// Code to create hgTracks menu bar

/* Copyright (C) 2014 The Regents of the University of California 
 * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */

#include "common.h"
#include "dystring.h"
#include "ensFace.h"
#include "agpFrag.h"
#include "ctgPos.h"
#include "hCommon.h"
#include "htmshell.h"
#include "hash.h"
#include "wikiLink.h"
#include "web.h"
#include "geoMirror.h"
#include "hgTracks.h"
#include "trackHub.h"
#include "extTools.h"
#include "trackVersion.h"
#include "chromAlias.h"

/* list of links to display in a menu */
/* a link with an empty name is displayed as a horizontal separator line */
struct hotLink
    {
    struct hotLink *next;
    char *name;
    char *url;
    char *id;
    char *mouseOver;
    char *onClick;
    char *shortcut;
    boolean inactive; /* greyed out */
    boolean external;
    };

static void appendLink(struct hotLink **links, char *url, char *name, char *id, boolean external)
{
// append to list of links for later printing and/or communication with javascript client
struct hotLink *link;
AllocVar(link);
link->name = cloneString(name);
link->url = cloneString(url);
link->id = cloneString(id);
link->external = external;
link->inactive = FALSE;
slAddTail(links, link);
}

static void appendLinkMaybeInactive(struct hotLink **links, char *url, char *name, char *id, 
    char *mouseOver, boolean external, boolean inactive)
{
appendLink(links, url, name, id, external);
struct hotLink *le = slLastEl(links);
le->inactive=inactive;
le->mouseOver=mouseOver;
}

static void appendLinkWithOnclick(struct hotLink **links, char *url, char *name, char *id, 
    char *mouseOver, char *onClick, char *shortcut, boolean external, boolean inactive)
{
appendLinkMaybeInactive(links, url, name, id, mouseOver, external, inactive);
struct hotLink *le = slLastEl(links);
le->onClick=onClick;
le->shortcut=shortcut;
}

static void appendLinkWithShortcut(struct hotLink **links, char *url, char *name, char *id, 
    char *mouseOver, char *shortcut, boolean external, boolean inactive)
{
appendLinkMaybeInactive(links, url, name, id, mouseOver, external, inactive);
struct hotLink *le = slLastEl(links);
le->shortcut=shortcut;
}

static void printEnsemblAnchor(char *database, char* archive,
                               char *chrName, int start, int end, struct hotLink **links)
/* Print anchor to Ensembl display on same window. */
{
char *scientificName = hScientificName(database);
char *dir = ensOrgNameFromScientificName(scientificName);
struct dyString *ensUrl;
char *name;
int localStart, localEnd;

name = chrName;

if (sameWord(scientificName, "Takifugu rubripes"))
    {
    /* for Fugu, must give scaffold, not chr coordinates */
    /* Also, must give "chrom" as "scaffold_N", name below. */
    if (differentWord(chromName,"chrM") &&
    !hScaffoldPos(database, chromName, winStart, winEnd,
                        &name, &localStart, &localEnd))
        /* position doesn't appear on Ensembl browser.
         * Ensembl doesn't show scaffolds < 2K */
        return;
    }
else if (sameWord(scientificName, "Gasterosteus aculeatus"))
    {
    if (differentWord("chrM", chrName))
    {
    char *fixupName = replaceChars(chrName, "chr", "group");
    name = fixupName;
    }
    }
else if (sameWord(scientificName, "Ciona intestinalis"))
    {
    if (stringIn("chr0", chrName))
	{
	char *fixupName = replaceChars(chrName, "chr0", "chr");
	name = fixupName;
	}
    }
else if (sameWord(scientificName, "Saccharomyces cerevisiae"))
    {
    if (stringIn("2micron", chrName))
	{
	char *fixupName = replaceChars(chrName, "2micron", "2-micron");
	name = fixupName;
	}
    }

if (sameWord(chrName, "chrM"))
    name = "chrMt";
ensUrl = ensContigViewUrl(database, dir, name, seqBaseCount, start+1, end, archive);
appendLink(links, ensUrl->string, "Ensembl", "ensemblLink", TRUE);
/* NOTE: you can not freeMem(dir) because sometimes it is a literal
 * constant */
freeMem(scientificName);
dyStringFree(&ensUrl);
}

