src/hg/instinct/hgHeatmap2/hgHeatmap2.h 1.51
1.51 2009/10/23 20:01:39 cszeto
Added local_url feature
Index: src/hg/instinct/hgHeatmap2/hgHeatmap2.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/hgHeatmap2/hgHeatmap2.h,v
retrieving revision 1.50
retrieving revision 1.51
diff -b -B -U 1000000 -r1.50 -r1.51
--- src/hg/instinct/hgHeatmap2/hgHeatmap2.h 2 Sep 2009 17:43:13 -0000 1.50
+++ src/hg/instinct/hgHeatmap2/hgHeatmap2.h 23 Oct 2009 20:01:39 -0000 1.51
@@ -1,415 +1,415 @@
/********************************************************************************/
/* Copyright 2007-2009 -- The Regents of the University of California */
/********************************************************************************/
/* hgHeatmap.h - Include file used by hgHeatmap.
* hgHeatmap is a CGI script that produces a web page containing
* a graphic with all chromosomes in genome */
#ifndef HGHEATMAP2_H
#define HGHEATMAP2_H
#define VERSION "1.5"
#define DEBUG_IMG 1 // Will always write new images.
#define MAX_NUM_RESPONSE 100 // maximum number of objects in JSON response
#define MIN_HEATMAP_HEIGHT 100 // minimum height of a heatmap
#include "cart.h"
#include "genoLay.h"
#include "hgHeatmapLib.h"
#include "featuresLib.h"
#include "filterFeatures.h"
#define DEBUG 0
/*** Prefixes for variables in cart we don't share with other apps. ***/
#define hghPrefix "hgHeatmap_"
#define hghDo hghPrefix "do"
#define hghTableName hghPrefix "tableName"
/*** Our various cart variables. ***/
#define hghHeatmap hghPrefix "heatmap"
#define hghDataSet hghPrefix "dataset"
#define hghDisplayType hghPrefix "display"
#define hghGhName hghPrefix "ghName"
#define hghMaxGapToFill hghPrefix "maxGapToFill"
#define hghImageWidth hghPrefix "imageWidth"
#define hghDataConfigPrefix hghPrefix "data_"
/** Commands from Javascript client **/
#define hgh2Prefix "hgh2_"
/* Obtaining Heatmaps */
#define hgh2Mode hgh2Prefix "mode"
#define hgh2Type hgh2Prefix "type"
#define hgh2Dataset hgh2Prefix "dataset"
#define hgh2ChromStart hgh2Prefix "chromStart"
#define hgh2ChromEnd hgh2Prefix "chromEnd"
#define hgh2GeneSets hgh2Prefix "geneSets"
#define hgh2UserGeneSet hgh2Prefix "userGeneSet"
#define hgh2Feature hgh2Prefix "feature"
#define hgh2FeatureList hgh2Prefix "featureList"
#define hgh2Width hgh2Prefix "width"
#define hgh2FeatureWidth hgh2Prefix "featureWidth"
#define hgh2SampleHeight hgh2Prefix "sampleHeight"
#define hgh2LowColor hgh2Prefix "lowColor"
#define hgh2ZeroColor hgh2Prefix "zeroColor"
#define hgh2HighColor hgh2Prefix "highColor"
/* Sorting heatmaps */
#define hgh2SortType hgh2Prefix "sortType"
#define hgh2FeatureSort hgh2Prefix "featureSort"
#define hgh2FeatureSortDir hgh2Prefix "featureSortDir"
#define hgh2SortChromStart hgh2Prefix "sortChromStart"
#define hgh2SortChromEnd hgh2Prefix "sortChromEnd"
#define hgh2SortGene hgh2Prefix "sortGene"
#define hgh2SortDir hgh2Prefix "sortDir"
/* Searching genesets */
#define hgh2MatchingGenes hgh2Prefix "matchingGenes"
#define hgh2MatchingGenesets hgh2Prefix "matchingGenesets"
/* Storin user genesets */
#define hgh2UserGenesetName hgh2Prefix "userGenesetName"
#define hgh2UserGenesetMembers hgh2Prefix "userGenesetMembers"
/* Subgrouping */
#define hgh2SubgroupNum hgh2Prefix "subgroupNum"
