/* mainPage - draws the main hgGenome page, including some controls
 * on the top and the graphic. */

/* 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 "psGfx.h"
#include "pscmGfx.h"
#include "linefile.h"
#include "hash.h"
#include "cheapcgi.h"
#include "htmshell.h"
#include "cart.h"
#include "hui.h"
#include "dbDb.h"
#include "ra.h"
#include "hdb.h"
#include "web.h"
#include "portable.h"
#include "hgColors.h"
#include "trackLayout.h"
#include "chromInfo.h"
#include "hvGfx.h"
#include "genoLay.h"
#include "cytoBand.h"
#include "hCytoBand.h"
#include "errCatch.h"
#include "chromGraph.h"
#include "customTrack.h"
#include "hPrint.h"
#include "jsHelper.h"
#include "hgGenome.h"
#include "trashDir.h"



static char *allColors[] = {
    "black", "blue", "purple", "red", "orange", "yellow", "green", "gray",
};

static char *defaultColors[maxLinesOfGraphs][maxGraphsPerLine] = {
    {"blue", "red", "black", "yellow", },
    {"gray", "purple", "green", "orange",},
    {"blue", "red", "black", "yellow", },
    {"gray", "purple", "green", "orange",},
    {"blue", "red", "black", "yellow", },
    {"gray", "purple", "green", "orange",},
};

char *graphColorAt(int row, int col)
/* Return graph color at given row/column, NULL if nonw. */
{
char *varName = graphColorVarName(row, col);
char *color = cartUsualString(cart, varName, defaultColors[row][col]);
if (color == NULL) color = defaultColors[0][0];
return color;
}

Color colorFromAscii(struct hvGfx *hvg, char *asciiColor)
/* Get color index for a named color. */
{
if (sameWord("red", asciiColor))
    return MG_RED;
else if (sameWord("blue", asciiColor))
    return MG_BLUE;
else if (sameWord("yellow", asciiColor))
    return hvGfxFindColorIx(hvg, 220, 220, 0);
else if (sameWord("purple", asciiColor))
    return hvGfxFindColorIx(hvg, 150, 0, 200);
else if (sameWord("orange", asciiColor))
    return hvGfxFindColorIx(hvg, 230, 120, 0);
else if (sameWord("green", asciiColor))
    return hvGfxFindColorIx(hvg, 0, 180, 0);
else if (sameWord("gray", asciiColor))
    return MG_GRAY;
else
    return MG_BLACK;
}

/* Page drawing stuff. */

void drawChromGraph(struct hvGfx *hvg, struct sqlConnection *conn, 
	struct genoLay *gl, char *chromGraph, int yOff, int height, Color color,
	boolean leftLabel, boolean rightLabel, boolean firstInRow)
/* Draw chromosome graph on all chromosomes in layout at given
 * y offset and height. */
{
boolean yellowMissing = getYellowMissing();
struct genoGraph *gg = hashFindVal(ggHash, chromGraph);
if (gg != NULL)
    {
    /* Get binary data source and scaling info etc. */
    struct chromGraphBin *cgb = gg->cgb;
    struct chromGraphSettings *cgs = gg->settings;
    int maxGapToFill = cgs->maxGapToFill;
    static struct rgbColor missingDataColor = { 180, 180, 120, 255};
    Color missingColor = hvGfxFindRgb(hvg, &missingDataColor);
    double pixelsPerBase = 1.0/gl->basesPerPixel;
    double gMin = cgs->minVal, gMax = cgs->maxVal, gScale;
    gScale = height/(gMax-gMin);

