src/hg/hgTracks/imageV2.c 1.1
1.1 2009/06/26 17:49:09 tdreszer
Initial check-in of new image V2.0 which will allow drag-reorder and drag-scroll. This is a work in progress and ifdef'd out of the build.
Index: src/hg/hgTracks/imageV2.c
===================================================================
RCS file: src/hg/hgTracks/imageV2.c
diff -N src/hg/hgTracks/imageV2.c
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ src/hg/hgTracks/imageV2.c 26 Jun 2009 17:49:09 -0000 1.1
@@ -0,0 +1,1020 @@
+/* hgTracks - Human Genome browser main cgi script. */
+#include "common.h"
+#include "hCommon.h"
+#include "linefile.h"
+#include "portable.h"
+#include "memalloc.h"
+#include "localmem.h"
+#include "obscure.h"
+#include "dystring.h"
+#include "hash.h"
+#include "jksql.h"
+#include "gfxPoly.h"
+#include "memgfx.h"
+#include "hvGfx.h"
+#include "psGfx.h"
+#include "cheapcgi.h"
+#include "hPrint.h"
+#include "htmshell.h"
+#include "cart.h"
+#include "hdb.h"
+#include "hui.h"
+#include "hgFind.h"
+#include "hgTracks.h"
+#include "trashDir.h"
+#include "grp.h"
+#include "versionInfo.h"
+#include "web.h"
+#include "cds.h"
+#include "cutterTrack.h"
+#include "wikiTrack.h"
+#include "ctgPos.h"
+#include "bed.h"
+#include "bigBed.h"
+#include "bedCart.h"
+#include "customTrack.h"
+#include "cytoBand.h"
+#include "ensFace.h"
+#include "liftOver.h"
+#include "pcrResult.h"
+#include "wikiLink.h"
+#include "jsHelper.h"
+#include "mafTrack.h"
+#include "hgConfig.h"
+#include "encode.h"
+#include "agpFrag.h"
+#include "imageV2.h"
+
+static char const rcsid[] = "$Id$";
+
+struct imgBox *theImgBox = NULL; // Make this global for now to avoid huge rewrite
+struct image *theOneImg = NULL; // Make this global for now to avoid huge rewrite
+struct imgTrack *curImgTrack = NULL; // Make this global for now to avoid huge rewrite
+struct imgSlice *curSlice = NULL; // Make this global for now to avoid huge rewrite
+struct mapSet *curMap = NULL; // Make this global for now to avoid huge rewrite
+//struct mapItem *curMapItem = NULL; // Make this global for now to avoid huge rewrite
+
+//#define IMAGEv2_UI
+#ifdef IMAGEv2_UI
+// IMAGEv2
+// The new way to do images
+// Terms:
+// "image box": The new version of the image on the html page. It is a table with rows that contain tracks which are made up of parts of images.
+// "imgBox": The C struct that contains all information to render the image box on the html page.
+// "imgTbl": The HTML structure that contains individual track images. The javascript client controls the imgTbl.
+// Thus cgi knows imgBox while html/js knows imgTbl.
+// "image": A single gif. An image may contain mutilple tracks.
+// Even as a single track and image may contain a data image, sideLabel and centerLabel
+// "map" or "mapSet": The image map for providing links to items in a data image.
+// An image and map are a 1 to 1 pair and pixel coordinates are alway image relative.
+// "slice" or "imgSlice": The cgi concept of the portion of an image that is sent to the html/js side.
+// Thus, if we are sending a 3X sized image, the "slice" spans the entire 3X.
+// Frequently a subset of an image, but possibly the whole image.
+// Even if the image is of a single track, it might still be cut into data image, sideLabel and centerLabel slices.
+// "sliceMap": The portion of a map that belongs to a slice. The pixel coordinates are always image relative, not sice relative.
+// "portal" or "imgPortal": The html/js concept of the portion of a slice that is visible in the browser.
+// Thus, if we are sending a 3X sized data image slice, the "portal" seen in the browser spans only 1X.
+// Frequently a subset of a slice, but possibly the whole image slice.
+// "imgTrack" or track image: The cgi side whole shabang for rendering one track.
+// It contains track specific information and three slices: data, sideLabel and centerLabel
+// The imgBox contains N imgTracks. Typically an ajax/JSON request gets a single imgTrack returned.
+// image box support: This can contain all the support variables that are global to the image box (like font size, box width, etc.).
+// At this point, lets not talk structure or cgi vs. html/js but leave this container as a concept that we know needs filling.
+// imgBox is the top level and contains all info to draw the image in HTML
+// - contains slList of all imgTrack structs shown
+// imgTrack contains all info to display one track/subtrack in the imgBox
+// - contains 3 imgSlice structs (data, centerLabel, sideLabel
+// imgSlice contains all info to display a portion of an image file
+// - contains 1 image struct
+// image contains all information about an image file and associated map box
+//
+//////// Maps
+//struct mapItem // IMAGEv2: single map item in an image map.
+// {
+// struct mapItem *next; // slList
+// char *linkVar; // the get variables associated with the map link
+// char *title; // item title
+// int topLeftX; // in pixels relative to image
+// int topLeftY; // in pixels relative to image
+// int bottomRightX; // in pixels relative to image
+// int bottomRightY; // in pixels relative to image
+// };
+//struct mapSet // IMAGEv2: full map for image OR partial map for slice
+// {
+// char *name; // to point an image to a map in HTML
+// struct image *parentImg; // points to the image this map belongs to
+// char *linkRoot; // the common or static portion of the link for the entire image
+// struct mapItem *items; // list of items
+// };
+struct mapSet *mapSetStart(char *name,struct image *img,char *linkRoot)
+/* Starts a map (aka mapSet) which is the seet of links and image locations used in HTML.
