFormat[i] ], s[i]);
    }
fprintf(f, "</span>");
}

void mafAndFoldHeader(FILE *f)
/* Print header for maf and fold the section*/
{
fprintf(f, "<center><h2> Multiple alignment and RNA secondary structure annotation </h2></center>");
}

void mkPosString(char *s, int size)
/* Make a string-ruler with a decimal every tenth position */
{
int i, d;
for (i = 0, d = 0; i < size; i++)
    if (i%10 == 0)
	{
	s[i] = '0' + d;
	d++;
	if (d == 10)
	  d = 0;
	}
    else
	s[i] = ' ';
s[size] = '\0';
}

char *mkScoreString(double *scores, int L, char *referenceText)
    /* allocate string of score symbols, adjust for gaps in reference sequene */
{
char *s = (char *) needMem(L+1);
char *scoreString = NULL;
int i, n;
for (i=0;i<L;i++)
    {
    n    = floor(10 *scores[i]);
    if (n == 10)
	n = 9;
    if (n < 0 || n > 9)
	errAbort( "Score not between 0 and 1\n" );
    s[i] = '0' + n;
    }
s[L] = 0;
scoreString = gapAdjustFold(s, referenceText);
freeMem(s);
return scoreString;
}

int *mkScoreColorFormat(double *scores, int L, char *referenceText)
  /* allocate string of score colors (gray shades), adjust for gaps in reference sequene */
{
int *v = NULL;
int *scoreColorFormat = NULL;
v = (int *) needMem(L *sizeof(int) );
doubleArray2binArray(scores, L, 0.0, 1.0, v, SCORE_SHADES_COUNT);
scoreColorFormat = gapIntArrayAdjust(v, referenceText);
freeMem(v);
return scoreColorFormat;
}

void defineMafSubstColors(int **p2mafColors)
/* Defines the colors used for maf coloring. Must corrspsond to the
 * markCompensatoryMutations function.*/
{
int *mafColors;
AllocArray(*p2mafColors, 8);
mafColors = *p2mafColors;
mafColors[0]    = LTGRAY;   /* not pairing */
mafColors[1]    = LTPURPLE; /* not pairing, substitution */
mafColors[2]    = BLACK;    /* compatible with pairing */
mafColors[3]    = BLUE;     /* compatible with pairing, single substitution  */
mafColors[4]    = GREEN;    /* compensatory change */
mafColors[5]    = RED;      /* not compatible with fold, single subs */
mafColors[6]    = ORANGE;   /* not compatible with fold, double subs */
mafColors[7]    = MAGENTA;  /* not compatible with fold, involves indel */
}

char *hDbOrganism(char *databaseIn)
/* Function to get organism from the genome db */
{
struct sqlConnection *connCentral = hConnectCentral();
char buf[256];
char query[256];
char *res = NULL;
char *database;
char *chp;

database = cloneString(databaseIn);

// process special case like "hg19.chr21"
chp = strstr(database, ".");
if (chp != NULL)
    {
    *chp = '\0';
    }

sqlSafef(query, sizeof(query), "select organism from dbDb where name = '%s'", database);
if(sqlQuickQuery(connCentral, query, buf, sizeof(buf)) == NULL)
    // this can happen in mirrors (see #8490).
    errAbort("organism '%s' not found in dbDb", database);
else
    res = cloneString(buf);
hDisconnectCentral(&connCentral);
freez(&database);
return res;
}


void htmlPrintMafAndFold(FILE *f, struct mafAli *maf, char *fold, double *scores, int lineSize)
/* HTML pretty print maf and fold to f. If scores is non-null then
 * scores are indicated below alignemnt.*/
{
struct mafComp *mc;
int  i, N, lineStart, lineEnd;
int  *pairList = NULL;
int  *mafColors = NULL;
int  **mafColorFormats = NULL;
int  *scoreColorFormat = NULL;
int  scoreColors[]  = {0x999999,0x888888,0x777777,0x666666,0x555555,0x444444,0x333333,0x222222,0x111111,0x000000};
char *scoreString = 0;
char *pairSymbols;
char *posString, *adjPosString;
char *adjFold;
char foldTag[]       = "SS anno";
char scoresTag[]     = "score  ";
char positionTag[]   = "offset";
char pairSymbolsTag[]= "pair symbol";
char *referenceText  = maf->components->text; /* first sequence in the alignment */
int  srcChars        = max( strlen(foldTag), strlen(pairSymbolsTag));
int  refLength       = strlen(referenceText);
int  foldLength      = strlen(fold);