    /* Draw significance threshold as a light blue line */
    if (leftLabel)
        {
	static struct rgbColor guidelineColor = { 220, 220, 255, 255};
	Color lightBlue = hvGfxFindRgb(hvg, &guidelineColor);
	struct slRef *ref;
	struct genoLayChrom *chrom;
	int rightX = gl->picWidth - gl->rightLabelWidth - gl->margin;
	int leftX = gl->leftLabelWidth + gl->margin;
	int width = rightX - leftX;
	double threshold = getThreshold();
	if (threshold >= gMin && threshold <= gMax)
	    {
	    int y = height - ((threshold - gMin)*gScale) + yOff;
	    for (ref = gl->leftList; ref != NULL; ref = ref->next)
		{
		chrom = ref->val;
		hvGfxBox(hvg, leftX, y + chrom->y, width, 1, lightBlue);
		}
	    ref = gl->bottomList;
	    if (ref != NULL)
		{
		chrom = ref->val;
		hvGfxBox(hvg, leftX, y + chrom->y, width, 1, lightBlue);
		}
	    }
	}

    /* Draw graphs on each chromosome */
    chromGraphBinRewind(cgb);
    while (chromGraphBinNextChrom(cgb))
	{
	struct genoLayChrom *chrom = hashFindVal(gl->chromHash, cgb->chrom);
	if (chrom)
	    {
	    int chromX = chrom->x, chromY = chrom->y;
	    int minY = chromY + yOff;
	    int maxY = chromY + yOff + height - 1;

	    if (chromGraphBinNextVal(cgb))
	        {
		/* Set clipping so can't scribble outside of box. */
		hvGfxSetClip(hvg, chromX, chromY, chrom->width+1, chrom->height);

		/* Handle first point as special case here, so don't
		 * have to test for first point in inner loop. */

		double x,lastX;
		int y,start,lastStart,lastY;

		start = lastStart = cgb->chromStart;
		x = lastX = pixelsPerBase*start + chromX;
		y = lastY = (height - ((cgb->val - gMin)*gScale)) + chromY+yOff;
		if (y < minY) y = minY;
		else if (y > maxY) y = maxY;

		struct pscmGfx *pscm = NULL;
		if (hvg->pixelBased)
		    {
    		    hvGfxDot(hvg, x, y, color);
		    }
		else
		    {
		    pscm = (struct pscmGfx *)hvg->vg->data;
		    pscmSetColor(pscm, color);
		    psFillEllipse(pscm->ps, x, y, 0.01, 0.01);
		    psSetLineWidth(pscm->ps, 0.01);
		    }

		/* Draw rest of points, connecting with line to previous point
		 * if not too far off. */
		while (chromGraphBinNextVal(cgb))
		    {
		    start = cgb->chromStart;
		    x = pixelsPerBase*start + chromX;
		    if (hvg->pixelBased)
			x = (int) x;
		    y = (height - ((cgb->val - gMin)*gScale)) + chromY+yOff;
		    if (y < minY) y = minY;
		    else if (y > maxY) y = maxY;
		    if (x != lastX || y != lastY)
		        {
			if (start - lastStart <= maxGapToFill)
			    {
			    if (hvg->pixelBased)
				hvGfxLine(hvg, lastX, lastY, x, y, color);
			    else
				{
				pscmSetColor(pscm, color);
				psDrawLine(pscm->ps, lastX, lastY, x, y);
				}
			    }
			else
			    {
			    if (yellowMissing && leftLabel)
			        {
				int width = x - lastX - 1;
				if (width > 0)
				    hvGfxBox(hvg, lastX+1, minY, width, height, missingColor);
				}
			    if (hvg->pixelBased)
				{
				hvGfxDot(hvg, x, y, color);
				}
			    else
				{
				pscmSetColor(pscm, color);
				psFillEllipse(pscm->ps, x, y, 0.01, 0.01);
				}
			    }
			}
		    lastX = x;
		    lastY = y;
		    lastStart = start;
		    }

		if (!hvg->pixelBased)
		    {
		    psSetLineWidth(pscm->ps, 1);
		    }

		hvGfxUnclip(hvg);
		}
	    }
	else
	    {
	    /* Just read and discard data. */
	    while (chromGraphBinNextVal(cgb))
	        ;
	    }
	}