+ Complete a map by adding items with mapItemAdd() */
+{
+struct mapSet *map;
+AllocVar(map);
+return mapSetUpdate(map,name,img,linkRoot);
+}
+struct mapSet *mapSetUpdate(struct mapSet *map,char *name,struct image *img,char *linkRoot)
+/* Updates an existing map (aka mapSet) */
+{
+if(name != NULL && differentStringNullOk(name,map->name))
+ {
+ if(map->name != NULL)
+ freeMem(map->name);
+ map->name = cloneString(name);
+ }
+if(img != NULL && img != map->parentImg)
+ map->parentImg = img;
+if(linkRoot != NULL && differentStringNullOk(linkRoot,map->linkRoot))
+ {
+ if(map->linkRoot != NULL)
+ freeMem(map->linkRoot);
+ map->linkRoot = cloneString(linkRoot);
+ }
+return map;
+}
+struct mapItem *mapSetItemAdd(struct mapSet *map,char *link,char *title,int topLeftX,int topLeftY,int bottomRightX,int bottomRightY)
+/* Added a single mapItem to a growing mapSet */
+{
+struct mapItem *item;
+AllocVar(item);
+if(title != NULL)
+ item->title = cloneString(title);
+if(link != NULL)
+ {
+ if(map->linkRoot != NULL && startsWith(map->linkRoot,link))
+ item->linkVar = cloneString(link + strlen(map->linkRoot));
+ else
+ item->linkVar = cloneString(link);
+ }
+item->topLeftX = topLeftX;
+item->topLeftY = topLeftY;
+item->bottomRightX = bottomRightX;
+item->bottomRightY = bottomRightY;
+slAddHead(&(map->items),item);
+//warn("Added map(%s) item '%s' count:%d",map->name,title,slCount(map->items));
+return map->items;
+}
+void mapItemFree(struct mapItem **pItem)
+/* frees all memory assocated with a single mapItem */
+{
+if(pItem != NULL && *pItem != NULL)
+ {
+ struct mapItem *item = *pItem;
+ if(item->title != NULL)
+ freeMem(item->title);
+ if(item->linkVar != NULL)
+ freeMem(item->linkVar);
+ freeMem(item);
+ *pItem = NULL;
+ }
+}
+boolean mapItemConsistentWithImage(struct mapItem *item,struct image *img,boolean verbose)
+/* Test whether a map item is consistent with the image it is supposed to be for */
+{
+if ((item->topLeftX < 0 || item->topLeftX >= img->width)
+|| (item->bottomRightX < 0 || item->bottomRightX > img->width || item->bottomRightX <= item->topLeftX)
+|| (item->topLeftY < 0 || item->topLeftY >= img->height)
+|| (item->bottomRightY < 0 || item->bottomRightY > img->height || item->bottomRightY <= item->topLeftY))
+ {
+ if (verbose)
+ warn("mapItem has coordinates (topX:%d topY:%d botX:%d botY:%d) outside of image (width:%d height:%d)",
+ item->topLeftX,item->topLeftY,item->bottomRightX,item->bottomRightY,img->width,img->height);
+ return FALSE;
+ }
+return TRUE;
+}
+boolean mapSetIsComplete(struct mapSet *map,boolean verbose)
+/* Tests the completeness and consistency of this map (mapSet) */
+{
+if (map == NULL)
+ {
+ if (verbose)
+ warn("map is NULL");
+ return FALSE;
+ }
+if (map->parentImg == NULL)
+ {
+ if (verbose)
+ warn("map is missing a parant image.");
+ return FALSE;
+ }
+if (map->parentImg->file == NULL)
+ {
+ if (verbose)
+ warn("map has image which has no file.");
+ return FALSE;
+ }
+if (map->items == NULL) // This is okay
+ {
+ //if (verbose)
+ // warn("map(%s) has no items.",(map->name?map->name:map->parentImg->file));
+ //return FALSE;
+ return TRUE; // Accept this as legitimate
+ }
+struct mapItem *item = map->items;
+for (;item != NULL; item = item->next)
+ {
+ if(!mapItemConsistentWithImage(item,map->parentImg,verbose))
+ return FALSE;
+ if(item->linkVar == NULL && map->linkRoot == NULL)
+ {
+ if (verbose)
+ warn("item for map(%s) has no link.",(map->name?map->name:map->parentImg->file));
+ return FALSE;
+ }
+ }
+return TRUE;
+}
+/* Tests the completeness and consistency of this imgTrack (not including slices) */
+void mapSetFree(struct mapSet **pMap)
+/* frees all memory (including items) assocated with a single mapSet */
+{
+if(pMap != NULL && *pMap != NULL)
+ {
+ struct mapSet *map = *pMap;
+ struct mapItem *item = NULL;
+ while((item = slPopHead(&(map->items))) != NULL )
+ mapItemFree(&item);
+ freeMem(map->name);
+ // Don't free parentImg, as it should be freed independently
+ freeMem(map->linkRoot);
+ freeMem(map);
+ *pMap = NULL;
+ }
+}
+
+//////// Images
+//struct image // IMAGEv2: single image which may have multiple imgSlices focused on it
+// {
+// struct image *next; // slList (Not yet used)
+// char *file; // name of file that hold the image
+// char *title; // image wide title
+// int width; // in pixels
+// int height; // in pixels
+// struct mapSet *map; // map assocated with this image (may be NULL)
+// };
+struct image *imgCreate(char *gif,char *title,int width,int height)
+/* Creates a single image container.