/* Adjust fold to gap structure in referenceText */
adjFold = gapAdjustFold(fold, referenceText);

/* make arrays for color formatting */
N = slCount(maf->components);
AllocArray(mafColorFormats, N);
for (i = 0; i < N; i++)
    AllocArray(mafColorFormats[i], refLength);
fold2pairingList(adjFold, refLength, &pairList);

for (mc = maf->components, i = 0; mc != NULL; mc = mc->next, i++)
    markCompensatoryMutations(mc->text, referenceText, pairList, mafColorFormats[i]);
defineMafSubstColors(&mafColors);

/* Make pos string */
posString = needMem(foldLength + 1);
mkPosString(posString, foldLength);
adjPosString = gapAdjustFold(posString, referenceText);

/* Make a symbol string indicating pairing partner */
pairSymbols = (char *) needMem(refLength + 1);
mkPairPartnerSymbols(pairList, pairSymbols, refLength);

/* Make the score string and its colorFormat */
if (scores)
     {
     scoreString      = mkScoreString(scores, foldLength, referenceText);
     scoreColorFormat = mkScoreColorFormat(scores, foldLength, referenceText);
     }

/* Find max. length of source (species) field. */
for (mc = maf->components; mc != NULL; mc = mc->next)
    {
    int len = strlen(mc->src)+strlen(hDbOrganism(mc->src)) + 1;
    if (srcChars < len)
        srcChars = len;
    }

/* Pretty print maf and fold */
fprintf(f, "<PRE><TT>");
for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd)
    {
    // int size;  unused variable
    char buf[256];
    lineEnd = lineStart + lineSize;
    if (lineEnd >= maf->textSize)
        lineEnd = maf->textSize;
    // size = lineEnd - lineStart;  unused variable
    fprintf(f, "%-*s %.*s\n", srcChars, positionTag, lineSize, adjPosString + lineStart);
    for (mc = maf->components, i = 0; mc != NULL; mc = mc->next, i++)
        {
	safef(buf, sizeof(buf), "%s/%s", mc->src, hDbOrganism(mc->src));
	fprintf(f, "%-*s ", srcChars, buf);
	htmlColorPrintString(f, mc->text + lineStart, mafColorFormats[i] + lineStart, mafColors, lineSize);
	fprintf(f, "\n");
	}
    fprintf(f, "%-*s %.*s\n", srcChars, foldTag, lineSize, adjFold + lineStart);
    fprintf(f, "%-*s %.*s\n", srcChars, pairSymbolsTag, lineSize, pairSymbols + lineStart);
    if (scores)
	{
	fprintf(f, "%-*s ", srcChars, scoresTag);
	htmlColorPrintString(f, scoreString + lineStart, scoreColorFormat + lineStart, scoreColors, lineSize);
	fprintf(f, "\n");
	}
    fprintf(f, "\n");
    }
fprintf(f, "</PRE></TT>");

/* clean up*/
freeMem(posString);
freeMem(adjPosString);
freeMem(adjFold);
freeMem(pairSymbols);
if (scores)
    {
    freeMem(scoreString);
    freeMem(scoreColorFormat);
    }
for (i = 0; i < N; i++)
    freeMem(mafColorFormats[i]);
freeMem(mafColorFormats);
}