#define hgh2Subgroup1Features hgh2Prefix "subgroup1Features"
#define hgh2Subgroup1Mins hgh2Prefix "subgroup1Mins"
#define hgh2Subgroup1Maxs hgh2Prefix "subgroup1Maxs"
#define hgh2Subgroup2Features hgh2Prefix "subgroup2Features"
#define hgh2Subgroup2Mins hgh2Prefix "subgroup2Mins"
#define hgh2Subgroup2Maxs hgh2Prefix "subgroup2Maxs"
#define hgh2Subgroup1CodedFeatures hgh2Prefix "subgroup1CodedFeatures"
#define hgh2Subgroup1Codes hgh2Prefix "subgroup1Codes"
#define hgh2Subgroup2CodedFeatures hgh2Prefix "subgroup2CodedFeatures"
#define hgh2Subgroup2Codes hgh2Prefix "subgroup2Codes"
#define hgh2StatsFxn hgh2Prefix "statsFxn"
/* Stats */
#define hgh2StatsCorrection hgh2Prefix "statsCorrection"
/* Save session */
#define hgh2Vars hgh2Prefix "vars"
#define hgh2Key hgh2Prefix "key"
/* User login */
#define hgh2UserLogin hgh2Prefix "login"
#define hgh2UserPass hgh2Prefix "pass"
#define hgh2UserId hgh2Prefix "userId"
#define hgh2UserTokenId hgh2Prefix "tokenId"
/* Tooltip */
#define hgh2Sample hgh2Prefix "sample"
#define hgh2Probe hgh2Prefix "probe"
/* Circle Map */
#define hgh2Gene hgh2Prefix "gene"
#define hgh2Summarize hgh2Prefix "summarize"
#define hgh2SummaryDisplay hgh2Prefix "summaryDisplay"
/*** Name prefixes to separate user from db graphs. */
#define hghUserTag "user: "
#define hghDbTag "db: "
#define hghVis hghPrefix "vis"
#define hghBetweenRowPad 3
#define hghBetweenVPad 2
#define SMALL_SPACING 1
#define hgHeatmapDefaultPixWidth 700
#define hgFeatureDefaultPixWidth 250
#define hgDefaultScalePixWidth 60
#define hgHeatmapDefaultCircleWidth 50
#define hgDefaultGenomeScalePixHeight 20
#define hgHeatmapDefaultLabelHeight 15
#define hgHeatmapDefaultSummaryHeight 150
#define hgSampleHeightDefault 1
#define hghSubgroupDefaultPixWidth 10
#define hghTrackContrlBar 10
#define hghFeatureLabel 80
#define hghGeneSetLabel 120
#define hghGeneLabelHeight 50
#define hghGeneLabelMinSize 7 /* max number of genes to display gene labels*/
#define hgh2SubgroupDefaultNum 2
#define hghBed5Height 40
#define hghProbCutoff 1.3 /* Equivalent of p<0.05 in -log10(p) */
/* ---- Global variables declared in hgHeatmap.c */
extern struct cart *cart; /* This holds cgi and other variables between clicks. */
struct hmPixel {
struct hmPixel *next;
int x;
int y;
int w;
int h;
double val;
int count;
Color color;
struct slDouble *valList;
double sum;
double avg;
double median; // median
double lowQ; // low quantile
double highQ; // high quantile
double lowW; // low whisker
double highW; // high whisker
double val2; // TODO: A temporary hack
int count2;
};
struct hmElement {
struct hmElement *next;
char *name;
int pixelStart;
int pixelEnd;
unsigned long baseStart; // only for chrom
unsigned long baseEnd; // only for chrom
char *shortLabel; // only for feature
char *longLabel; // only for feature
char *probeName; // only for geneset hmElement
struct bed *bed; // only for geneset hmElement
};
struct heatmapLay {
struct heatmapLay *next;
char *name;
int width;
int height;
int genesetLabelHeight;
int sampleHeight;
double basesPerPixel;
int pixelStart;
int pixelEnd;
MgFont *font;
int fontHeight;
/* For scales */
int maxValPos;
double maxVal;
int minValPos;
double minVal;
struct hmElement *elements;
struct rgbColor *lowColor;
struct rgbColor *zeroColor;
struct rgbColor *highColor;