+ A map map be added with imgMapStart(),mapSetItemAdd() */
+{
+struct image *img;
+AllocVar(img);
+if(gif != NULL)
+ img->file = cloneString(gif);
+if(title != NULL)
+ img->title = cloneString(title);
+img->height = height;
+img->width = width;
+img->map = NULL;
+return img;
+}
+struct mapSet *imgMapStart(struct image *img,char *name,char *linkRoot)
+/* Starts a map associated with an image. Map items can then be added to the returned pointer with mapSetItemAdd() */
+{
+if(img->map != NULL)
+ {
+ warn("imgAddMap() but map already exists. Being replaced.");
+ mapSetFree(&(img->map));
+ }
+img->map = mapSetStart(name,img,linkRoot);
+return img->map;
+}
+struct mapSet *imgGetMap(struct image *img)
+/* Gets the map associated with this image. Map items can then be added to the map with mapSetItemAdd() */
+{
+return img->map;
+}
+void imgFree(struct image **pImg)
+/* frees all memory assocated with an image (including a map) */
+{
+if(pImg != NULL && *pImg != NULL)
+ {
+ struct image *img = *pImg;
+ mapSetFree(&(img->map));
+ freeMem(img->file);
+ freeMem(img->title);
+ freeMem(img);
+ *pImg = NULL;
+ }
+}
+
+//////// Slices
+//struct imgSlice // IMAGEv2: the portion of an image that is displayable for one track
+// {
+// struct imgSlice *next; // slList
+// enum sliceType type; // Type of slice (currently only 3)
+// struct image *parentImg;// the actual image/gif
+// char *title; // slice wide title
+// struct mapSet *map; // A slice specific map. It contains a subset of the img->map. Coordinates must be img relative NOT slice relative!
+// int width; // in pixels (differs from img->width if img contains sideLabel)
+// int height; // in pixels (differs from img->height if img contains centerLabel and/or multiple tracks)
+// int offsetX; // offset from left (when img->width > slice->width)
+// int offsetY; // offset from top (when img->height > slice->height)
+// };
+struct imgSlice *sliceCreate(enum sliceType type,struct image *img,char *title,int width,int height,int offsetX,int offsetY)
+/* Creates of a slice which is a portion of an image.
+ A slice specific map map be added with sliceMapStart(),mapSetItemAdd() */
+{
+struct imgSlice *slice;
+AllocVar(slice);
+slice->map = NULL; // This is the same as defaulting to slice->parentImg->map
+return sliceUpdate(slice,type,img,title,width,height,offsetX,offsetY);
+}
+struct imgSlice *sliceUpdate(struct imgSlice *slice,enum sliceType type,struct image *img,char *title,int width,int height,int offsetX,int offsetY)
+/* updates an already created slice */
+{
+slice->type = type;
+if(img != NULL && slice->parentImg != img)
+ slice->parentImg = img;
+if(title != NULL && differentStringNullOk(title,img->title))
+ {
+ if(img->title != NULL)
+ freeMem(img->title);
+ img->title = cloneString(title);
+ }
+slice->width = width;
+slice->height = height;
+slice->offsetX = offsetX;
+slice->offsetY = offsetY;
+return slice;
+}
+char *sliceTypeToString(enum sliceType type)
+/* Translate enum slice type to string */
+{
+switch(type)
+ {
+ case isData: return "data";
+ case isSide: return "side";
+ case isCenter: return "center";
+ default: return "unknown";
+ }
+}
+struct mapSet *sliceMapStart(struct imgSlice *slice,char *name,char *linkRoot)
+/* Adds a slice specific map to a slice of an image. Map items can then be added to the returned pointer with mapSetItemAdd()*/
+{
+if(slice->parentImg == NULL)
+ {
+ warn("sliceAddMap() but slice has no image.");
+ return NULL;
+ }
+if(slice->map != NULL && slice->map != slice->parentImg->map)
+ {
+ warn("sliceAddMap() but slice already has its own map. Being replaced.");
+ mapSetFree(&(slice->map));
+ }
+char qualifiedName[128];
+safef(qualifiedName,sizeof(qualifiedName),"%s_%s",sliceTypeToString(slice->type),name);
+slice->map = mapSetStart(qualifiedName,slice->parentImg,linkRoot);
+return slice->map;
+}
+struct mapSet *sliceGetMap(struct imgSlice *slice,boolean sliceSpecific)
+/* Gets the map associate with a slice which male be sliceSpecific or it map belong to the slices' image.