void mafAndFoldLegend(FILE *f)
/* Print legend for the maf and fold section */
{
char *s          = "0123456789";
int colorFormat[] = {0,1,2,3,4,5,6,7,8,9};
int colors[]      = {0x999999,0x888888,0x777777,0x666666,0x555555,0x444444,0x333333,0x222222,0x111111,0x000000};
fprintf(f, "<h3> Color legend </h3>");
fprintf(f, "<TABLE BORDER=0>");
fprintf(f, "<TR> <TD style='color:#%06X;'> GRAY:       </TD> "
           "<TD> Not part of annotated pair, no substitution. <BR>             </TD> </TR>",
           LTGRAY);
fprintf(f, "<TR> <TD style='color:#%06X;'> LT. PURPLE: </TD> "
           "<TD> Not part of annotated pair, substitution. <BR>                </TD> </TR>",
           LTPURPLE);
fprintf(f, "<TR> <TD style='color:#%06X;'> BLACK:      </TD> "
           "<TD> Compatible with annotated pair, no substitutions.<BR>         </TD> </TR>",
           BLACK);
fprintf(f, "<TR> <TD style='color:#%06X;'> BLUE:       </TD> "
           "<TD> Compatible with annotated pair, single substitution.<BR>      </TD> </TR>",
           BLUE);
fprintf(f, "<TR> <TD style='color:#%06X;'> GREEN:      </TD> "
           "<TD> Compatible with annotated pair, double substitution.<BR>      </TD> </TR>",
           GREEN);
fprintf(f, "<TR> <TD style='color:#%06X;'> RED:        </TD> "
           "<TD> Not compatible with annotated pair, single substitution. <BR> </TD> </TR>",
           RED);
fprintf(f, "<TR> <TD style='color:#%06X;'> ORANGE:     </TD> "
           "<TD> Not compatible with annotated pair, double substitution. <BR> </TD> </TR>",
           ORANGE);
fprintf(f, "<TR> <TD style='color:#%06X;'> MAGENTA:    </TD> "
           "<TD> Not compatible with annotated pair, involves gap. <BR>        </TD> </TR>",
           MAGENTA);
fprintf(f, "</TABLE>");
/* Score legend */
fprintf(f, "<BR>SCORE:   min ");
htmlColorPrintString(f, s, colorFormat, colors, 0);
fprintf(f, " max");
}

struct mafAli *mafFromRnaSecStrItem(char *mafTrack, struct rnaSecStr *item)
{
struct mafAli *maf;
maf = hgMafFrag(database, mafTrack, item->chrom, item->chromStart, item->chromEnd, item->strand[0], NULL, NULL);
return maf;
}

void mafSortBySpeciesOrder(struct mafAli *maf, char *speciesOrder)
/* Sort maf components by species. Excised from mafClick.c. */
{
int speciesCt;
char *species[256];
struct mafComp **newOrder, *mcThis;
int i;
int mcCount;

mcCount = 0;
speciesCt = chopLine(cloneString(speciesOrder), species);
newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *));
newOrder[mcCount++] = maf->components;

for (i = 0; i < speciesCt; i++)
  {
    if ((mcThis = mafMayFindCompSpecies(maf, species[i], '.')) == NULL)
	continue;
    newOrder[mcCount++] = mcThis;
  }

maf->components = NULL;
for (i = 0; i < mcCount; i++)
  {
    newOrder[i]->next = 0;
    slAddHead(&maf->components, newOrder[i]);
  }

slReverse(&maf->components);
}

void htmlPrintSecStr(FILE *f, char *table, struct rnaSecStr *item, int start)
/* Print out the details for an rnaStruct* table. */
{
// grab the sequence
struct dnaSeq *seq = hChromSeq(database, item->chrom, item->chromStart, item->chromEnd);
touppers(seq->dna);
if (item->strand[0] == '-')
    reverseComplement(seq->dna, seq->size);
toRna(seq->dna);

// make sure the dna is not longer than the paren string
seq->dna[strlen(item->secStr)] = 0;

char *rnaPlotPath = cfgOptionDefault("rnaPlotPath", "../cgi-bin/RNAplot");
mkdirTrashDirectory(table);

char psName[512];
safef(psName, sizeof(psName), "../trash/%s/%s_%s.ps", table, table, item->name);
char *plotCmd[] = {rnaPlotPath, NULL};
struct pipeline *plStruct = pipelineOpen1(plotCmd, pipelineWrite | pipelineNoAbort, "/dev/null", NULL, 0);
FILE *of = pipelineFile(plStruct);
if (of != NULL)
    {
    fprintf(of, ">%s\n", psName);        /* This tells where to put file. */
    fprintf(of, "%s\n%s\n", seq->dna, item->secStr);
    }
pipelineClose(&plStruct);