    /* Draw labels. */
    if (withLabels && (leftLabel || rightLabel))
        {
	int lineY = yOff;
	int i,j;
	int spaceWidth = tl.nWidth;
	int tickWidth = spaceWidth*2/3;
	int fontPixelHeight = mgFontPixelHeight(gl->font);
	for (i=0; i<gl->lineCount; ++i)
	    {
	    hvGfxSetClip(hvg, 0, lineY, gl->picWidth, gl->lineHeight);
	    for (j=0; j< cgs->linesAtCount; ++j)
	        {
		double lineAt = cgs->linesAt[j];
		int y = (height - ((lineAt - gMin)*gScale)) + lineY;
		int textTop = y - fontPixelHeight/2+1;
		int textBottom = textTop + fontPixelHeight;
		char label[24];
		safef(label, sizeof(label), "%g", lineAt);
		if (leftLabel)
		    {
		    hvGfxBox(hvg, gl->margin + gl->leftLabelWidth - tickWidth-1, y,
		    	tickWidth, 1, color);
		    if (textTop >= lineY && textBottom < lineY + height)
			{
			hvGfxTextRight(hvg, gl->margin, textTop, 
			    gl->leftLabelWidth-spaceWidth, fontPixelHeight,
			    color, gl->font, label);
			}
		    }
		if (rightLabel)
		    {
		    hvGfxBox(hvg, 
		    	gl->picWidth - gl->margin - gl->rightLabelWidth+1, 
		    	y, tickWidth, 1, color);
		    if (textTop >= lineY && textBottom < lineY + height)
			{
			hvGfxText(hvg,
			    gl->picWidth - gl->margin - gl->rightLabelWidth + spaceWidth,
			    textTop, color, gl->font, label);
			}
		    }
		}
	    lineY += gl->lineHeight;
	    hvGfxUnclip(hvg);
	    }
	}
    }
}

void genomeGif(struct sqlConnection *conn, struct genoLay *gl,
	int graphRows, int graphCols, int oneRowHeight, char *psOutput)
/* Create genome GIF file and HTML that includes it. */
{
struct hvGfx *hvg;
struct tempName gifTn;
Color shadesOfGray[10];
int maxShade = ArraySize(shadesOfGray)-1;
int spacing = 1;
int yOffset = 2*spacing;
int innerHeight = oneRowHeight - 3*spacing;
int i,j;


if (psOutput)
    {
    hvg = hvGfxOpenPostScript(gl->picWidth, gl->picHeight, psOutput);
    }
else
    {

    /* Create gif file and make reference to it in html. */
    trashDirFile(&gifTn, "hgg", "ideo", ".png");
    hvg = hvGfxOpenPng(gl->picWidth, gl->picHeight, gifTn.forCgi, FALSE);

    hPrintf("<INPUT TYPE=IMAGE SRC=\"%s\" BORDER=1 WIDTH=%d HEIGHT=%d NAME=\"%s\">",
		gifTn.forHtml, gl->picWidth, gl->picHeight, hggClick);
    }

/* Get our grayscale. */
hMakeGrayShades(hvg, shadesOfGray, maxShade);

/* Draw the labels and then the chromosomes. */
genoLayDrawChromLabels(gl, hvg, MG_BLACK);
genoLayDrawBandedChroms(gl, hvg, database, conn, 
	shadesOfGray, maxShade, MG_BLACK);

/* Draw chromosome graphs. */
for (i=0; i<graphRows; ++i)
    {
    boolean firstInRow = TRUE;
    for (j=graphCols-1; j>=0; --j)
	{
	char *graph = graphSourceAt(i,j);
	if (graph != NULL && graph[0] != 0)
	    {
	    Color color = colorFromAscii(hvg, graphColorAt(i,j));
	    drawChromGraph(hvg, conn, gl, graph, 
		    gl->betweenChromOffsetY + yOffset, 
		    innerHeight,  color, j==0, j==1, firstInRow);
	    firstInRow = FALSE;
	    }
	}
    yOffset += oneRowHeight;
    }

hvGfxBox(hvg, 0, 0, gl->picWidth, 1, MG_GRAY);
hvGfxBox(hvg, 0, gl->picHeight-1, gl->picWidth, 1, MG_GRAY);
hvGfxBox(hvg, 0, 0, 1, gl->picHeight, MG_GRAY);
hvGfxBox(hvg, gl->picWidth-1, 0, 1, gl->picHeight, MG_GRAY);
hvGfxClose(&hvg);
}

void graphDropdown(struct sqlConnection *conn, char *varName, char *curVal, char *event, char *js)
/* Make a drop-down with available chrom graphs */
{
int totalCount = 1;
char **menu, **values;
int i = 0;
struct slRef *ref;
for (ref = ggList; ref != NULL; ref = ref->next)
    {
    struct genoGraph *gg = ref->val;
    if (gg->isComposite == FALSE)
	totalCount++;
    }

