/* joinedRmskClick - Click handler for joinedRmskTrack.  This is based
 *                   loosely on the original rmsk click handler inside
 *                   of hgc.c.
 *
 *  Written by Robert Hubley 12/2012
 */

/* 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 "hgc.h"
#include "rmskOut2.h"
#include "rmskAlign.h"
#include "rmskJoined.h"
#include "hCommon.h"


void printAlignment (struct rmskAlign *ra)
/*
 * Print RepeatMasker alignment data stored in RM's cAlign format.
 * The format is basically a lightly compressed diff format where
 * the query and subject are merged into one squence line. The
 * runs of exact matching sequences are interrupted by either
 * single base substitutions annotated as queryBase "/" subjectBase,
 * insertions in the subject annotated as "+ACTAT+", or deletions
 * in the query annotated as "-ACTTTG-".
 */
{
int alignLength = 80;
char querySeq[alignLength + 1];
char diffSeq[alignLength + 1];
char subjSeq[alignLength + 1];
int inSub = 0;
int inDel = 0;
int inIns = 0;

int aIdx = 0;
int sIdx = 0;
int qCnt = 0;
int sCnt = 0;
int qStart = ra->genoStart;
int sStart = ra->repStart;
if (ra->strand[0] == '-')
    sStart = ra->repEnd;

int maxNameLen =
    (strlen (ra->genoName) >
     strlen (ra->repName) ? strlen (ra->genoName) : strlen (ra->repName));

while (ra->alignment[aIdx] != '\0')
    {
    if (ra->alignment[aIdx] == '/')
        inSub = 1;
    else if (ra->alignment[aIdx] == '-')
        inDel ^= 1;
    else if (ra->alignment[aIdx] == '+')
        inIns ^= 1;
    else
	{
	if (inSub)
	    {
	    subjSeq[sIdx - 1] = ra->alignment[aIdx];
	    if ((querySeq[sIdx - 1] == 'C' &&
		 subjSeq[sIdx - 1] == 'T') ||
		(querySeq[sIdx - 1] == 'T' &&
		 subjSeq[sIdx - 1] == 'C') ||
		(querySeq[sIdx - 1] == 'A' &&
		 subjSeq[sIdx - 1] == 'G') ||
		(querySeq[sIdx - 1] == 'G' && subjSeq[sIdx - 1] == 'A'))
	    diffSeq[sIdx - 1] = 'i';
	    else if ((index ("BDHVRYKMSWNX", querySeq[sIdx - 1]) != NULL) ||
		     (index ("BDHVRYKMSWNX", subjSeq[sIdx - 1]) != NULL))
	        diffSeq[sIdx - 1] = '?';
	    else
	        diffSeq[sIdx - 1] = 'v';
	    inSub = 0;
	    }
	else if (inDel)
	    {
	    querySeq[sIdx] = ra->alignment[aIdx];
	    subjSeq[sIdx] = '-';
	    diffSeq[sIdx] = '-';
	    qCnt++;
	    sIdx++;
	    }
	else if (inIns)
	    {
	    querySeq[sIdx] = '-';
	    subjSeq[sIdx] = ra->alignment[aIdx];
	    diffSeq[sIdx] = '-';
	    sCnt++;
	    sIdx++;
	    }
	else
	    {
	    diffSeq[sIdx] = ' ';
	    querySeq[sIdx] = ra->alignment[aIdx];
	    subjSeq[sIdx] = ra->alignment[aIdx];
	    sCnt++;
	    qCnt++;
	    sIdx++;
	    }
	if (sIdx == alignLength)
	    {
	    querySeq[sIdx] = '\0';
	    diffSeq[sIdx] = '\0';
	    subjSeq[sIdx] = '\0';
	    printf ("%*s %10d %s %d\n", maxNameLen, ra->genoName, qStart,
		    querySeq, (qStart + qCnt - 1));
	    printf ("%*s            %s\n", maxNameLen, " ", diffSeq);
	    if (ra->strand[0] == '+')
	        printf ("%*s %10d %s %d\n", maxNameLen, ra->repName, sStart,
		    subjSeq, (sStart + sCnt - 1));
	    else
	        printf ("%*s %10d %s %d\n", maxNameLen, ra->repName, sStart,
		    subjSeq, (sStart - sCnt + 1));
	    printf ("\n");
	    qStart += qCnt;
	    if (ra->strand[0] == '+')
	        sStart += sCnt;
	    else
	        sStart -= sCnt;
	    qCnt = 0;
	    sCnt = 0;
	    sIdx = 0;
	    }
	}
    aIdx++;
    }
if (sIdx)
    {
    querySeq[sIdx] = '\0';
    diffSeq[sIdx] = '\0';
    subjSeq[sIdx] = '\0';
    printf ("%*s %10d %s %d\n", maxNameLen, ra->genoName, qStart, querySeq,
	    (qStart + qCnt - 1));
    printf ("%*s            %s\n", maxNameLen, " ", diffSeq);
    if (ra->strand[0] == '+')
        printf ("%*s %10d %s %d\n", maxNameLen, ra->repName, sStart, subjSeq,
	    (sStart + sCnt - 1));
    else
        printf ("%*s %10d %s %d\n", maxNameLen, ra->repName, sStart, subjSeq,
	    (sStart - sCnt + 1));
    ;
    }
}