};
/* next two structs are used to group datasets for display */
struct dataset {
struct dataset *next;
char *name;
char *shortLabel;
char *longLabel;
- char *url;
+ char *local_url;
int expCount;
};
struct datasetGroup {
struct datasetGroup *next;
char *name;
struct dataset *datasets;
};
/*** Routines from hgHeatmap.h ***/
int heatmapHeight(struct genoHeatmap *gh);
/* Return height of heatmap. This is only for those experiments that will be displayed. */
int heatmapFullHeight(struct genoHeatmap *gh);
/* Return height of the heatmap, analysis result, and gene labels if there are */
int heatmapFullHeightWithLabels(struct genoHeatmap *gh);
/* Return height of the heatmap section, after evaluation all related labels */
char *dataSetRaName();
/* Return the dataset configuration ra file name */
int experimentHeight();
/* Return height of an experiment */
int experimentCount(struct genoHeatmap *gh);
/* Return the number of experiments */
char *getPathwayDb();
struct sqlConnection *getPathwayDbConn();
struct sqlConnection *getFeatureDbConn(struct genoHeatmap *gh);
//char *chromLayout();
/* Return one of above strings specifying layout. */
struct genoLay *defaultLayoutH(struct genoLay *gl, int width, int height);
/* Layout area based on previously layed out, horizontally extend on the right with width and height */
struct genoLay *defaultLayoutV(struct genoLay *gl, int width, int height);
/* Layout area based on previously layed out, vertically extend in below with width and height */
struct genoLay *ggLayout(struct sqlConnection *conn);
/* Figure out how to lay out image. */
void heatmapLayResetMinMax(struct heatmapLay *hlList);
struct heatmapLay *chromLayout(struct sqlConnection *conn, struct genoHeatmap *gh,
char *chromStart, int startBase,
char *chromEnd, int endBase,
int width, int sampleHeight);
/* Layout chromosome view */
struct heatmapLay *genesetLayout(struct genoHeatmap *gh,
char *geneSetNames,
int width, int sampleHeight);
/* Layout geneset view */
struct heatmapLay *featureLayout(struct genoHeatmap *gh, int width, int sampleHeight);
/* Layout feature panel */
/*** Routine related to mainPage.c ***/
void mainPage(struct sqlConnection *conn, char *tableName);
/* Do main page of application: hotlinks bar, controls, graphic. */
char *genomeGif(struct sqlConnection *conn, struct heatmapLay *hl,
struct genoHeatmap *gh);
char *genomeLabelsGif(struct sqlConnection *conn, struct heatmapLay *hl);
char *genesetGif(struct sqlConnection *conn, struct heatmapLay *hl,
struct genoHeatmap *gh);
char *genesetLabelsGif(struct sqlConnection *conn, struct heatmapLay *hl);
char *genomeSummaryGif(struct sqlConnection *conn, struct heatmapLay *hl,
struct genoHeatmap *gh, struct slName *sampleList,
int totalH, int subset, int subsetNum);
char *genesetSummaryGif(struct sqlConnection *conn, struct heatmapLay *hl,
struct genoHeatmap *gh, struct slName *sampleList,
int totalH, int subset, int subsetNum);
char *featureGif(struct sqlConnection *conn, struct heatmapLay *hl,
struct genoHeatmap *gh, char *tableName);
char *featureSummaryGif(struct sqlConnection *conn, struct heatmapLay *hl,
struct genoHeatmap *gh, char *tableName, struct slName *sampleList,
int buffer, int subset, int subsetNum);