AllocArray(menu, totalCount);
AllocArray(values, totalCount);
menu[0] = "-- nothing --";
values[0] = "";

for (ref = ggList; ref != NULL; ref = ref->next)
    {    
    struct genoGraph *gg = ref->val;
    if (gg->isComposite == FALSE)
	{
	++i;
	menu[i] = gg->shortLabel;
	values[i] = gg->name;
	}
    }
cgiMakeDropListFull(varName, menu, values, totalCount, curVal, event, js);
freez(&menu);
freez(&values);
}

void colorDropdown(int row, int col, char *event, char *js)
/* Put up color drop down menu. */
{
char *varName = graphColorVarName(row, col);
char *curVal = graphColorAt(row, col);
cgiMakeDropListFull(varName, allColors, allColors, ArraySize(allColors), curVal, event, js);
}

static void addThresholdGraphCarries(struct dyString *dy, int graphRows, int graphCols, boolean cgaOnly)
/* Add javascript that carries over threshold and graph vars
 * to new form. */
{
if (cgaOnly)
    return;
jsTextCarryOver(dy, getThresholdName());
int i,j;
for (i=0; i<graphRows; ++i)
    for (j=0; j<graphCols; ++j)
        {
	jsDropDownCarryOver(dy, graphVarName(i,j));
	jsDropDownCarryOver(dy, graphColorVarName(i,j));
	}
}

static struct dyString *onChangeStart(int graphRows, int graphCols, boolean cgaOnly)
/* Return common prefix to onChange javascript string */
{
struct dyString *dy = jsOnChangeStart();
addThresholdGraphCarries(dy, graphRows, graphCols, cgaOnly);
return dy;
}

static char *onChangeClade(int graphRows, int graphCols, boolean cgaOnly)
/* Return javascript executed when they change clade. */
{
struct dyString *dy = onChangeStart(graphRows, graphCols, cgaOnly);
jsDropDownCarryOver(dy, "clade");
dyStringAppend(dy, " document.hiddenForm.org.value=0;");
dyStringAppend(dy, " document.hiddenForm.db.value=0;");
return jsOnChangeEnd(&dy);
}

static char *onChangeOrg(int graphRows, int graphCols, boolean cgaOnly)
/* Return javascript executed when they change organism. */
{
struct dyString *dy = onChangeStart(graphRows, graphCols, cgaOnly);
jsDropDownCarryOver(dy, "clade");
jsDropDownCarryOver(dy, "org");
dyStringAppend(dy, " document.hiddenForm.db.value=0;");
return jsOnChangeEnd(&dy);
}

static void saveOnChangeOtherFunction(int graphRows, int graphCols, boolean cgaOnly)
/* Write out Javascript function to save vars in hidden
 * form and submit. */
{
struct dyString *dy = dyStringNew(4096);
dyStringAppend(dy, 
"var submitted=false;\n"
"function changeOther()\n"
"{\n"
"if (!submitted)\n"
"    {\n"
"    submitted=true;\n"
"    ");
addThresholdGraphCarries(dy, graphRows, graphCols, cgaOnly);
jsDropDownCarryOver(dy, "clade");
jsDropDownCarryOver(dy, "org");
jsDropDownCarryOver(dy, "db");
dyStringAppend(dy, "document.hiddenForm.submit();\n");
dyStringAppend(dy, 
"    }\n"
"}\n"
);
jsInline(dy->string);
}

static char *onChangeOther()
/* Return javascript executed when they change database. */
{
return "changeOther();";
}

boolean renderGraphic(struct sqlConnection *conn, char *psOutput)
/* draw just the graphic */
{
struct genoLay *gl;
int graphRows = linesOfGraphs();
int graphCols = graphsPerLine();
boolean result = FALSE;
if (ggList != NULL)
    {
    /* Get genome layout.  This can fail so it is wrapped in an error
     * catcher. */
    struct errCatch *errCatch = errCatchNew();
    if (errCatchStart(errCatch))
	{
	gl = ggLayout(conn, graphRows, graphCols);