static void fr2ScaffoldEnsemblLink(char *archive, struct hotLink **links)
/* print out Ensembl link to appropriate scaffold there */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr = NULL;
char **row = NULL;
char query[256];
sqlSafef(query, sizeof(query),
"select * from chrUn_gold where chrom = '%s' and chromStart<%u and chromEnd>%u",
chromName, winEnd, winStart);
sr = sqlGetResult(conn, query);

int itemCount = 0;
struct agpFrag *agpItem = NULL;
while ((row = sqlNextRow(sr)) != NULL)
    {
    agpFragFree(&agpItem);  // if there is a second one
    agpItem = agpFragLoad(row+1);
    ++itemCount;
    if (itemCount > 1)
	break;
    }
sqlFreeResult(&sr);
hFreeConn(&conn);
if (1 == itemCount)
    {   // verify *entirely* within single contig
    if ((winEnd <= agpItem->chromEnd) &&
	(winStart >= agpItem->chromStart))
	{
	int agpStart = winStart - agpItem->chromStart;
	int agpEnd = agpStart + winEnd - winStart;
	printEnsemblAnchor(database, archive, agpItem->frag,
                           agpStart, agpEnd, links);
	}
    }
agpFragFree(&agpItem);  // the one we maybe used
}

void freeLinksAndConvert(struct hotLink *links, struct dyString *menuHtml)
/* convert the links to html strings and append to the dyString "menu", destroying the links */
{
int len = slCount(links);
int i = 0;
struct hotLink *link = NULL;
for(i = 0, link = links; link != NULL; i++, link = link->next)
    {
    char class[100];
    if(i == 0)
        safef(class, sizeof(class), "first");
    else if (i + 1 == len)
        safef(class, sizeof(class), "last");
    else if (isEmpty(link->name))
        safef(class, sizeof(class), "horizSep");
    else
        class[0] = 0;
    dyStringAppend(menuHtml, "<li");
    char *encodedName = htmlEncode(link->name);
    if(*class)
        dyStringPrintf(menuHtml, " class='%s'", class);
    dyStringPrintf(menuHtml, ">\n");

    if (!isEmpty(link->name))
        {
        dyStringPrintf(menuHtml, "<a href='%s'", link->url);
        if (link->mouseOver)
            dyStringPrintf(menuHtml, " title='%s'", link->mouseOver); 
        if (link->onClick)
	    {
	    jsOnEventById("click", link->id, link->onClick);
	    }
        dyStringPrintf(menuHtml, " id='%s'", link->id);
	if (link->external)
	    dyStringAppend(menuHtml, " TARGET='_blank'");
        dyStringPrintf(menuHtml, ">%s</a>\n", encodedName);
        }
    if (!isEmpty(link->shortcut))
        dyStringPrintf(menuHtml, "<span class='shortcut'>%s</span>", link->shortcut);

    dyStringPrintf(menuHtml, "</li>\n");
    freez(&encodedName);

    freez(&link->name);
    freez(&link->url);
    freez(&link->id);
    }
slFreeList(links);
}

void printMenuBar()
/* Put up the special menu bar for hgTracks. */
{
struct hotLink *links = NULL;
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
    conn = hAllocConn(database);
char *menuStr, buf[4096], uiVars[1024];
safef(uiVars, sizeof(uiVars), "%s=%s", cartSessionVarName(), cartSessionId(cart));

menuStr = menuBar(cart, database);

/* hide Projects dropdown (just used by static and gateway pages */
menuStr = replaceChars(menuStr, "<!-- OPTIONAL_PROJECT_MENU_START -->", "<!-- OPTIONAL_PROJECT_MENU_START");
menuStr = replaceChars(menuStr, "<!--OPTIONAL_PROJECT_MENU_END -->", "OPTIONAL_PROJECT_MENU_END -->");

// Add Recommended Track Sets to Genome Browser menu (if any for this assembly)
// TODO: consider splitting the recommended track sets config file into separate files by database,
//       so we don't need to read file to see whether to add menu item
if (recTrackSetsEnabled() && recTrackSetsForDb())
    {
    #define recTrackSetsMenuItemId     "recTrackSetsMenuItem"
    struct dyString *menuItemDs = dyStringCreate("<li><a href='#' id='%s'>Recommended Track Sets</a></li>",
                                       recTrackSetsMenuItemId);
    menuStr = replaceChars(menuStr, "<!-- OPTIONAL_RECOMMENDED_TRACK_SETS_MENU -->", 
                                dyStringCannibalize(&menuItemDs));
    if (stringIn(recTrackSetsMenuItemId, menuStr))
        jsOnEventById("click", recTrackSetsMenuItemId, "showRecTrackSetsPopup(); return false;");
    }