+ Map items can then be added to the map returned with mapSetItemAdd() */
+{
+if(!sliceSpecific && slice->map == NULL && slice->parentImg != NULL)
+ return slice->parentImg->map;
+return slice->map;
+}
+struct mapSet *sliceMapFindOrStart(struct imgSlice *slice,char *name,char *linkRoot)
+/* Finds the slice specific map or starts it */
+{
+struct mapSet *map = sliceGetMap(slice,TRUE); // Must be specific to this slice
+if (map == NULL)
+ map = sliceMapStart(slice,name,linkRoot);
+return map;
+}
+struct mapSet *sliceMapUpdateOrStart(struct imgSlice *slice,char *name,char *linkRoot)
+/* Updates the slice specific map or starts it */
+{
+struct mapSet *map = sliceGetMap(slice,TRUE); // Must be specific to this slice
+if (map == NULL)
+ return sliceMapStart(slice,name,linkRoot);
+char qualifiedName[128];
+safef(qualifiedName,sizeof(qualifiedName),"%s_%s",sliceTypeToString(slice->type),name);
+return mapSetUpdate(map,qualifiedName,slice->parentImg,linkRoot);
+}
+/* Adds a slice specific map to a slice of an image. Map items can then be added to the returned pointer with mapSetItemAdd()*/
+boolean sliceIsConsistent(struct imgSlice *slice,boolean verbose)
+/* Test whether the slice and it's associated image and map are consistent with each other */
+{
+if (slice == NULL)
+ {
+ if (verbose)
+ warn("slice is NULL");
+ return FALSE;
+ }
+if (slice->parentImg == NULL)
+ {
+ if (verbose)
+ warn("slice(%s) has no image",sliceTypeToString(slice->type));
+ return FALSE;
+ }
+if (slice->width == 0 || slice->width > slice->parentImg->width)
+ {
+ if (verbose)
+ warn("slice(%s) has an invalid width %d (image width %d)",
+ sliceTypeToString(slice->type),slice->width,slice->parentImg->width);
+ return FALSE;
+ }
+if (slice->height == 0 || slice->height > slice->parentImg->height)
+ {
+ if (verbose)
+ warn("slice(%s) has an invalid height %d (image height %d)",
+ sliceTypeToString(slice->type),slice->height,slice->parentImg->height);
+ return FALSE;
+ }
+if (slice->offsetX >= slice->parentImg->width
+|| slice->offsetY >= slice->parentImg->height)
+ {
+ if (verbose)
+ warn("slice(%s) has an invalid X:%d or Y:%d offset (image width:%d height:%d)",
+ sliceTypeToString(slice->type),slice->offsetX,slice->offsetY,
+ slice->parentImg->width,slice->parentImg->height);
+ return FALSE;
+ }
+if (slice->map != NULL)
+ {
+ if(!mapSetIsComplete(slice->map,verbose))
+ {
+ warn("slice(%s) has bad map",sliceTypeToString(slice->type));
+ return FALSE;
+ }
+
+ struct mapItem *item = slice->map->items;
+ for (;item != NULL; item = item->next)
+ {
+ if(!mapItemConsistentWithImage(item,slice->parentImg,verbose))
+ {
+ warn("slice(%s) map is inconsistent with slice image",sliceTypeToString(slice->type));
+ return FALSE;
+ }
+ }
+ }
+return TRUE;
+}
+void sliceFree(struct imgSlice **pSlice)
+/* frees all memory assocated with a slice (not including the image or a map belonging to the image) */
+{
+if(pSlice != NULL && *pSlice != NULL)
+ {
+ struct imgSlice *slice = *pSlice;
+ // Don't free parentImg: remember that a slice is a portion of an image
+ struct mapSet *map = sliceGetMap(slice,TRUE);// Only one that belongs to slice, not image
+ if(map != NULL)
+ mapSetFree(&map);
+ freeMem(slice->title);
+ freeMem(slice);
+ *pSlice = NULL;
+ }
+}
+
+//////// imgTracks
+//struct imgTrack // IMAGEv2: imageBox conatins list of displayed imageTracks
+// {
+// struct imgTrack *next; // slList
+// struct trackDb *tdb; // trackDb entry (should this be struct track* entry?)
+// char *name; // It is possible to have an imgTrack without a tdb, but then it mist have a name
+// char *db; // Image for db (species) (assert imgTrack matches imgBox)
+// char *chrom; // Image for chrom (assert imgTrack matches imgBox)
+// int chromStart; // Image start (absolute, not portal position)
+// int chromEnd; // Image end (absolute, not portal position)
+// boolean plusStrand; // Image covers plus strand, not minus strand
+// boolean showCenterLabel; // Initially display center label? TODO: Isn't this redundent with vis?
+// enum trackVisibility vis; // Current visibility of track image
+// struct imgSlice *slices; // Currently there should be three slices for every track: data, centerLabel, sideLabel
+// };
+struct imgTrack *imgTrackStart(struct trackDb *tdb,char *name,char *db,char *chrom,int chromStart,int chromEnd,boolean plusStrand,boolean showCenterLabel,enum trackVisibility vis,boolean reorderable)
+/* Starts an image track which will contain all image slices needed to render one track
+ Must completed by adding slices with imgTrackAddSlice() */
+{
+struct imgTrack *imgTrack; // gifTn.forHtml, pixWidth, mapName
+AllocVar(imgTrack);
+return imgTrackUpdate(imgTrack,tdb,name,db,chrom,chromStart,chromEnd,plusStrand,showCenterLabel,vis,reorderable);
+}
+struct imgTrack *imgTrackUpdate(struct imgTrack *imgTrack,struct trackDb *tdb,char *name,char *db,char *chrom,int chromStart,int chromEnd,boolean plusStrand,boolean showCenterLabel,enum trackVisibility vis,boolean reorderable)
+/* Updates an already existing image track */
+{
+if(tdb != NULL && tdb != imgTrack->tdb)
+ imgTrack->tdb = tdb;
+if(name != NULL && differentStringNullOk(imgTrack->name,name))
+ {
+ if(imgTrack->name != NULL)
+ freeMem(imgTrack->name);