char *subgroupGif(struct genoHeatmap *gh, char *tableName, int width, int sampleHeight);
char *genomeStatsGif(struct sqlConnection *conn, struct heatmapLay *hl,
struct genoHeatmap *gh, float colorCutoff);
char *genesetStatsGif(struct sqlConnection *conn, struct heatmapLay *hl,
struct genoHeatmap *gh, float colorCutoff);
void geneSetsAddPathwayLayout(struct geneSet *geneSets, struct hash *geneHash);
void geneSetsChromLayout(struct geneSet *geneSets);
char *simpleScaleGif(struct heatmapLay *hl, struct genoHeatmap *gh, int subset, int subsetNum);
char *genomeScaleGif(struct heatmapLay *hl, double numBases);
void hghDoUsualHttp();
/* Wrap html page dispatcher with code that writes out
* HTTP header and write cart back to database. */
/*** Functions imported from other modules. ***/
void printMainHelp();
/* Put up main page help info. */
char *cartSettingsString(char *prefix, char *functionName);
void trashDirMD5File(struct tempName *tn, char *dirName, char *suffix, char *strToHash);
char *retrieveSettings(struct cart *cart, char *key);
/* Retrieves settings according to unique key... if key is NULL, then session according to
* user id is returned. If no session exists, NULL is returned. */
int saveUserSettings(struct cart *cart, char *vars);
/* Saves settings in vars to mysql database, one entry in db per user-id.
* -1 is returned if problem occurred. */
struct slName *getGenesMatchingList(char *searchGenes);
struct slName *getGenesMatching(char *searchGene);
struct slName *getGenesNotMatching(char *searchGenes);
struct slName *getGenesetsMatching(struct cart *cart, char *searchGenes, char *searchGenesets);
char *getDescriptionOfGeneset(char *geneset);
char *storeUserGeneset(struct cart *cart, char *name, char *geneList);
struct geneSet *getAllPathways(struct cart *cart, char *db, char *pathwayNames);
struct slName *getGenesInGeneset(struct cart *cart, char *geneset);
char *annotationGif(struct heatmapLay *hl, char *table);
void vgMakeColorGradient(struct vGfx *vg,
struct rgbColor *start, struct rgbColor *end,
int steps, Color *colorIxs);
boolean singleChromImage(struct heatmapLay *hl);
char *md5HashString(char *str);
char *toolTipByProbe(struct genoHeatmap *gh, char *sampleId, char *probeId);
char *toolTipByFeature(struct genoHeatmap *gh, char *sampleId, char *feature);
char *toolTipByPatient(struct genoHeatmap *gh, char *sampleId);
char *toolTipByChromPos(struct genoHeatmap *gh, char *sampleId,
char *chrom, int chromStart, int chromStop);
char *toolTipGeneTrackByChromPos(char *db, char *tableName, char *chromName,
int chromStart, int chromStop, int maxNumGenes);
void verticalTextRight(struct vGfx *vg, int x, int y,
int width, int height, int colorIx, MgFont *font, char *string);
void drawLayoutLines(struct vGfx *vg, struct heatmapLay *hlList, int width);
void heatmapLaySetDefaultColor(struct heatmapLay *hl, char *platform);
/* Moving all circle map to own file, to prepare for making it separate CGI */
void modeGetCircleMap();
void setupFeatureVisibility(struct genoHeatmap *gh);
void setupSort(struct genoHeatmap *gh);
char *getId(struct sqlConnection *conn, char *table, char *key, char *sample, char *value);
/* get patient ID from sample (or experiment) Id */
void setSubgroups(struct genoHeatmap *gh);
#endif /* HGHEATMAP2_H */