1. rtracklayer
  2. Commit f470dd1f4bdf47125e0297207c7a05a03d2c34a4
Browse code

Updates to UCSC library

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rtracklayer@57674 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 26/08/2011 13:57:00
Showing 42 changed files
src/ucsc/_bwgInternal.h
History View file @ f470dd1f
1 1 
deleted file mode 100644
... ... 
@@ -1,74 +0,0 @@
1 
-/* Stuff that should be in ucsc/bwgInternal.h, but wasn't, so
2 
-   rtracklayer put it here. */
3 
-
4 
-struct bwgBedGraphItem
5 
-/* An bedGraph-type item in a bwgSection. */
6 
-{
7 
-  struct bwgBedGraphItem *next;	/* Next in list. */
8 
-  bits32 start,end;		/* Range of chromosome covered. */
9 
-  float val;			/* Value. */
10 
-};
11 
-
12 
-struct bwgVariableStepItem
13 
-/* An variableStep type item in a bwgSection. */
14 
-{
15 
-  struct bwgVariableStepItem *next;	/* Next in list. */
16 
-  bits32 start;		/* Start position in chromosome. */
17 
-  float val;			/* Value. */
18 
-};
19 
-
20 
-struct bwgVariableStepPacked
21 
-/* An variableStep type item in a bwgSection. */
22 
-{
23 
-  bits32 start;		/* Start position in chromosome. */
24 
-  float val;			/* Value. */
25 
-};
26 
-
27 
-struct bwgFixedStepItem
28 
-/* An fixedStep type item in a bwgSection. */
29 
-{
30 
-  struct bwgFixedStepItem *next;	/* Next in list. */
31 
-  float val;			/* Value. */
32 
-};
33 
-
34 
-struct bwgFixedStepPacked
35 
-/* An fixedStep type item in a bwgSection. */
36 
-{
37 
-  float val;			/* Value. */
38 
-};
39 
-
40 
-union bwgItem
41 
-/* Union of item pointers for all possible section types. */
42 
-{
43 
-  struct bwgBedGraphItem *bedGraphList;		/* A linked list */
44 
-  struct bwgFixedStepPacked *fixedStepPacked;		/* An array */
45 
-  struct bwgVariableStepPacked *variableStepPacked;	/* An array */
46 
-  /* No packed format for bedGraph... */
47 
-};
48 
-
49 
-struct bwgSection
50 
-/* A section of a bigWig file - all on same chrom.  This is a somewhat fat data
51 
- * structure used by the bigWig creation code.  See also bwgSection for the
52 
- * structure returned by the bigWig reading code. */
53 
-{
54 
-  struct bwgSection *next;		/* Next in list. */
55 
-  char *chrom;			/* Chromosome name. */
56 
-  bits32 start,end;			/* Range of chromosome covered. */
57 
-  enum bwgSectionType type;
58 
-  union bwgItem items;		/* List/array of items in this section. */
59 
-  bits32 itemStep;			/* Step within item if applicable. */
60 
-  bits32 itemSpan;			/* Item span if applicable. */
61 
-  bits16 itemCount;			/* Number of items in section. */
62 
-  bits32 chromId;			/* Unique small integer value for chromosome. */
63 
-  bits64 fileOffset;			/* Offset of section in file. */
64 
-};
65 
-
66 
-void bwgCreate(struct bwgSection *sectionList, struct hash *chromSizeHash,
67 
-               int blockSize, int itemsPerSlot, boolean doCompress,
68 
-               char *fileName);
69 
-
70 
-struct bbiFile *bigWigFileOpen(char *fileName);
71 
-
72 
-struct bbiInterval *bigWigIntervalQuery(struct bbiFile *bwf, char *chrom,
73 
-                                        bits32 start, bits32 end,
74 
-                                        struct lm *lm);
src/ucsc/_cheapcgi.c
History View file @ f470dd1f
... ... 
@@ -1,4 +1,4 @@
1 
-/* rtracklayer took out this little utility from cheapcgi.c */
1 
+/* rtracklayer took out these little utilities from cheapcgi.c */
2 2
3 3 
 #include "common.h"
4 4
... ... 
@@ -28,3 +28,49 @@ void cgiDecode(char *in, char *out, int inLength)
28 28 
     }
29 29 
   *out++ = 0;
30 30 
 }
31 
+
32 
+char *cgiEncode(char *inString)
33 
+/* Return a cgi-encoded version of inString.
34 
+ * Alphanumerics kept as is, space translated to plus,
35 
+ * and all other characters translated to %hexVal. */
36 
+{
37 
+  char c;
38 
+  int outSize = 0;
39 
+  char *outString, *out, *in;
40 
+
41 
+  if (inString == NULL)
42 
+    return(cloneString(""));
43 
+
44 
+  /* Count up how long it will be */
45 
+  in = inString;
46 
+  while ((c = *in++) != 0)
47 
+    {
48 
+      if (isalnum(c) || c == ' ' || c == '.' || c == '_')
49 
+        outSize += 1;
50 
+      else
51 
+        outSize += 3;
52 
+    }
53 
+  outString = needMem(outSize+1);
54 
+
55 
+  /* Encode string */
56 
+  in = inString;
57 
+  out = outString;
58 
+  while ((c = *in++) != 0)
59 
+    {
60 
+      if (isalnum(c) || c == '.' || c == '_')
61 
+        *out++ = c;
62 
+      else if (c == ' ')
63 
+        *out++ = '+';
64 
+      else
65 
+        {
66 
+          unsigned char uc = c;
67 
+          char buf[4];
68 
+          *out++ = '%';
69 
+          safef(buf, sizeof(buf), "%02X", uc);
70 
+          *out++ = buf[0];
71 
+          *out++ = buf[1];
72 
+        }
73 
+    }
74 
+  *out++ = 0;
75 
+  return outString;
76 
+}
src/ucsc/_portimpl.c
History View file @ f470dd1f
... ... 