+ imgTrack->name = cloneString(name);
+ }
+if(db != NULL && db != imgTrack->db)
+ imgTrack->db = db; // NOTE: Not allocated
+if(chrom != NULL && chrom != imgTrack->chrom)
+ imgTrack->chrom = chrom; // NOTE: Not allocated
+imgTrack->chromStart = chromStart;
+imgTrack->chromEnd = chromEnd;
+imgTrack->plusStrand = plusStrand;
+imgTrack->showCenterLabel = showCenterLabel;
+imgTrack->vis = vis;
+imgTrack->reorderable = reorderable;
+return imgTrack;
+}
+struct imgSlice *imgTrackSliceAdd(struct imgTrack *imgTrack,enum sliceType type, struct image *img,char *title,int width,int height,int offsetX,int offsetY)
+/* Adds slices to an image track. Expected are types: isData, isSide and isCenter */
+{
+struct imgSlice *slice = sliceCreate(type,img,title,width,height,offsetX,offsetY);
+slAddHead(&(imgTrack->slices),slice);
+return imgTrack->slices;
+}
+struct imgSlice *imgTrackSliceGetByType(struct imgTrack *imgTrack,enum sliceType type)
+/* Gets a specific slice already added to an image track. Expected are types: isData, isSide and isCenter */
+{
+struct imgSlice *slice;
+for(slice = imgTrack->slices;slice != NULL;slice=slice->next)
+ {
+ if(slice->type == type)
+ return slice;
+ }
+return NULL;
+}
+struct imgSlice *imgTrackSliceFindOrAdd(struct imgTrack *imgTrack,enum sliceType type, struct image *img,char *title,int width,int height,int offsetX,int offsetY)
+/* Find the slice or adds it */
+{
+struct imgSlice *slice = imgTrackSliceGetByType(imgTrack,type);
+if (slice == NULL)
+ slice = imgTrackSliceAdd(imgTrack,type,img,title,width,height,offsetX,offsetY);
+return slice;
+}
+struct imgSlice *imgTrackSliceUpdateOrAdd(struct imgTrack *imgTrack,enum sliceType type, struct image *img,char *title,int width,int height,int offsetX,int offsetY)
+/* Updates the slice or adds it */
+{
+struct imgSlice *slice = imgTrackSliceGetByType(imgTrack,type);
+if (slice == NULL)
+ return imgTrackSliceAdd(imgTrack,type,img,title,width,height,offsetX,offsetY);
+return sliceUpdate(slice,type,img,title,width,height,offsetX,offsetY);
+}
+
+struct mapSet *imgTrackGetMapByType(struct imgTrack *imgTrack,enum sliceType type)
+/* Gets the map assocated with a specific slice belonging to the imgTrack */
+{
+struct imgSlice *slice = imgTrackSliceGetByType(imgTrack,type);
+if(slice == NULL)
+ return NULL;
+return sliceGetMap(slice,FALSE); // Map could belong to image or could be slice specific
+}
+
+boolean imgTrackIsComplete(struct imgTrack *imgTrack,boolean verbose)
+/* Tests the completeness and consistency of this imgTrack (including slices) */
+{
+if (imgTrack == NULL)
+ {
+ if (verbose)
+ warn("imgTrack is NULL");
+ return FALSE;
+ }
+if (imgTrack->tdb == NULL && imgTrack->name == NULL)
+ {
+ if (verbose)
+ warn("imgTrack has no tdb or name");
+ return FALSE;
+ }
+char * name = (imgTrack->name != NULL ? imgTrack->name : imgTrack->tdb->tableName);
+if (imgTrack->db == NULL)
+ {
+ if (verbose)
+ warn("imgTrack(%s) has no db.",name);
+ return FALSE;
+ }
+if (imgTrack->db == NULL)
+ {
+ if (verbose)
+ warn("imgTrack(%s) has no chrom.",name);
+ return FALSE;
+ }
+if (imgTrack->chromStart >= imgTrack->chromEnd)
+ {
+ if (verbose)
+ warn("imgTrack(%s) for %s.%s:%d-%d has bad genome range.",name,
+ imgTrack->db,imgTrack->chrom,imgTrack->chromStart,imgTrack->chromEnd);
+ return FALSE;
+ }
+if(imgTrack->slices == NULL)
+ {
+ if (verbose)
+ warn("imgTrack(%s) has no slices.",name);
+ return FALSE;
+ }
+// Can have no more than one of each type of slice
+boolean found[isMaxSliceTypes] = { FALSE,FALSE,FALSE,FALSE};
+struct imgSlice *slice = imgTrack->slices;
+for(; slice != NULL; slice = slice->next )
+ {
+ if(found[slice->type])
+ {
+ if (verbose)
+ warn("imgTrack(%s) found more than one slice of type %s.",
+ name,sliceTypeToString(slice->type));
+ return FALSE;
+ }
+ found[slice->type] = TRUE;
+
+ if(!sliceIsConsistent(slice,verbose))
+ {
+ if (verbose)
+ warn("imgTrack(%s) has bad slice",name);
+ return FALSE;
+ }
+ }
+if(!found[isData])
+ {
+ if (verbose)
+ warn("imgTrack(%s) has no DATA slice.",name);
+ return FALSE;
+ }
+
+return TRUE;
+}
+void imgTrackFree(struct imgTrack **pImgTrack)
+/* frees all memory assocated with an imgTrack (including slices) */
+{
+if(pImgTrack != NULL && *pImgTrack != NULL)
+ {
+ struct imgTrack *imgTrack = *pImgTrack;
+ struct imgSlice *slice;
+ while((slice = slPopHead(&(imgTrack->slices))) != NULL )
+ sliceFree(&slice);
+ freeMem(imgTrack->name);
+ freeMem(imgTrack);
+ *pImgTrack = NULL;
+ }
+}
+
+
+//////// Image Box
+//struct imgBox // IMAGEv2: imageBox conatins all the definitions to draw an image in hgTracks
+// {
+// char *db; // database (species)
+// char *chrom; // chrom
+// int chromStart; // imageBox displays this position (though images may cover more)
+// int chromEnd; // imageBox displays this position (though images may cover more)
+// boolean plusStrand; // imgBox currently shows plus strand, not minus strand
+// boolean showSideLabel; // Initially display side label? (use 'plusStrand' for left/right)
+// struct image *images; // Contains all images for the imgBox. TEMPORARY: hgTracks creates it's current one image and I'll store it here
+// struct image *bgImg; // When track images are transparent, bgImage contains blue lines that are db coordinate granularity.