	/* Draw picture. Enclose in table to add a couple of pixels between
	 * it and controls on IE. */
	genomeGif(conn, gl, graphRows, graphCols, graphHeight()+betweenRowPad, psOutput);
	result = TRUE;
	}
    errCatchEnd(errCatch);
    if (errCatch->gotError)
	warn("%s", errCatch->message->string);
    errCatchFree(&errCatch); 
    }
else
    {
    hPrintf("<BR><B>No graph data is available for this assembly.  "
	    "Upload your own data or import from a table or custom track.</B>");
    }
return result;
}

void handlePostscript(struct sqlConnection *conn)
/* Deal with Postscript output. */
{
struct tempName psTn;
char *pdfFile = NULL;
trashDirFile(&psTn, "hgg", "hgg", ".eps");
cartWebStart(cart, database, "%s Genome Graphs", genome);
printf("<H1>PDF Output</H1>\n");

boolean result = renderGraphic(conn, psTn.forCgi);
if (result)
    {
    printf("EPS (PostScript) output has been discontinued in pursuit of additional features\n");
    printf("that are not PostScript-compatible.  If you require PostScript output for your\n");
    printf("workflow, please <a href='https://genome.ucsc.edu/contacts.html'>reach out to us</a>\n");
    printf("and let us know what your needs are - we may be able to help.\n");
    pdfFile = convertEpsToPdf(psTn.forCgi);
    if(pdfFile != NULL)
	{
	printf("<BR><BR>PDF can be viewed with Adobe Acrobat Reader.<BR>\n");
	printf("<A TARGET=_blank HREF=\"%s\">Click here</A> "
	       "to download the current browser graphic in PDF.", pdfFile);
	}
    else
	printf("<BR><BR>PDF format not available");
    freez(&pdfFile);
    }
printf("<BR><BR><A HREF=\"../cgi-bin/hgGenome\">Return</A>");
cartWebEnd();
}



void mainPage(struct sqlConnection *conn)
/* Do main page of application:  hotlinks bar, controls, graphic. */
{
int graphRows = linesOfGraphs();
int graphCols = graphsPerLine();
int i, j;
int realCount = 0;
char *scriptName = "../cgi-bin/hgGenome";

cartWebStart(cart, database, "%s Genome Graphs", genome);

/* Start form and save session var. */
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=GET>\n", scriptName);
cartSaveSession(cart);



/* it might be a non-chrom based assembly */

// defined externally in import.c at the moment
extern struct slName *getChroms();
/* Get a chrom list. */


struct slName *chromList = getChroms();
int count = slCount(chromList);
boolean cgaOnly = FALSE;
if ((count > 500) || (count == 0))
    {
    cgaOnly = TRUE;
    }


jsInit();
saveOnChangeOtherFunction(graphRows, graphCols, cgaOnly);
char *jsOther = onChangeOther();

/* Print clade, genome and assembly line. */
hPrintf("<TABLE>");
boolean gotClade = hGotClade();
if (gotClade)
    {
    hPrintf("<TR><TD><B>clade:</B>\n");
    printCladeListHtml(hGenome(database), "change", onChangeClade(graphRows, graphCols, cgaOnly));
    htmlNbSpaces(3);
    hPrintf("<B>genome:</B>\n");
    printGenomeListForCladeHtml(database, "change", onChangeOrg(graphRows, graphCols, cgaOnly));
    }
else
    {
    hPrintf("<TR><TD><B>genome:</B>\n");
    printGenomeListHtml(database, "change", onChangeOrg(graphRows, graphCols, cgaOnly));
    }
htmlNbSpaces(3);
hPrintf("<B>assembly:</B>\n");
printAssemblyListHtml(database, "change", jsOther);
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>");