void printOutTableHeader (char strand)
/* Print the appropriate HTML table header
 * given the strand of the element.
 */
{
const char *hd1_style =
    "style=\"background-color:#C2C9E0; font-size:14px; padding:4px 14px;\"";
const char *hd1span_style =
    "style=\"background-color:#6678B1; font-size:14px; padding:4px 14px;\"";
const char *hd2_style =
    "style=\"background-color:#C2C9E0; font-size:14px; padding:4px 14px; "
    "border-bottom: 2px solid #6678B1;\"";
printf ("  <thead>\n");
printf ("    <tr>\n");
printf ("      <th %s>bit/sw</th>\n", hd1_style);
printf ("      <th %s>perc</th>\n", hd1_style);
printf ("      <th %s>perc</th>\n", hd1_style);
printf ("      <th %s>perc</th>\n", hd1_style);
printf ("      <th colspan=\"4\" %s>query</th>\n", hd1span_style);
printf ("      <th %s></th>\n", hd1_style);
printf ("      <th colspan=\"5\" %s>matching repeat</th>\n", hd1span_style);
printf ("      <th %s></th>\n", hd1_style);
printf ("    </tr>\n");
printf ("    <tr>\n");
printf ("      <th %s>score</th>\n", hd2_style);
printf ("      <th %s>div.</th>\n", hd2_style);
printf ("      <th %s>del.</th>\n", hd2_style);
printf ("      <th %s>ins.</th>\n", hd2_style);
printf ("      <th %s>sequence</th>\n", hd2_style);
printf ("      <th %s>begin</th>\n", hd2_style);
printf ("      <th %s>end</th>\n", hd2_style);
printf ("      <th %s>remaining</th>\n", hd2_style);
printf ("      <th %s>orient.</th>\n", hd2_style);
printf ("      <th %s>name</th>\n", hd2_style);
printf ("      <th %s>class/family</th>\n", hd2_style);
if (strand == 'C')
    {
    printf ("      <th %s>remaining</th>\n", hd2_style);
    printf ("      <th %s>end</th>\n", hd2_style);
    printf ("      <th %s>begin</th>\n", hd2_style);
    }
else
    {
    printf ("      <th %s>begin</th>\n", hd2_style);
    printf ("      <th %s>end</th>\n", hd2_style);
    printf ("      <th %s>remaining</th>\n", hd2_style);
    }
printf ("      <th %s>id</th>\n", hd2_style);
printf ("    </tr>\n");
printf ("  </thead>\n");
}


void doJRepeat (struct trackDb *tdb, char *repeat)
/* Main entry point */
{
const char *data_style = "style=\"padding:0px 6px;\"";
char *table = (tdb ? tdb->table : tdb->track);
char outTable[64];
char alignTable[64];