+// int portalStart; // initial visible portal within html image table (db coodinates) [May be obsoleted by js client]
+// int portalEnd; // initial visible portal within html image table (db coodinates) [May be obsoleted by js client]
+// int portalWidth; // in pixels (note that width in visible position within image position (db coodinates)
+// // TODO: I am certain there are more details needed
+// struct imgTrack *imgTracks; // slList of all images to display
+// };
+struct imgBox *imgBoxStart(char *db,char *chrom,int chromStart,int chromEnd,boolean plusStrand,boolean showSideLabel,int portalWidth)
+/* Starts an imgBox which should contain all info needed to draw the hgTracks image with multiple tracks
+ The image box must be completed using imgBoxImageAdd() and imgBoxTrackAdd() */
+{
+struct imgBox * imgBox; // gifTn.forHtml, pixWidth, mapName
+AllocVar(imgBox);
+if(db != NULL)
+ imgBox->db = cloneString(db); // NOTE: Is allocated
+if(chrom != NULL)
+ imgBox->chrom = cloneString(chrom); // NOTE: Is allocated
+imgBox->chromStart = chromStart;
+imgBox->chromEnd = chromEnd;
+imgBox->plusStrand = plusStrand;
+imgBox->showSideLabel = showSideLabel;
+imgBox->images = NULL;
+imgBox->bgImg = NULL;
+int oneThird = (chromEnd - chromStart)/3; // TODO: Currently defaulting to 1/3 of image width
+imgBox->portalStart = chromStart + oneThird;
+imgBox->portalEnd = chromEnd - oneThird;
+imgBox->portalWidth = portalWidth;
+// images are added with imgBoxImageAdd()
+// imgTracks are added with imgBoxTrackAdd()
+// Plans for slices and maps: Fill in imgTracks with slices as the map is created.
+return imgBox;
+}
+
+struct image *imgBoxImageAdd(struct imgBox *imgBox,char *gif,char *title,int width,int height,boolean backGround)
+/* Adds an image to an imgBox. The image may be extended with imgMapStart(),mapSetItemAdd() */
+{
+struct image *img = imgCreate(gif,title,width,height);
+if(backGround)
+ {
+ if(imgBox->bgImg != NULL)
+ {
+ warn("imgBoxImageAdd() for background but already exists. Being replaced.");
+ imgFree(&(imgBox->bgImg));
+ }
+ imgBox->bgImg = img;
+ return imgBox->bgImg;
+ }
+slAddHead(&(imgBox->images),img);
+return imgBox->images;
+}
+struct image *imgBoxImageFind(struct imgBox *imgBox,char *gif)
+/* Finds a specific image already added to this imgBox */
+{
+struct image *img = NULL;
+for (img = imgBox->images; img != NULL; img = img->next )
+ {
+ if (sameOk(img->file,gif))
+ return img;
+ }
+return NULL;
+}
+//boolean imgBoxImageRemove(struct imgBox *imgBox,struct image *img)
+//{
+//return slRemoveEl(&(imgBox->images),img);
+//}
+
+struct imgTrack *imgBoxTrackAdd(struct imgBox *imgBox,struct trackDb *tdb,char *name,enum trackVisibility vis,boolean showCenterLabel,boolean reorderable)
+/* Adds an imgTrack to an imgBox. The imgTrack needs to be extended with imgTrackAddSlice() */
+{
+struct imgTrack *imgTrack = imgTrackStart(tdb,name,imgBox->db,imgBox->chrom,imgBox->chromStart,imgBox->chromEnd,imgBox->plusStrand,showCenterLabel,vis,reorderable);
+slAddHead(&(imgBox->imgTracks),imgTrack);
+return imgBox->imgTracks;
+}
+struct imgTrack *imgBoxTrackFind(struct imgBox *imgBox,struct trackDb *tdb,char *name)
+/* Finds a specific imgTrack already added to this imgBox */
+{
+struct imgTrack *imgTrack = NULL;
+for (imgTrack = imgBox->imgTracks; imgTrack != NULL; imgTrack = imgTrack->next )
+ {
+ if (name != NULL && sameOk(name,imgTrack->name))
+ return imgTrack;
+ else if (imgTrack->tdb == tdb)
+ return imgTrack;
+ }
+return NULL;
+}
+struct imgTrack *imgBoxTrackFindOrAdd(struct imgBox *imgBox,struct trackDb *tdb,char *name,enum trackVisibility vis,boolean showCenterLabel,boolean reorderable)
+/* Find the imgTrack, or adds it if not found */
+{
+struct imgTrack *imgTrack = imgBoxTrackFind(imgBox,tdb,name);
+if( imgTrack == NULL)
+ imgTrack = imgBoxTrackAdd(imgBox,tdb,name,vis,showCenterLabel,reorderable);
+return imgTrack;
+}
+struct imgTrack *imgBoxTrackUpdateOrAdd(struct imgBox *imgBox,struct trackDb *tdb,char *name,enum trackVisibility vis,boolean showCenterLabel,boolean reorderable)
+/* Updates the imgTrack, or adds it if not found */
+{
+struct imgTrack *imgTrack = imgBoxTrackFind(imgBox,tdb,name);
+if( imgTrack == NULL)
+ return imgBoxTrackAdd(imgBox,tdb,name,vis,showCenterLabel,reorderable);
+
+return imgTrackUpdate(imgTrack,tdb,name,imgBox->db,imgBox->chrom,imgBox->chromStart,imgBox->chromEnd,imgBox->plusStrand,showCenterLabel,vis,reorderable);