@@ -10,47 +10,38 @@ void makeDirsOnPath(char *pathName)
10 10 
  * (It's not considered a problem for the directory to already
11 11 
  * exist. ) */
12 12 
 {
13 
-/* Save a copy of current directory. */
14 
-char *curDir = cloneString(getCurrentDir());
15 13
16 
-/* Return current directory.  Abort if it fails. */
17 
-/* Make local copy of pathName. */
18 
-int len = strlen(pathName);
19 
-char pathCopy[len+1];
20 
-strcpy(pathCopy, pathName);
14 
+  /* shortcut for paths that already exist */
15 
+  if (fileExists(pathName))
16 
+    return;
21 17
22 
-/* Start at root if it's an absolute path name. */
23 
-char *s = pathCopy, *e;
24 
-if (pathCopy[0] == '/')
25 
-  {
26 
-setCurrentDir("/");
27 
-++s;
28 
-}
18 
+  /* Make local copy of pathName. */
19 
+  int len = strlen(pathName);
20 
+  char pathCopy[len+1];
21 
+  strcpy(pathCopy, pathName);
29 22
30 
-/* Step through it one slash at a time - changing directory if possible
31 
- * else making directory if possible, else dying. */
32 
-for (; !isEmpty(s); s = e)
33 
-  {
34 
-/* Find end of this section and terminate string there. */
35 
-e = strchr(s, '/');
36 
-if (e != NULL)
37 
-  *e++ = 0;
23 
+  /* Tolerate double-slashes in path, everyone else does it. */
38 24
39 
-/* Cd there.  If that fails mkdir there and then cd there. */
40 
-if (!maybeSetCurrentDir(s))
41 
-  {
42 
-if (!makeDir(s))
43 
-  {
44 
-break;
45 
-}
46 
-setCurrentDir(s);
47 
-}
48 
-}
49 
-setCurrentDir(curDir);
50 
-freeMem(curDir);
25 
+  /* Start at root if it's an absolute path name. */
26 
+  char *s = pathCopy, *e;
27 
+  while (*s++ == '/')
28 
+    /* do nothing */;
29 
+
30 
+  /* Step through it one slash at a time
31 
+   * making directory if possible, else dying. */
32 
+  for (; !isEmpty(s); s = e)
33 
+    {
34 
+      /* Find end of this section and terminate string there. */
35 
+      e = strchr(s, '/');
36 
+      if (e != NULL)
37 
+	*e = 0;
38 
+      makeDir(pathCopy);
39 
+      if (e != NULL)
40 
+	*e++ = '/';
41 
+    }
51 42 
 }
52 43
53 
-/* some shared utilities */
44 
+/* some shared utilities (osunix.c) */
54 45
55 46 
 struct fileInfo *newFileInfo(char *name, off_t size, bool isDir, int statErrno,
56 47 
                              time_t lastAccess)
src/ucsc/_portimpl.h
History View file @ f470dd1f
57 48 
new file mode 100644
... ... 
@@ -0,0 +1,6 @@
1 
+/* Utilities that rtracklayer made common between win9x and unix */
2 
+
3 
+struct fileInfo *newFileInfo(char *name, off_t size, bool isDir, int statErrno,
4 
+                             time_t lastAccess);
5 
+
6 
+int cmpFileInfo(const void *va, const void *vb);
src/ucsc/bbiFile.h
History View file @ f470dd1f
... ... 
@@ -49,13 +49,14 @@
49 49 
  *                 sumData      4 bytes float
50 50 
  *                 sumSquares   4 bytes float
51 51 
  *         zoom index        	cirTree index
52 
+ *     magic# 		4 bytes - same as magic number at start of header
52 53 
  */
53 54
54 55 
 #ifndef CIRTREE_H
55 56 
 #include "cirTree.h"
56 57 
 #endif
57 58
58 
-#define bbiCurrentVersion 3
59 
+#define bbiCurrentVersion 4
59 60 
 /* Version history (of file format, not utilities - corresponds to version field in header)
60 61 
  *    1 - Initial release
61 62 
  *    1 - Unfortunately when attempting a transparent change to encoders, made the sectionCount
... ... 
@@ -66,6 +67,8 @@
66 67 
  *        zoom in files made by bedToBigBed and bedGraphToBigWig.  (The older wigToBigWig was fine.)
67 68 
  *        Added totalSummary section.
68 69 
  *    3 - Adding zlib compression.  Only active if uncompressBufSize is non-zero in header.
70 
+ *    4 - Fixed problem in encoder for the max field in zoom levels higher than the first one.
71 
+ *        Added an extra sig at end of file.
69 72 
  */
70 73
71 74 
 struct bbiZoomLevel
... ... 