char pngName[256];
char *rootName = cloneString(psName);
 
chopSuffix(rootName);
safef(pngName, sizeof(pngName), "%s.png", rootName);

char outputBuf[1024];
safef(outputBuf, sizeof outputBuf, "-sOutputFile=%s", pngName);
char *pipeCmd[] = {"gs", "-sDEVICE=png16m", outputBuf, "-dBATCH","-dNOPAUSE","-q", psName, NULL};
struct pipeline *pl = pipelineOpen1(pipeCmd, pipelineWrite | pipelineNoAbort, "/dev/null", NULL, 0);
int sysRet = pipelineWait(pl);
if (sysRet != 0)
    errAbort("System call returned %d for:\n  %s", sysRet, pipelineDesc(pl));

printf("<a target=blank href='http://pseudoviewer.inha.ac.kr/WSPV_quickSender.asp?seq=%s&str=%s&start=%d'>Display on PseudoViewer</a><BR>", seq->dna, item->secStr, start);
htmlHorizontalLine();
printf("RNAFold diagram:<BR>");
printf("<IMG SRC='%s' border = '2'>", pngName);
}

void htmlPrintSecStrEvofoldDrawing(FILE *f, struct rnaSecStr *item)
{
char fileName[512];
struct dnaSeq *seq;
seq = hChromSeq(database, item->chrom, item->chromStart, item->chromEnd);
touppers(seq->dna);
if (item->strand[0] == '-')
    reverseComplement(seq->dna, seq->size);
memSwapChar(seq->dna, seq->size, 'T', 'U');

safef(fileName, sizeof(fileName), "/gbdb/%s/evoFold/%s/%s.png",
       database, item->chrom, item->name);
if (fileExists(fileName))
    {
    fprintf(f, "<center><h2> RNA secondary structure drawing </h2></center>");
    fprintf(f,"<B>");

    // Could consider to serve up all EvoFold .png files from our public server in the future
    // fprintf(f,"<IMG SRC=\"http://genome.ucsc.edu/evoFold/%s/%s/%s.png\" border = '2' "
    //           "ALT=\"ERROR: VARA plotting failed.\"</B><BR>",
    fprintf(f,"<IMG SRC=\"../evoFold/%s/%s/%s.png\" border = '2' ALT=\"ERROR: symlink to file not found.\"</B><BR>",
            database, item->chrom, item->name);
    fprintf(f,"</B>");
    }

freeMem(seq);
printf("<p>The UCSC Genome Browser mirror site at the Molecular Diagnostic Laboratory (MDL) at Aarhus University Hospital Skejby in Denmark offers a VARNA Java applet to view the above RNA structure with more options, ");
printf("<A HREF=\"");
printf("http://genome-mirror.moma.ki.au.dk/cgi-bin/hgc?db=%s&c=%s&l=%d&r=%d&o=%d&t=%d"
        "&g=evofold&i=%s",database, item->chrom, item->chromStart, item->chromEnd, 
        item->chromStart, item->chromEnd, cgiEncode(item->name)); 
        // c, l and r are needed because mirror may have no cart for us. Not actually used, however.
printf("\" TARGET=_blank>%s</A>.", "click here to go to genome-mirror.moma.ki.au.dk");
fprintf(f,"  <B><FONT COLOR = RED>NOTE:</FONT> some operating system/browser combinations require ");
fprintf(f," the latest version of Java for this to work properly.</FONT></B></P>");
}

void htmlPrintSecStrEvofoldV2Drawing(FILE *f, struct rnaSecStr *item)
{
char fileName[512];
struct dnaSeq *seq;
seq = hChromSeq(database, item->chrom, item->chromStart, item->chromEnd);
touppers(seq->dna);
if (item->strand[0] == '-')
    reverseComplement(seq->dna, seq->size);
memSwapChar(seq->dna, seq->size, 'T', 'U');

safef(fileName, sizeof(fileName), "/gbdb/%s/evoFoldV2/%s/%s.png",
       database, item->chrom, item->name);
if (fileExists(fileName))
    {
    fprintf(f, "<center><h2> RNA secondary structure drawing </h2></center>");
    fprintf(f,"<B>");