/* Currently using a fixed table name design
 * with support for two datasets ( baseline and current ).
 * The baseline dataset is the run which all the other
 * tracks are based upon.  The current can be any more
 * recent run of RepeatMasker.
 */
if (startsWith ("rmskJoinedCurrent", table))
    {
    strcpy (alignTable, "rmskAlignCurrent");
    strcpy (outTable, "rmskOutCurrent");
    }
else if (startsWith ("rmskJoinedBaseline", table))
    {
    strcpy (alignTable, "rmskAlignBaseline");
    strcpy (outTable, "rmskOutBaseline");
    }

cartWebStart (cart, database, "%s", tdb->longLabel);

int offset = cartInt (cart, "o");
if (offset >= 0)
    {
    struct sqlConnection *conn2 = hAllocConn (database);
    struct sqlResult *sr2;
    char **row;
    char query[256];
    char qTable[HDB_MAX_TABLE_STRING];
    boolean hasBin;

    int start = cartInt (cart, "o");

    if (hTableExists (database, table))
	{
	if (!hFindSplitTable (database, seqName, table, qTable, sizeof(qTable), &hasBin))
	    errAbort("track %s not found", table);
    
	sqlSafef (query, sizeof (query),
	       "select * from %s where chrom = '%s' and alignStart >= %d"
	       " and id = %s", qTable, seqName, start-1, repeat);

	sr2 = sqlGetResult (conn2, query);
	if ((row = sqlNextRow (sr2)) != NULL)
	    {
	    struct rmskJoined *rmJoin = rmskJoinedLoad (row + hasBin);

	    char class[32];
	    class[0] = '\0';
	    char family[32];
	    family[0] = '\0';
	    char *poundPtr = index (rmJoin->name, '#');
	    if (poundPtr)
		{
		// Terminate name string properly
		safecpy (class, sizeof (class), poundPtr + 1);
		*poundPtr = '\0';
		char *slashPtr = index (class, '/');
		if (slashPtr)
		    {
		    // Terminate class string properly
		    safecpy (family, sizeof (family), slashPtr + 1);
		    *slashPtr = '\0';
		    }
		}

	    printf ("<b>Repeat:</b> %s<br>\n", rmJoin->name);
	    printf ("<b>Class:</b> %s<br>\n", class);
	    printf ("<b>Family:</b> %s<br>\n", family);
	    printf ("<b>Orientation:</b> %s<br>\n", rmJoin->strand);
	    printf ("<b>Joined Element Genomic Range:</b> %s:%d-%d<br>\n",
		    rmJoin->chrom, rmJoin->alignStart+1, rmJoin->alignEnd);
	    printf ("<br><br>\n");
	    }
	sqlFreeResult (&sr2);
	}

    /*
     * Locate *.out annotation for this element
     */
    if (hTableExists (database, outTable))
	{
	int isFirst = 0;
	struct rmskOut2 *ro;
	if (!hFindSplitTable (database, seqName, outTable, qTable, sizeof(qTable), &hasBin))
	    errAbort("track %s not found", outTable);
	sqlSafef (query, sizeof (query),
	       "select * from %s where genoName = '%s' and genoStart >= %d"
	       " and id = %s", qTable, seqName, start-1, repeat);
	sr2 = sqlGetResult (conn2, query);
	printf ("<h4>RepeatMasker Annotation:</h4>\n");
	printf
	    ("The RepeatMasker annotation line(s) for this element. "
	     "If the element is fragmented the output will contain one "
	     "line per joined fragment.<p>\n");
	printf ("<table cellspacing=\"0\">\n");
	while ((row = sqlNextRow (sr2)) != NULL)
	    {
	    ro = rmskOut2Load (row + hasBin);
	    if (!isFirst++)
	        printOutTableHeader (ro->strand[0]);
	    printf ("  <tr>\n");
	    printf ("    <td %s>%d</td>\n", data_style, ro->swScore);
	    printf ("    <td %s>%3.1f</td>\n", data_style,
		    (double) ro->milliDiv * (double) 0.01);
	    printf ("    <td %s>%3.1f</td>\n", data_style,
		    (double) ro->milliDel * (double) 0.01);
	    printf ("    <td %s>%3.1f</td>\n", data_style,
		    (double) ro->milliIns * (double) 0.01);
	    printf ("    <td %s>%s</td>\n", data_style, ro->genoName);
	    printf ("    <td %s>%d</td>\n", data_style, ro->genoStart + 1);
	    printf ("    <td %s>%d</td>\n", data_style, ro->genoEnd);
	    printf ("    </A>");
	    printf ("    <td %s>(%d)</td>\n", data_style, ro->genoLeft);
	    printf ("    <td %s>%s</td>\n", data_style, ro->strand);
	    printf ("    <td %s>%s</td>\n", data_style, ro->repName);
	    printf ("    <td %s>%s/%s</td>\n", data_style, ro->repClass,
		    ro->repFamily);
	    printf ("    <td %s>%d</td>\n", data_style, ro->repStart);
	    printf ("    <td %s>%d</td>\n", data_style, ro->repEnd);
	    printf ("    <td %s>(%d)</td>\n", data_style, ro->repLeft);
	    printf ("    <td %s>%d</td>\n", data_style, ro->id);
	    printf ("  <td>\n");
	    printf ("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">Browser</A>",
		    hgTracksPathAndSettings (), database, seqName,
		    ro->genoStart + 1, ro->genoEnd);
	    char *tbl = cgiUsualString ("table", cgiString ("g"));
	    printf
		(" - <A HREF=\"%s&o=%d&g=getDna&i=%s%s%s%s%s&c=%s&l=%d&r=%d&"
		 "strand=%s&table=%s\">"
		 "DNA</A>\n", hgcPathAndSettings (), ro->genoStart,
                 (ro->repName != NULL ? cgiEncode (ro->repName) : ""),
                 cgiEncode("#"),
		 (ro->repClass != NULL ? cgiEncode (ro->repClass) : ""),
                 cgiEncode("/"),
		 (ro->repFamily != NULL ? cgiEncode (ro->repFamily) : ""),
		 seqName, ro->genoStart, ro->genoEnd, cgiEncode (ro->strand),
		 tbl);