@@ -349,4 +352,10 @@ bits64 bbiWriteSummaryAndIndex(struct bbiSummary *summaryList,
349 352 
 /* Write out summary and index to summary, returning start position of
350 353 
  * summary index. */
351 354
355 
+boolean bbiFileCheckSigs(char *fileName, bits32 sig, char *typeName);
356 
+/* check file signatures at beginning and end of file */
357 
+
358 
+time_t bbiUpdateTime(struct bbiFile *bbi);
359 
+/* return bbi->udc->updateTime */
360 
+
352 361 
 #endif /* BBIFILE_H */
src/ucsc/bbiRead.c
History View file @ f470dd1f
... ... 
@@ -37,6 +37,44 @@ for (level = levelList; level != NULL; level = level->next)
37 37 
 return closestLevel;
38 38 
 }
39 39
40 
+boolean bbiFileCheckSigs(char *fileName, bits32 sig, char *typeName)
41 
+/* check file signatures at beginning and end of file */
42 
+{
43 
+int fd = mustOpenFd(fileName, O_RDONLY);
44 
+bits32 magic;
45 
+boolean isSwapped = FALSE;
46 
+
47 
+// look for signature at the beginning of the file
48 
+mustReadFd(fd, &magic, sizeof(magic));
49 
+
50 
+if (magic != sig)
51 
+    {
52 
+    magic = byteSwap32(magic);
53 
+    isSwapped = TRUE;
54 
+    if (magic != sig)
55 
+        return FALSE;
56 
+    }
57 
+
58 
+// look for signature at the end of the file
59 
+mustLseek(fd, -sizeof(magic), SEEK_END);
60 
+mustReadFd(fd, &magic, sizeof(magic));
61 
+mustCloseFd(&fd);
62 
+
63 
+if (isSwapped)
64 
+    {
65 
+    magic = byteSwap32(magic);
66 
+    if (magic != sig)
67 
+        return FALSE;
68 
+    }
69 
+else
70 
+    {
71 
+    if (magic != sig)
72 
+        return FALSE;
73 
+    }
74 
+
75 
+return TRUE;
76 
+}
77 
+
40 78 
 struct bbiFile *bbiFileOpen(char *fileName, bits32 sig, char *typeName)
41 79 
 /* Open up big wig or big bed file. */
42 80 
 {
... ... 
@@ -551,11 +589,11 @@ if (start >= end)
551 589 
     return result;
552 590 
 bzero(summary, summarySize * sizeof(summary[0]));
553 591
554 
-/* Figure out what size of data we want.  We actually want to get 4 data points per summary
592 
+/* Figure out what size of data we want.  We actually want to get 2 data points per summary
555 593 
  * value if possible to minimize the effect of a data point being split between summary pixels. */
556 594 
 bits32 baseSize = end - start;
557 595 
 int fullReduction = (baseSize/summarySize);
558 
-int zoomLevel = fullReduction/4;
596 
+int zoomLevel = fullReduction/2;
559 597 
 if (zoomLevel < 0)
560 598 
     zoomLevel = 0;
561 599
... ... 
@@ -692,3 +730,9 @@ else if (bbi->version == 1)
692 730 
 return res;
693 731 
 }
694 732
733 
+time_t bbiUpdateTime(struct bbiFile *bbi)
734 
+/* return bbi->udc->updateTime */
735 
+{
736 
+struct udcFile *udc = bbi->udc;
737 
+return udcUpdateTime(udc);
738 
+}
src/ucsc/bbiWrite.c
History View file @ f470dd1f
... ... 
@@ -7,6 +7,7 @@
7 7 
 #include "cirTree.h"
8 8 
 #include "bPlusTree.h"
9 9 
 #include "bbiFile.h"
10 
+#include "obscure.h"
10 11
11 12 
 void bbiWriteDummyHeader(FILE *f)
12 13 
 /* Write out all-zero header, just to reserve space for it. */
... ... 
@@ -30,6 +31,16 @@ writeOne(f, sum->sumData);
30 31 
 writeOne(f, sum->sumSquares);
31 32 
 }
32 33
34 
+static int bbiChromInfoCmp(const void *va, const void *vb)
35 
+/* Sort bbiChromInfo.  Unlike most of our sorts this is single rather
36 
+ * than double indirect. */
37 
+{
38 
+const struct bbiChromInfo *a = (const struct bbiChromInfo *)va;
39 
+const struct bbiChromInfo *b = (const struct bbiChromInfo *)vb;
40 
+return strcmp(a->name, b->name);
41 
+}
42 
+
43 
+
33 44 
 void bbiWriteChromInfo(struct bbiChromUsage *usageList, int blockSize, FILE *f)
34 45 
 /* Write out information on chromosomes to file. */
35 46 
 {
... ... 
@@ -52,6 +63,9 @@ for (i=0, usage = usageList; i<chromCount; ++i, usage = usage->next)
52 63 
     chromInfoArray[i].size = usage->size;
53 64 
     }
54 65
66 
+/* Sort so the b-Tree actually works. */
67 
+qsort(chromInfoArray, chromCount, sizeof(chromInfoArray[0]), bbiChromInfoCmp);
68 
+
55 69 
 /* Write chromosome bPlusTree */
56 70 
 int chromBlockSize = min(blockSize, chromCount);
57 71 
 bptFileBulkIndexToOpenFile(chromInfoArray, sizeof(chromInfoArray[0]), chromCount, chromBlockSize,
... ... 