+}
+//boolean imgBoxTrackRemove(struct imgBox *imgBox,struct imgTrack *imgTrack)
+//{
+//return slRemoveEl(&(imgBox->imgTracks),imgTrack);
+//}
+
+boolean imgBoxIsComplete(struct imgBox *imgBox,boolean verbose)
+/* Tests the completeness and consistency of an imgBox. */
+{
+if (imgBox == NULL)
+ {
+ if (verbose)
+ warn("No imgBox.");
+ return FALSE;
+ }
+if (imgBox->db == NULL)
+ {
+ if (verbose)
+ warn("imgBox has no db.");
+ return FALSE;
+ }
+if (imgBox->db == NULL)
+ {
+ if (verbose)
+ warn("imgBox has no chrom.");
+ return FALSE;
+ }
+if (imgBox->chromStart >= imgBox->chromEnd)
+ {
+ if (verbose)
+ warn("imgBox(%s.%s:%d-%d) has bad genome range.",imgBox->db,imgBox->chrom,imgBox->chromStart,imgBox->chromEnd);
+ return FALSE;
+ }
+if (imgBox->portalStart >= imgBox->portalEnd
+|| imgBox->portalStart < imgBox->chromStart
+|| imgBox->portalEnd > imgBox->chromEnd )
+ {
+ if (verbose)
+ warn("imgBox(%s.%s:%d-%d) has bad portal range: %d-%d",imgBox->db,imgBox->chrom,imgBox->chromStart,imgBox->chromEnd,imgBox->portalStart,imgBox->portalEnd);
+ return FALSE;
+ }
+
+// Must have images
+if (imgBox->images == NULL)
+ {
+ if (verbose)
+ warn("imgBox(%s.%s:%d-%d) has no images",imgBox->db,imgBox->chrom,imgBox->chromStart,imgBox->chromEnd);
+ return FALSE;
+ }
+// Must have tracks
+if (imgBox->imgTracks == NULL)
+ {
+ if (verbose)
+ warn("imgBox(%s.%s:%d-%d) has no imgTracks",imgBox->db,imgBox->chrom,imgBox->chromStart,imgBox->chromEnd);
+ return FALSE;
+ }
+struct imgTrack *imgTrack = NULL;
+for (imgTrack = imgBox->imgTracks; imgTrack != NULL; imgTrack = imgTrack->next )
+ {
+ if(!imgTrackIsComplete(imgTrack,verbose))
+ {
+ if (verbose)
+ warn("imgBox(%s.%s:%d-%d) has bad track",imgBox->db,imgBox->chrom,imgBox->chromStart,imgBox->chromEnd);
+ return FALSE;
+ }
+ if(differentWord(imgTrack->db, imgBox->db)
+ || differentWord(imgTrack->chrom, imgBox->chrom)
+ || imgTrack->chromStart != imgBox->chromStart
+ || imgTrack->chromEnd != imgBox->chromEnd
+ || imgTrack->plusStrand != imgBox->plusStrand)
+ {
+ if (verbose)
+ warn("imgBox(%s.%s:%d-%d) has inconsistent imgTrack for %s.%s:%d-%d",
+ imgBox->db, imgBox->chrom, imgBox->chromStart, imgBox->chromEnd,
+ imgTrack->db,imgTrack->chrom,imgTrack->chromStart,imgTrack->chromEnd);
+ return FALSE;
+ }
+ // Every track must have slices
+ if (imgTrack->slices == NULL)
+ {
+ if (verbose)
+ warn("imgBox(%s.%s:%d-%d) has no slices",
+ imgBox->db,imgBox->chrom,imgBox->chromStart,imgBox->chromEnd);
+ return FALSE;
+ }
+ struct imgSlice *slice = NULL;
+ for (slice = imgTrack->slices; slice != NULL; slice = slice->next )
+ {
+ if(!sliceIsConsistent(slice,verbose))
+ {
+ if (verbose)
+ warn("imgBox(%s.%s:%d-%d) has bad slice",imgBox->db,imgBox->chrom,imgBox->chromStart,imgBox->chromEnd);
+ return FALSE;
+ }
+ // Every slice must point to an image owned by the imgBox
+ if(slIxFromElement(imgBox->images,slice->parentImg) == -1)
+ {
+ if (verbose)
+ warn("imgBox(%s.%s:%d-%d) has slice(%s) for unknown image (%s)",
+ imgBox->db,imgBox->chrom,imgBox->chromStart,imgBox->chromEnd,
+ sliceTypeToString(slice->type),slice->parentImg->file);
+ return FALSE;
+ }
+ }
+ }
+return TRUE;
+}
+
+void imgBoxFree(struct imgBox **pImgBox)
+/* frees all memory assocated with an imgBox (including images and imgTracks) */
+{
+if(pImgBox != NULL && *pImgBox != NULL)
+ {
+ struct imgBox *imgBox = *pImgBox;
+ struct imgTrack *imgTrack = NULL;
+ while((imgTrack = slPopHead(&(imgBox->imgTracks))) != NULL )
+ imgTrackFree(&imgTrack);
+ struct image *img = NULL;
+ while((img = slPopHead(&(imgBox->images))) != NULL )
+ imgFree(&img);
+ imgFree(&(imgBox->bgImg));
+ freeMem(imgBox->db);
+ freeMem(imgBox->chrom);
+ freeMem(imgBox);
+ *pImgBox = NULL;
+ }
+}
+
+// Now the real work:
+void imageMapDraw(struct mapSet *map,char *name)
+/* writes an image map as HTML */
+{
+//warn("Drawing map_%s %s",name,(map == NULL?"map is NULL":map->items == NULL?"map->items is NULL":"Should draw!"));
+if(map == NULL || map->items == NULL)
+ return;
+
+hPrintf("<MAP name='map_%s'>\n", name); // map_ prefix is implicit
+struct mapItem *item = map->items;
+for(;item!=NULL;item=item->next)
+ {
+ hPrintf("<AREA SHAPE=RECT COORDS='%d,%d,%d,%d'",
+ item->topLeftX, item->topLeftY, item->bottomRightX, item->bottomRightY);
+ // TODO: remove static portion of the link and handle in js
+ if(map->linkRoot != NULL)