	    printf ("  </td>\n");

	    printf ("  </tr>\n");

	    }
	sqlFreeResult (&sr2);
	printf ("</table>\n");
	}

    printf ("<br><br>\n");

    /*
     * Locate *.align data for this element
     */
    if (hTableExists (database, alignTable))
	{
	struct rmskAlign *ro;
	if (!hFindSplitTable (database, seqName, alignTable, qTable, sizeof(qTable), &hasBin))
	    errAbort("track %s not found", alignTable);
	sqlSafef (query, sizeof (query),
	       "select * from %s where genoName = '%s' and genoStart >= %d"
	       " and id = %s", qTable, seqName, start-1, repeat);
	sr2 = sqlGetResult (conn2, query);
	printf ("<h4>RepeatMasker Alignments:</h4>\n");
	printf
	    ("The raw alignment data used by RepeatMasker to generate "
	     "the final annotation call for this element. NOTE: The "
	     "aligned sequence names and consensus positions may differ "
	     "from the final annotation.<p>\n");
	printf ("<table>\n");
	while ((row = sqlNextRow (sr2)) != NULL)
	    {
	    ro = rmskAlignLoad (row + hasBin);
	    printf ("  <tr>\n");
	    printf ("    <td>%d</td>\n", ro->swScore);
	    printf ("    <td>%3.2f</td>\n",
		    (double) ro->milliDiv * (double) 0.01);
	    printf ("    <td>%3.2f</td>\n",
		    (double) ro->milliDel * (double) 0.01);
	    printf ("    <td>%3.2f</td>\n",
		    (double) ro->milliIns * (double) 0.01);
	    printf ("    <td>%s</td>\n", ro->genoName);
	    printf ("    <td>%d</td>\n", ro->genoStart + 1);
	    printf ("    <td>%d</td>\n", ro->genoEnd);
	    printf ("    <td>(%d)</td>\n", ro->genoLeft);
	    printf ("    <td>%s</td>\n", ro->strand);
	    printf ("    <td>%s</td>\n", ro->repName);
	    printf ("    <td>%s/%s</td>\n", ro->repClass, ro->repFamily);
	    if (ro->strand[0] == '-')
		{
		printf ("    <td>(%d)</td>\n", ro->repLeft);
		printf ("    <td>%d</td>\n", ro->repEnd);
		printf ("    <td>%d</td>\n", ro->repStart);
		}
	    else
		{
		printf ("    <td>%d</td>\n", ro->repStart);
		printf ("    <td>%d</td>\n", ro->repEnd);
		printf ("    <td>(%d)</td>\n", ro->repLeft);
		}
	    printf ("    <td>%d</td>\n", ro->id);
	    printf ("    </tr><tr><td colspan=\"15\"><pre>\n");
	    printAlignment (ro);
	    printf ("    </pre><td></tr>\n");
	    }
	sqlFreeResult (&sr2);
	printf ("</table>\n");
	}
    hFreeConn (&conn2);
    }
printTrackHtml (tdb);
}