@@ -130,6 +144,9 @@ int lastStart = -1;
130 144 
 bits32 id = 0;
131 145 
 bits64 totalBases = 0, bedCount = 0;
132 146 
 int minDiff = BIGNUM;
147 
+
148 
+lineFileRemoveInitialCustomTrackLines(lf);
149 
+
133 150 
 for (;;)
134 151 
     {
135 152 
     int rowSize = lineFileChopNext(lf, row, ArraySize(row));
... ... 
@@ -139,6 +156,16 @@ for (;;)
139 156 
     char *chrom = row[0];
140 157 
     int start = lineFileNeedNum(lf, row, 1);
141 158 
     int end = lineFileNeedNum(lf, row, 2);
159 
+    if (start >= end)
160 
+        {
161 
+	if (start == end)
162 
+	    errAbort("line %d of %s: start and end coordinates the same\n"
163 
+	             "They need to be at least one apart"
164 
+		     , lf->lineIx, lf->fileName);
165 
+	else
166 
+	    errAbort("end (%d) before start (%d) line %d of %s",
167 
+	    	end, start, lf->lineIx, lf->fileName);
168 
+	}
142 169 
     ++bedCount;
143 170 
     totalBases += (end - start);
144 171 
     if (usage == NULL || differentString(usage->name, chrom))
... ... 
@@ -149,10 +176,14 @@ for (;;)
149 176 
 	    	lf->fileName, lf->lineIx);
150 177 
 	    }
151 178 
 	hashAdd(uniqHash, chrom, NULL);
179 
+	struct hashEl *chromHashEl = hashLookup(chromSizesHash, chrom);
180 
+	if (chromHashEl == NULL)
181 
+	    errAbort("%s is not found in chromosome sizes file", chrom);
182 
+	int chromSize = ptToInt(chromHashEl->val);
152 183 
 	AllocVar(usage);
153 184 
 	usage->name = cloneString(chrom);
154 185 
 	usage->id = id++;
155 
-	usage->size = hashIntVal(chromSizesHash, chrom);
186 
+	usage->size = chromSize;
156 187 
 	slAddHead(&usageList, usage);
157 188 
 	lastStart = -1;
158 189 
 	}
... ... 
@@ -222,7 +253,7 @@ while (start < end)
222 253 
 	newSum->minVal = minVal;
223 254 
 	newSum->maxVal = maxVal;
224 255 
 	sum = newSum;
225 
-        slAddHead(pOutList, sum);
256 
+	slAddHead(pOutList, sum);
226 257 
 	}
227 258
228 259 
     /* Figure out amount of overlap between current summary and item */
... ... 
@@ -519,7 +550,7 @@ else
519 550 
     twiceReduced->end = sum->end;
520 551 
     twiceReduced->validCount += sum->validCount;
521 552 
     if (sum->minVal < twiceReduced->minVal) twiceReduced->minVal = sum->minVal;
522 
-    if (sum->maxVal < twiceReduced->maxVal) twiceReduced->maxVal = sum->maxVal;
553 
+    if (sum->maxVal > twiceReduced->maxVal) twiceReduced->maxVal = sum->maxVal;
523 554 
     twiceReduced->sumData += sum->sumData;
524 555 
     twiceReduced->sumSquares += sum->sumSquares;
525 556 
     }
src/ucsc/bigBed.h
History View file @ f470dd1f
... ... 
@@ -68,35 +68,8 @@ char *bigBedAutoSqlText(struct bbiFile *bbi);
68 68 
 struct asObject *bigBedAs(struct bbiFile *bbi);
69 69 
 /* Get autoSql object definition if any associated with file. */
70 70
71 
-void bigBedFileCreate(
72 
-	char *inName, 	  /* Input file in a tabular bed format <chrom><start><end> + whatever. */
73 
-	char *chromSizes, /* Two column tab-separated file: <chromosome> <size>. */
74 
-	int blockSize,	  /* Number of items to bundle in r-tree.  1024 is good. */
75 
-	int itemsPerSlot, /* Number of items in lowest level of tree.  64 is good. */
76 
-	bits16 definedFieldCount,  /* Number of defined bed fields - 3-16 or so.  0 means all fields
77 
-				    * are the defined bed ones. */
78 
-	char *asFileName, /* If non-null points to a .as file that describes fields. */
79 
-	boolean clip,     /* If set silently clip out of bound coordinates. */
80 
-	char *outName);   /* BigBed output file name. */
81 
-/* Convert tab-separated bed file to binary indexed, zoomed bigBed version. */
82 
-
83 
-void bigBedFileCreateDetailed(
84 
-	struct ppBed *pbList, 	  /* Input bed data. Must be sorted. */
85 
-	bits64 pbCount,           /* size of input pbList */
86 
-	double pbAverageSize,     /* average size of elements in pbList */
87 
-	char *inName,             /* Input file name (for error message reporting) */
88 
-	struct hash *chromHash,   /* Hash containing sizes of all chroms. */
89 
-	int blockSize,	  /* Number of items to bundle in r-tree.  1024 is good. */
90 
-	int itemsPerSlot, /* Number of items in lowest level of tree.  64 is good. */
91 
-	bits16 definedFieldCount, /* Number of defined bed fields - 3-16 or so.  0 means all fields
92 
-				    * are the defined bed ones. */
93 
-	bits16 fieldCount,        /* actual field count from input data. */
94 
-	char *asFileName,         /* If non-null points to a .as file that describes fields. */
95 
-	struct asObject *as,      /* If non-null contains as object that describes fields. */
96 
-	bits64 fullSize,          /* full size of ppBed on disk */
97 
-	char *outName);            /* BigBed output file name. */
98 
-/* create zoomed bigBed version from ppBed list. */
99 
-
71 
+boolean bigBedFileCheckSigs(char *fileName);
72 
+/* check file signatures at beginning and end of file */
100 73
101 74 
 #endif /* BIGBED_H */
102 75
src/ucsc/bigWig.h
History View file @ f470dd1f
... ... 