// Create top items in view menu
safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.psOutput=on", uiVars);
appendLink(&links, buf, "PDF", "pdfLink", FALSE);
safef(buf, sizeof(buf), "%s&o=%d&g=getDna&i=mixed&c=%s&l=%d&r=%d&db=%s&%s",
      hgcNameAndSettings(), winStart, chromName, winStart, winEnd, database, uiVars);
//appendLink(&links, buf, "DNA", "dnaLink", FALSE);
appendLinkWithShortcut(&links, buf, "DNA", "dnaLink", "Show DNA sequence in view", "v d", FALSE, FALSE);
safef(buf, sizeof(buf), "../cgi-bin/hgConvert?hgsid=%s&db=%s", cartSessionId(cart), database);
appendLink(&links, buf, "In Other Genomes (Convert)", "convertMenuLink", FALSE);

// add the sendTo menu
if (fileExists("extTools.ra"))
    {
    appendLinkWithOnclick(&links, "#", "In External Tools", "extToolLink", "Show current sequence on a third-party website", "showExtToolDialog(); return false;", "s t", FALSE, FALSE);
    }


// Add link-outs to other dbs as appropriate for this assembly
if (differentWord(database,"susScr2"))
    {
    /* Print Ensembl anchor for latest assembly of organisms we have
     * supported by Ensembl == if versionString from trackVersion exists */
    struct trackVersion *trackVersion = getTrackVersion(database, "ensGene");

    if ((conn != NULL) && sqlTableExists(conn, UCSC_TO_ENSEMBL))
        printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links);
    else if (sameWord(database,"hg19"))
        {
        printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links);
        }
    else if (sameWord(database,"hg18"))
        {
        printEnsemblAnchor(database, "ncbi36", chromName, winStart, winEnd, &links);
        }
    else if (sameWord(database,"oryCun2") || sameWord(database,"anoCar2") || sameWord(database,"calJac3"))
        {
        printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links);
        }
    else if ((trackVersion != NULL) && !isEmpty(trackVersion->version))
        {
        char *archive = NULL;
        if (!isEmpty(trackVersion->dateReference) && differentWord("current", trackVersion->dateReference))
            archive = cloneString(trackVersion->dateReference);
        /*  Can we perhaps map from a UCSC random chrom to an Ensembl contig ? */
        if (isUnknownChrom(database, chromName))
            {
            //	which table to check
            char *ctgPos = "ctgPos";

            if (sameWord(database,"fr2"))
                fr2ScaffoldEnsemblLink(archive, &links);
            else if (hTableExists(database, UCSC_TO_ENSEMBL))
                printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links);
            else if (hTableExists(database, ctgPos))
                /* see if we are entirely within a single contig */
                {
                struct sqlResult *sr = NULL;
                char **row = NULL;
                char query[256];
                sqlSafef(query, sizeof(query),
                      "select * from %s where chrom = '%s' and chromStart<%u and chromEnd>%u",
                      ctgPos, chromName, winEnd, winStart);
                sr = sqlGetResult(conn, query);

                int itemCount = 0;
                struct ctgPos *ctgItem = NULL;
                while ((row = sqlNextRow(sr)) != NULL)
                    {
                    ctgPosFree(&ctgItem);   // if there is a second one
                    ctgItem = ctgPosLoad(row);
                    ++itemCount;
                    if (itemCount > 1)
                        break;
                    }
                sqlFreeResult(&sr);
                if (1 == itemCount)
                    {   // verify *entirely* within single contig
                    if ((winEnd <= ctgItem->chromEnd) &&
                        (winStart >= ctgItem->chromStart))
                        {
                        int ctgStart = winStart - ctgItem->chromStart;
                        int ctgEnd = ctgStart + winEnd - winStart;
                        printEnsemblAnchor(database, archive, ctgItem->contig,
                                           ctgStart, ctgEnd, &links);
                        }
                    }
                ctgPosFree(&ctgItem);   // the one we maybe used
                }
            }
        else
            {
            printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links);
            }
        }
    }
hFreeConn(&conn);