if (cgaOnly)
    {
    if (count > 500)  /* Too-many-chrom assembly */
	{
	warn("Sorry, too many chromosomes. "
	    "This one has %d. Please select another organism or assembly.", count);
	}
    else if (count == 0)  /* non-chrom assembly */
	{
	warn("Sorry, can only do genome layout on assemblies mapped to chromosomes. "
	    "This one has no usable chromosomes. Please select another organism or assembly.");
	}
    }
else
    {

    /* Draw graph controls. */
    hPrintf("<TABLE>");
    for (i=0; i<graphRows; ++i)
	{
	hPrintf("<TR>");
	hPrintf("<TD><B>graph</B></TD>");
	for (j=0; j<graphCols; ++j)
	    {
	    char *varName = graphVarName(i,j);
	    char *curVal = cartUsualString(cart, varName, "");
	    if (curVal[0] != 0)
		++realCount;
	    hPrintf("<TD>");
	    graphDropdown(conn, varName, curVal, "change", jsOther);
	    hPrintf(" <B>in</B> ");
	    colorDropdown(i, j, "change", jsOther);
	    if (j != graphCols-1) hPrintf(",");
	    hPrintf("</TD>");
	    }
	hPrintf("</TR>");
	}
    hPrintf("</TABLE>");
    cgiMakeButton(hggUpload, "upload");
    hPrintf(" ");
    cgiMakeButton(hggImport, "import");
    hPrintf(" ");
    cgiMakeButton(hggConfigure, "configure");
    hPrintf(" ");
    cgiMakeOptionalButton(hggCorrelate, "correlate", realCount < 2);
    hPrintf(" <B>significance threshold:</B>");
    hPrintf("<INPUT TYPE=\"TEXT\" NAME=\"%s\" id='%s' SIZE=\"%d\" VALUE=\"%g\">"
	    , getThresholdName(),  getThresholdName(), 3, getThreshold());
    jsOnEventById("change"  , getThresholdName(), "changeOther();");
    jsOnEventById("keypress", getThresholdName(), "return submitOnEnter(event,document.mainForm);");
    hPrintf(" ");
    cgiMakeOptionalButton(hggBrowse, "browse regions", realCount == 0);
    hPrintf(" ");
    cgiMakeOptionalButton(hggSort, "sort genes", 
	    realCount == 0 || !hgNearOk(database));
    hPrintf("<BR>");

    hPrintf("<TABLE CELLPADDING=2><TR><TD>\n");

    boolean result = renderGraphic(conn, NULL);

    hPrintf("</TD></TR></TABLE>\n");
    if (result)
	/* Write a little click-on-help */
	hPrintf("<i>Click on a chromosome to open Genome Browser at that position.</i>");


    }  /* end else non-chrom assembly */

hPrintf("</FORM>\n");

/* Hidden form - fo the benefit of javascript. */
    {
    /* Copy over both the regular, non-changing variables, and
    * also all the source/color pairs that depend on the 
    * configuration. */
    static char *regularVars[] = {
      "clade", "org", "db",
      };
    int regularCount = ArraySize(regularVars);
    int varCount = regularCount + 1 + 2 * graphRows * graphCols;
    int varIx = regularCount;
    char **allVars;
    AllocArray(allVars, varCount);
    CopyArray(regularVars, allVars, regularCount);
    allVars[varIx++] = cloneString(getThresholdName());
    for (i=0; i<graphRows; ++i)
        {
	for (j=0; j<graphCols; ++j)
	    {
	    allVars[varIx++] = cloneString(graphVarName(i,j));
	    allVars[varIx++] = cloneString(graphColorVarName(i,j));
	    }
	}
    jsCreateHiddenForm(cart, scriptName, allVars, varCount);
    }

webNewSection("Using Genome Graphs");
printMainHelp();
cartWebEnd();
}