@@ -23,6 +23,9 @@
23 23 
 #include "bbiFile.h"
24 24 
 #endif
25 25
26 
+#ifndef BITS_H
27 
+#include "bits.h"
28 
+#endif
26 29
27 30 
 void bigWigFileCreate(
28 31 
 	char *inName, 		/* Input file in ascii wiggle format. */
... ... 
@@ -66,5 +69,44 @@ double bigWigSingleSummary(struct bbiFile *bwf, char *chrom, int start, int end,
66 69 
     enum bbiSummaryType summaryType, double defaultVal);
67 70 
 /* Return the summarized single value for a range. */
68 71
72 
+boolean isBigWig(char *fileName);
73 
+/* Peak at a file to see if it's bigWig */
74 
+
75 
+boolean bigWigFileCheckSigs(char *fileName);
76 
+/* check file signatures at beginning and end of file */
77 
+
78 
+/* bigWigValsOnChrom - a little system for optimizing bigWig use when doing a pass over the
79 
+ * whole chromosome.   How it is used typically is:
80 
+ *      struct bigWigValsOnChrom *chromVals = bigWigValsOnChromNew();
81 
+ *      for (chrom = chromList; chrom != NULL; chrom = chrom->next)
82 
+ *          {
83 
+ *          if (bigWigValsOnChromFetchData(chromVals, chrom->name, bigWig))
84 
+ *              // do stuff using the valBuf, or covBuf fields which have
85 
+ *              // the big wig data unpacked into them. Can use chromSize and chrom too
86 
+ *          }
87 
+ *       bigWigValsOnChromFree(&chromVals);  */
88 
+
89 
+struct bigWigValsOnChrom
90 
+/* Object for bulk access a chromosome at a time.  This is faster than
91 
+ * doing bigWigInterval queries when you have ~3000 or more queries. */
92 
+     {
93 
+     struct bigWigValsOnChrom *next;
94 
+     char *chrom;	/* Current chromosome. */
95 
+     long chromSize;	/* Size of current chromosome. */
96 
+     long bufSize;	/* Size of allocated buffer */
97 
+     double *valBuf;	/* A value for each base on chrom. Zero where no data. */
98 
+     Bits *covBuf;	/* A bit for each base with data. */
99 
+     };
100 
+
101 
+struct bigWigValsOnChrom *bigWigValsOnChromNew();
102 
+/* Allocate new empty bigWigValsOnChromStructure. */
103 
+
104 
+void bigWigValsOnChromFree(struct bigWigValsOnChrom **pChromVals);
105 
+/* Free up bigWigValsOnChrom */
106 
+
107 
+boolean bigWigValsOnChromFetchData(struct bigWigValsOnChrom *chromVals, char *chrom,
108 
+	struct bbiFile *bigWig);
109 
+/* Fetch data for chromosome from bigWig. Returns FALSE if not data on that chrom. */
110 
+
69 111 
 #endif /* BIGWIG_H */
70 112
src/ucsc/bwgCreate.c
History View file @ f470dd1f
... ... 