char *gcfId = hNcbiGcfId(database);
char *gcaId = hNcbiGcaId(database);
if (isNotEmpty(gcfId))	/* GCF has priority over GCA */
    {
    char *ncbiChr = chromAliasNCBI(database, chromName, gcfId);
    safef(buf, sizeof(buf),
          "https://www.ncbi.nlm.nih.gov/genome/gdv/browser/"
          "?context=genome&acc=%s&chr=%s&from=%d&to=%d",
          gcfId, ncbiChr, winStart+1, winEnd);
    appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
    }
else if (isNotEmpty(gcaId))
    {
    char *ncbiChr = chromAliasNCBI(database, chromName, gcaId);
    safef(buf, sizeof(buf),
          "https://www.ncbi.nlm.nih.gov/genome/gdv/browser/"
          "?context=genome&acc=%s&chr=%s&from=%d&to=%d",
          gcaId, ncbiChr, winStart+1, winEnd);
    appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
    }
else if (startsWith("oryLat", database))
    {
    safef(buf, sizeof(buf), "http://medaka.utgenome.org/browser_ens_jump.php?revision=version1.0&chr=chromosome%s&start=%d&end=%d",
          skipChr(chromName), winStart+1, winEnd);
    appendLink(&links, buf, "UTGB", "medakaLink", TRUE);
    }
else if (sameString(database, "cb3"))
    {
    safef(buf, sizeof(buf), "http://www.wormbase.org/db/seq/gbrowse/briggsae?name=%s:%d-%d",
          skipChr(chromName), winStart+1, winEnd);
    appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
    }
else if (sameString(database, "cb4"))
    {
    safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_briggsae?name=%s:%d-%d",
          chromName, winStart+1, winEnd);
    appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
    }
else if (sameString(database, "ce10"))
    {
    safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_elegans?name=%s:%d-%d",
          skipChr(chromName), winStart+1, winEnd);
    appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
    }
else if (sameString(database, "ce4"))
    {
    safef(buf, sizeof(buf), "http://ws170.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d",
          skipChr(chromName), winStart+1, winEnd);
    appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
    }
else if (sameString(database, "ce2"))
    {
    safef(buf, sizeof(buf), "http://ws120.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d",
          skipChr(chromName), winStart+1, winEnd);
    appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
    }

// finish View menu
appendLink(&links, "", "", "", FALSE); // separator line
safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgTracksConfigPage=configure", uiVars);
appendLinkWithShortcut(&links, buf, "Configure Browser", "configureMenuLink", "Open configuration menu", "c f", FALSE, FALSE);

// multi-region
appendLinkWithOnclick(&links, "#", "Multi-Region", "multiRegionLink", "Show multi-region options", "popUpHgt.hgTracks('multi-region config'); return false;", "", FALSE, FALSE);

safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.reset=on", uiVars);
appendLinkWithShortcut(&links, buf, "Default Tracks", "defaultTracksMenuLink", "Show only default tracks", "d t", FALSE, FALSE);
safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.defaultImgOrder=on", uiVars);
appendLinkWithShortcut(&links, buf, "Default Track Order", "defaultTrackOrderMenuLink", "Re-order tracks to be in default order", "d o", FALSE, FALSE);
appendLinkWithOnclick(&links, "#", "Remove all highlights", "cleaerHighlightLink", "Remove all highlights on all genomes", "highlightCurrentPosition('clear'); $('ul.nice-menu li ul').hide();", "h c", FALSE, FALSE);
appendLinkWithShortcut(&links, "../cgi-bin/cartReset", "Reset All User Settings", "cartResetMenuLink", "Clear user data, e.g. active tracks, track configuration, custom data, ...", "c r", FALSE, FALSE);

struct dyString *viewMenu = dyStringCreate("<li class='menuparent' id='view'><span>View</span>\n<ul>\n");
freeLinksAndConvert(links, viewMenu);
dyStringAppend(viewMenu, "</ul>\n</li>\n");

menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", dyStringCannibalize(&viewMenu));
menuStr = replaceChars(menuStr, "id=\"main-menu-whole\"", "id=\"hgTracks-main-menu-whole\"");
menuStr = replaceChars(menuStr, "id=\"home-link\"", "id=\"hgTracks-home-link\"");


hPuts(menuStr);
freez(&menuStr);

}