+ hPrintf(" HREF='%s%s'",map->linkRoot,(item->linkVar != NULL?item->linkVar:""));
+ else if(item->linkVar != NULL)
+ hPrintf(" HREF='%s'",item->linkVar);
+ else
+ warn("map item has no url!");
+
+ if(item->title != NULL)
+ hPrintf(" TITLE='%s'", item->title );
+ hPrintf(">\n" );
+ }
+hPrintf("</MAP>\n");
+}
+void sliceAndMapDraw(struct imgSlice *slice,char *name)
+/* writes a slice of an image and any assocated image map as HTML */
+{
+hPrintf("<div style='width:%dpx; height:%dpx; overflow:hidden;'",slice->width,slice->height);
+if(slice->type==isData)
+ hPrintf(" class='panDiv'");
+hPrintf(">\n");
+
+struct mapSet *map = sliceGetMap(slice,FALSE); // Could be the image map or slice specific
+if(map)
+ imageMapDraw(map,name);
+
+hPrintf("<IMG id='img_%s' src='%s' style='position:relative; left:-%dpx; top: -%dpx; border:0;'",
+ name,slice->parentImg->file,slice->offsetX,slice->offsetY);
+if(map && map->items)
+ hPrintf(" usemap='#map_%s'",name);
+if(slice->type==isSide)
+ hPrintf(" class='sideLab'");
+else if(slice->type==isCenter)
+ hPrintf(" class='centerLab'");
+else if(slice->type==isData)
+ hPrintf(" class='panImg'");
+//hPrintf(" title='[%s] width:%d height: %d offsetX: %d offsetY: %d'",
+// sliceTypeToString(slice->type),slice->width,slice->height,slice->offsetX,slice->offsetY);
+if(slice->title != NULL)
+ hPrintf(" title='%s'",slice->title); // Adds slice wide title
+else if(slice->parentImg->title != NULL)
+ hPrintf(" title='%s'",slice->parentImg->title);// Adds image wide title
+hPrintf("></div>");
+}
+void imageBoxDraw(struct imgBox *imgBox)
+/* writes a entire imgBox including all tracksas HTML */
+{
+if(!imgBoxIsComplete(imgBox,TRUE))
+ return;
+char name[128];
+
+// TODO: Add in sorting
+if(differentStringNullOk(imgBox->imgTracks->name,RULER_TRACK_NAME))
+ slReverse(&(imgBox->imgTracks));
+
+hPrintf("<!--------------- IMAGEv2 ---------------->\n");
+//commonCssStyles();
+jsIncludeFile("jquery.tablednd.js", NULL);
+// TODO: jsIncludeFile("dragScroll.js", NULL);
+hPrintf("<style type='text/css'>\n");
+hPrintf(".trDrag {opacity:0.4; padding:1px; background-color:red;}\n");// outline:red solid thin;}\n"); // opacity for FF, padding/bg for IE
+hPrintf(".dragHandle {cursor: s-resize;}\n");
+hPrintf("div.dragZoom { cursor: text; }\n");
+//hPrintf("div.panDiv { width: %dpx; overflow: hidden; }\n",imgBox->portalWidth);
+//hPrintf("div.panDivScroller { width: %dpx; overflow: hidden; }\n",imgBox->portalWidth);
+//hPrintf("img.panImg { position: relative; left: -%dpx; top: 0px; border: 0; }\n",imgBox->portalWidth);
+//hPrintf("img.centerLab { position: relative; left: -%dpx; top: 0px; border: 0; }\n",imgBox->portalWidth);
+//hPrintf("img.sideLab { border: 0; }\n");
+hPrintf("</style>\n");
+
+hPrintf("<TABLE id='imgTbl' border=0 cellspacing=0 cellpadding=0");
+hPrintf(" width=%d",imgBox->portalWidth);
+hPrintf(" class='tableWithDragAndDrop' style='border:1px solid blue;border-collapse:separate'");
+hPrintf(">\n");
+
+struct imgTrack *imgTrack = imgBox->imgTracks;
+for(;imgTrack!=NULL;imgTrack=imgTrack->next)
+ {
+ char *trackName = (imgTrack->name != NULL ? imgTrack->name : imgTrack->tdb->tableName );
+ hPrintf("<TR id='tr_%s'%s>\n",trackName,
+ (imgTrack->reorderable?" class='trDraggable'":" class='nodrop nodrag'"));
+ // leftLabel
+ if(imgBox->showSideLabel && imgBox->plusStrand)
+ {
+ safef(name,sizeof(name),"left_%s",trackName);
+ hPrintf("<TD id='td_%s'%s>\n",name,
+ (imgTrack->reorderable?" class='dragHandle' title='Drag to reorder'":""));
+ sliceAndMapDraw(imgTrackSliceGetByType(imgTrack,isSide), name);
+ hPrintf("</TD>");
+ }
+ // Main/Data image region
+ hPrintf("<TD id='td_data_%s' width=%d>\n", trackName, imgBox->portalWidth);
+ // centerLabel
+ if(imgTrack->showCenterLabel)
+ {
+ safef(name, sizeof(name), "center_%s", trackName);
+ sliceAndMapDraw(imgTrackSliceGetByType(imgTrack,isCenter), name);
+ //hPrintf("<BR>\n");
+ }
+ // data image
+ safef(name, sizeof(name), "data_%s", trackName);
+ sliceAndMapDraw(imgTrackSliceGetByType(imgTrack,isData), name);
+ hPrintf("</TD>");
+
+ // rightLabel
+ if(imgBox->showSideLabel && !imgTrack->plusStrand)
+ {
+ safef(name, sizeof(name), "right_%s", trackName);
+ hPrintf("<TD id='td_%s'>\n", name);
+ sliceAndMapDraw(imgTrackSliceGetByType(imgTrack,isSide), name);
+ hPrintf("</TD>");
+ }
+ hPrintf("</TR>");
+ }
+hPrintf("</TABLE>\n");
+hPrintf("<!--------------- IMAGEv2 ---------------->\n");
+}
+#endif//def IMAGEv2_UI