@@ -15,70 +15,7 @@
15 15 
 #include "bwgInternal.h"
16 16 
 #include "bigWig.h"
17 17
18 
-static char const rcsid[] = "$Id: bwgCreate.c,v 1.22 2009/11/25 07:17:25 kent Exp $";
19 
-
20 
-struct bwgBedGraphItem
21 
-/* An bedGraph-type item in a bwgSection. */
22 
-    {
23 
-    struct bwgBedGraphItem *next;	/* Next in list. */
24 
-    bits32 start,end;		/* Range of chromosome covered. */
25 
-    float val;			/* Value. */
26 
-    };
27 
-
28 
-struct bwgVariableStepItem
29 
-/* An variableStep type item in a bwgSection. */
30 
-    {
31 
-    struct bwgVariableStepItem *next;	/* Next in list. */
32 
-    bits32 start;		/* Start position in chromosome. */
33 
-    float val;			/* Value. */
34 
-    };
35 
-
36 
-struct bwgVariableStepPacked
37 
-/* An variableStep type item in a bwgSection. */
38 
-    {
39 
-    bits32 start;		/* Start position in chromosome. */
40 
-    float val;			/* Value. */
41 
-    };
42 
-
43 
-struct bwgFixedStepItem
44 
-/* An fixedStep type item in a bwgSection. */
45 
-    {
46 
-    struct bwgFixedStepItem *next;	/* Next in list. */
47 
-    float val;			/* Value. */
48 
-    };
49 
-
50 
-struct bwgFixedStepPacked
51 
-/* An fixedStep type item in a bwgSection. */
52 
-    {
53 
-    float val;			/* Value. */
54 
-    };
55 
-
56 
-union bwgItem
57 
-/* Union of item pointers for all possible section types. */
58 
-    {
59 
-    struct bwgBedGraphItem *bedGraphList;		/* A linked list */
60 
-    struct bwgFixedStepPacked *fixedStepPacked;		/* An array */
61 
-    struct bwgVariableStepPacked *variableStepPacked;	/* An array */
62 
-    /* No packed format for bedGraph... */
63 
-    };
64 
-
65 
-struct bwgSection
66 
-/* A section of a bigWig file - all on same chrom.  This is a somewhat fat data
67 
- * structure used by the bigWig creation code.  See also bwgSection for the
68 
- * structure returned by the bigWig reading code. */
69 
-    {
70 
-    struct bwgSection *next;		/* Next in list. */
71 
-    char *chrom;			/* Chromosome name. */
72 
-    bits32 start,end;			/* Range of chromosome covered. */
73 
-    enum bwgSectionType type;
74 
-    union bwgItem items;		/* List/array of items in this section. */
75 
-    bits32 itemStep;			/* Step within item if applicable. */
76 
-    bits32 itemSpan;			/* Item span if applicable. */
77 
-    bits16 itemCount;			/* Number of items in section. */
78 
-    bits32 chromId;			/* Unique small integer value for chromosome. */
79 
-    bits64 fileOffset;			/* Offset of section in file. */
80 
-    };
81 
-
18 
+static char const rcsid[] = "$Id: bwgCreate.c,v 1.27 2010/06/10 20:13:29 braney Exp $";
82 19
83 20 
 static int bwgBedGraphItemCmp(const void *va, const void *vb)
84 21 
 /* Compare to sort based on query start. */
... ... 
@@ -200,7 +137,7 @@ return bufSize;
200 137 
 }
201 138
202 139
203 
-static int bwgSectionCmp(const void *va, const void *vb)
140 
+int bwgSectionCmp(const void *va, const void *vb)
204 141 
 /* Compare to sort based on chrom,start,end.  */
205 142 
 {
206 143 
 const struct bwgSection *a = *((struct bwgSection **)va);
... ... 
@@ -338,7 +275,7 @@ struct lm *lmLocal = lmInit(0);
338 275 
  * adding values from single column to list. */
339 276 
 char *words[2];
340 277 
 char *line;
341 
-struct bwgVariableStepItem *item, *itemList = NULL;
278 
+struct bwgVariableStepItem *item, *nextItem, *itemList = NULL;
342 279 
 int originalSectionSize = 0;
343 280 
 while (lineFileNextReal(lf, &line))
344 281 
     {
... ... 
@@ -372,6 +309,20 @@ while (lineFileNextReal(lf, &line))
372 309 
     }
373 310 
 slSort(&itemList, bwgVariableStepItemCmp);
374 311
312 
+/* Make sure no overlap between items. */
313 
+if (itemList != NULL)
314 
+    {
315 
+    item = itemList;
316 
+    for (nextItem = item->next; nextItem != NULL; nextItem = nextItem->next)
317 
+        {
318 
+	if (item->start + span > nextItem->start)
319 
+	    errAbort("Overlap on %s between items starting at %d and %d.\n"
320 
+	             "Please remove overlaps and try again",
321 
+		    chrom, item->start, nextItem->start);
322 
+	item = nextItem;
323 
+	}
324 
+    }
325 
+
375 326 
 /* Break up into sections of no more than items-per-slot size. */
376 327 
 int sizeLeft = originalSectionSize;
377 328 
 for (item = itemList; item != NULL; )
... ... 
@@ -435,7 +386,7 @@ else
435 386 
     errAbort("Unknown type %s\n", typeWord);
436 387
437 388 
 /* Set up defaults for values we hope to parse out of rest of line. */
438 
-int span = 1;
389 
+int span = 0;
439 390 
 bits32 step = 0;
440 391 
 bits32 start = 0;
441 392 
 char *chrom = NULL;
... ... 
@@ -468,8 +419,8 @@ while ((varEqVal = nextWord(&initialLine)) != NULL)
468 419 
  * rest of section. */
469 420 
 if (chrom == NULL)
470 421 
     errAbort("Missing chrom= setting line %d of %s\n", lf->lineIx, lf->fileName);
471 
-bits32 chromSize = hashIntVal(chromSizeHash, chrom);
472 
-if (start >= chromSize)
422 
+bits32 chromSize = (chromSizeHash ? hashIntVal(chromSizeHash, chrom) : BIGNUM);
423 
+if (start > chromSize)
473 424 
     {
474 425 
     warn("line %d of %s: chromosome %s has %u bases, but item starts at %u",
475 426 
     	lf->lineIx, lf->fileName, chrom, chromSize, start);
... ... 
@@ -482,6 +433,8 @@ if (type == bwgTypeFixedStep)
482 433 
 	errAbort("Missing start= setting line %d of %s\n", lf->lineIx, lf->fileName);
483 434 
     if (step == 0)
484 435 
 	errAbort("Missing step= setting line %d of %s\n", lf->lineIx, lf->fileName);
436 
+    if (span == 0)
437 
+	span = step;
485 438 
     parseFixedStepSection(lf, clipDontDie, lm, itemsPerSlot,
486 439 
     	chrom, chromSize, span, start-1, step, pSectionList);
487 440 
     }
... ... 