    // Could consider to serve up all EvoFold .png files from our public server in the future
    // fprintf(f,"<IMG SRC=\"http://genome.ucsc.edu/evoFold/%s/%s/%s.png\" border = '2' ALT=\"ERROR: VARA plotting failed.\"</B><BR>",
    fprintf(f,"<IMG SRC=\"../evoFoldV2/%s/%s/%s.png\" border = '2' ALT=\"ERROR:  symlink to file not found.\"</B><BR>",
            database, item->chrom, item->name);
    fprintf(f,"</B>");
    }

freeMem(seq);
printf("<p>The UCSC Genome Browser mirror site at the Molecular Diagnostic Laboratory (MDL) at Aarhus University Hospital Skejby in Denmark offers a VARNA Java applet to view the above RNA structure with more options, ");
printf("<A HREF=\"");
printf("http://genome-mirror.moma.ki.au.dk/cgi-bin/hgc?db=%s&c=%s&l=%d&r=%d&o=%d&t=%d"
        "&g=evofoldV2&i=%s", database, item->chrom, item->chromStart, item->chromEnd, 
        item->chromStart, item->chromEnd, cgiEncode(item->name));  
        // c, l and r are needed because mirror may have no cart for us. Not actually used, however.
printf("\" TARGET=_blank>%s</A>.", "click here to go to genome-mirror.moma.ki.au.dk");
fprintf(f," <B><FONT COLOR = RED>NOTE:</FONT> some operating system/browser combinations require ");
fprintf(f," the latest version of Java for this to work properly.</FONT></B></P>");
}

void doRnaSecStr(struct trackDb *tdb, char *itemName)
/* Handle click on rnaSecStr type elements. */
{
char *table = tdb->table;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
struct rnaSecStr *item;
char extraWhere[256];
char **row;
int  rowOffset = 0;
char *mafTrack = trackDbSetting(tdb, "mafTrack");
int start = cartInt(cart, "o");
struct mafAli *maf = NULL;
char option[128];
char *speciesOrder = NULL;
boolean hasConf = sqlColumnExists(conn, table, "conf");

/* print header */
genericHeader(tdb, itemName);
/* printRfamUrl(itemName); */
genericBedClick(conn, tdb, itemName, start, 6);

/* get the rnaSecStr and maf from db */
sqlSafef(extraWhere, sizeof extraWhere, "chromStart = %d and name = '%s'", start, itemName);
sr   = hExtendedChromQuery(conn, table, seqName, extraWhere,  FALSE, NULL, &rowOffset);
row  = sqlNextRow(sr);
if (hasConf)
    item = rnaSecStrLoadConf(row + rowOffset);
else
    item = rnaSecStrLoad(row + rowOffset);
if (mafTrack)
    {
    htmlHorizontalLine();
    maf  = mafFromRnaSecStrItem(mafTrack, item);

    /* order maf by species */
    safef(option, sizeof(option), "%s.speciesOrder", tdb->track);
    speciesOrder = cartUsualString(cart, option, NULL);
    if (speciesOrder == NULL)
      speciesOrder = trackDbSetting(tdb, "speciesOrder");
    if (speciesOrder)
      mafSortBySpeciesOrder(maf, speciesOrder);

    mafAndFoldHeader(stdout);
    htmlPrintMafAndFold(stdout, maf, item->secStr, item->conf, 100);

    mafAndFoldLegend(stdout);
    }

/* Draw structure for rnaStruct* table */
if (startsWith("rnaStruct", tdb->table))
    {
    htmlHorizontalLine();
    htmlPrintSecStr(stdout, tdb->table, item, start);
    }
if (sameWord(tdb->table, "evofold"))
    {
    htmlHorizontalLine();
    htmlPrintSecStrEvofoldDrawing(stdout, item);
    }

/* Draw structure for evoFoldV2 */
if (sameWord(tdb->table, "evofoldV2"))
    {
    htmlHorizontalLine();
    htmlPrintSecStrEvofoldV2Drawing(stdout, item);
    }

/* track specific html */
printTrackHtml(tdb);

/* clean up */
mafAliFree(&maf);
rnaSecStrFree(&item);
sqlFreeResult(&sr);
hFreeConn(&conn);
}