@@ -491,6 +444,8 @@ else
491 444 
 	errAbort("Extra start= setting line %d of %s\n", lf->lineIx, lf->fileName);
492 445 
     if (step != 0)
493 446 
 	errAbort("Extra step= setting line %d of %s\n", lf->lineIx, lf->fileName);
447 
+    if (span == 0)
448 
+	span = 1;
494 449 
     parseVariableStepSection(lf, clipDontDie, lm, itemsPerSlot,
495 450 
     	chrom, chromSize, span, pSectionList);
496 451 
     }
... ... 
@@ -546,7 +501,7 @@ while (lineFileNextReal(lf, &line))
546 501 
         {
547 502 
 	lmAllocVar(chromHash->lm, chrom);
548 503 
 	hashAddSaveName(chromHash, chromName, chrom, &chrom->name);
549 
-	chrom->size = hashIntVal(chromSizeHash, chromName);
504 
+	chrom->size = (chromSizeHash ? hashIntVal(chromSizeHash, chromName) : BIGNUM);
550 505 
 	slAddHead(&chromList, chrom);
551 506 
 	}
552 507
... ... 
@@ -574,10 +529,22 @@ while (lineFileNextReal(lf, &line))
574 529 
     }
575 530 
 slSort(&chromList, bedGraphChromCmpName);
576 531
532 
+/* Loop through each chromosome and output the item list, broken into sections
533 
+ * for that chrom. */
577 534 
 for (chrom = chromList; chrom != NULL; chrom = chrom->next)
578 535 
     {
579 536 
     slSort(&chrom->itemList, bwgBedGraphItemCmp);
580 537
538 
+    /* Check to make sure no overlap between items. */
539 
+    struct bwgBedGraphItem *item = chrom->itemList, *nextItem;
540 
+    for (nextItem = item->next; nextItem != NULL; nextItem = nextItem->next)
541 
+        {
542 
+	if (item->end > nextItem->start)
543 
+	    errAbort("Overlap between %s %d %d and %s %d %d.\nPlease remove overlaps and try again",
544 
+	        chrom->name, item->start, item->end, chrom->name, nextItem->start, nextItem->end);
545 
+	item = nextItem;
546 
+	}
547 
+
581 548 
     /* Break up into sections of no more than items-per-slot size. */
582 549 
     struct bwgBedGraphItem *startItem, *endItem, *nextStartItem = chrom->itemList;
583 550 
     for (startItem = chrom->itemList; startItem != NULL; startItem = nextStartItem)
... ... 
@@ -832,8 +799,7 @@ return outList;
832 799 
 }
833 800
834 801 
 void bwgCreate(struct bwgSection *sectionList, struct hash *chromSizeHash,
835 
-               int blockSize, int itemsPerSlot, boolean doCompress,
836 
-               char *fileName)
802 
+	int blockSize, int itemsPerSlot, boolean doCompress, char *fileName)
837 803 
 /* Create a bigWig file out of a sorted sectionList. */
838 804 
 {
839 805 
 bits64 sectionCount = slCount(sectionList);
... ... 
@@ -862,12 +828,12 @@ struct bbiChromInfo *chromInfoArray;
862 828 
 int chromCount, maxChromNameSize;
863 829 
 bwgMakeChromInfo(sectionList, chromSizeHash, &chromCount, &chromInfoArray, &maxChromNameSize);
864 830
865 
-/* Figure out initial summary level - starting with a summary 20 times the amount
831 
+/* Figure out initial summary level - starting with a summary 10 times the amount
866 832 
  * of the smallest item.  See if summarized data is smaller than half input data, if
867 833 
  * not bump up reduction by a factor of 2 until it is, or until further summarying
868 834 
  * yeilds no size reduction. */
869 835 
 int  minRes = bwgAverageResolution(sectionList);
870 
-int initialReduction = minRes*20;
836 
+int initialReduction = minRes*10;
871 837 
 bits64 fullSize = bwgTotalSectionSize(sectionList);
872 838 
 bits64 maxReducedSize = fullSize/2;
873 839 
 struct bbiSummary *firstSummaryList = NULL, *summaryList = NULL;
... ... 
@@ -878,8 +844,7 @@ for (;;)
878 844 
     bits64 summarySize = bbiTotalSummarySize(summaryList);
879 845 
     if (doCompress)
880 846 
 	{
881 
-        summarySize *= 4;	// Compensate for summary not compressing as well as primary data
882 
-	initialReduction *= 4;
847 
+        summarySize *= 2;	// Compensate for summary not compressing as well as primary data
883 848 
 	}
884 849 
     if (summarySize >= maxReducedSize && summarySize != lastSummarySize)
885 850 
         {
... ... 
@@ -1049,18 +1014,30 @@ for (i=0; i<summaryCount; ++i)
1049 1014 
     writeOne(f, reductionIndexOffsets[i]);
1050 1015 
     }
1051 1016
1017 
+/* Write end signature. */
1018 
+fseek(f, 0L, SEEK_END);
1019 
+writeOne(f, sig);
1020 
+
1052 1021 
 /* Clean up */
1053 1022 
 freez(&chromInfoArray);
1054 1023 
 carefulClose(&f);
1055 1024 
 }
1056 1025
1057 
-struct bwgSection *bwgParseWig(char *fileName, boolean clipDontDie, struct hash *chromSizeHash,
1058 
-	int maxSectionSize, struct lm *lm)
1026 
+struct bwgSection *bwgParseWig(
1027 
+	char *fileName,       /* Name of ascii wig file. */
1028 
+	boolean clipDontDie,  /* Skip items outside chromosome rather than aborting. */
1029 
+	struct hash *chromSizeHash,  /* If non-NULL items checked to be inside chromosome. */
1030 
+	int maxSectionSize,   /* Biggest size of a section.  100 - 100,000 is usual range. */
1031 
+	struct lm *lm)	      /* Memory pool to allocate from. */
1059 1032 
 /* Parse out ascii wig file - allocating memory in lm. */
1060 1033 
 {
1061 1034 
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
1062 1035 
 char *line;
1063 1036 
 struct bwgSection *sectionList = NULL;
1037 
+
1038 
+/* remove initial browser and track lines */
1039 
+lineFileRemoveInitialCustomTrackLines(lf);
1040 
+
1064 1041 
 while (lineFileNextReal(lf, &line))
1065 1042 
     {
1066 1043 
     verbose(2, "processing %s\n", line);
... ... 
@@ -1089,7 +1066,7 @@ while (lineFileNextReal(lf, &line))
1089 1066 
     }
1090 1067 
 slSort(&sectionList, bwgSectionCmp);
1091 1068
1092 
-/* Check for overlap. */
1069 
+/* Check for overlap at section level. */
1093 1070 
 struct bwgSection *section, *nextSection;
1094 1071 
 for (section = sectionList; section != NULL; section = nextSection)
1095 1072 
     {
src/ucsc/bwgInternal.h
History View file @ f470dd1f
... ... 
@@ -14,8 +14,93 @@ enum bwgSectionType
14 14 
     bwgTypeFixedStep=3,
15 15 
     };
16 16
17 
-struct bwgSection *bwgParseWig(char *fileName, boolean clipDontDie, struct hash *chromSizeHash,
18 
-	int maxSectionSize, struct lm *lm);
17 
+struct bwgBedGraphItem
18 
+/* An bedGraph-type item in a bwgSection. */
19 
+    {
20 
+    struct bwgBedGraphItem *next;	/* Next in list. */
21 
+    bits32 start,end;		/* Range of chromosome covered. */
22 
+    float val;			/* Value. */
23 
+    };
24 
+
25 
+struct bwgVariableStepItem
26 
+/* An variableStep type item in a bwgSection. */
27 
+    {
28 
+    struct bwgVariableStepItem *next;	/* Next in list. */
29 
+    bits32 start;		/* Start position in chromosome. */
30 
+    float val;			/* Value. */
31 
+    };
32 
+
33 
+struct bwgVariableStepPacked
34 
+/* An variableStep type item in a bwgSection. */
35 
+    {
36 
+    bits32 start;		/* Start position in chromosome. */
37 
+    float val;			/* Value. */
38 
+    };
39 
+
40 
+struct bwgFixedStepItem
41 
+/* An fixedStep type item in a bwgSection. */
42 
+    {
43 
+    struct bwgFixedStepItem *next;	/* Next in list. */
44 
+    float val;			/* Value. */
45 
+    };
46 
+
47 
+struct bwgFixedStepPacked
48 
+/* An fixedStep type item in a bwgSection. */
49 
+    {
50 
+    float val;			/* Value. */
51 
+    };
52 
+
53 
+union bwgItem
54 
+/* Union of item pointers for all possible section types. */
55 
+    {
56 
+    struct bwgBedGraphItem *bedGraphList;		/* A linked list */
57 
+    struct bwgFixedStepPacked *fixedStepPacked;		/* An array */
58 
+    struct bwgVariableStepPacked *variableStepPacked;	/* An array */
59 
+    /* No packed format for bedGraph... */
60 
+    };
61 
+
62 
+struct bwgSection
63 
+/* A section of a bigWig file - all on same chrom.  This is a somewhat fat data
64 
+ * structure used by the bigWig creation code.  See also bwgSection for the
65 
+ * structure returned by the bigWig reading code. */
66 
+    {
67 
+    struct bwgSection *next;		/* Next in list. */
68 
+    char *chrom;			/* Chromosome name. */
69 
+    bits32 start,end;			/* Range of chromosome covered. */
70 
+    enum bwgSectionType type;
71 
+    union bwgItem items;		/* List/array of items in this section. */
72 
+    bits32 itemStep;			/* Step within item if applicable. */
73 
+    bits32 itemSpan;			/* Item span if applicable. */
74 
+    bits16 itemCount;			/* Number of items in section. */
75 
+    bits32 chromId;			/* Unique small integer value for chromosome. */
76 
+    bits64 fileOffset;			/* Offset of section in file. */
77 
+    };
78 
+
79 
+struct bwgSectionHead
80 
+/* A header from a bigWig file section - similar to above bug what is on disk. */
81 
+    {
82 
+    bits32 chromId;	/* Chromosome short identifier. */
83 
+    bits32 start,end;	/* Range covered. */
84 
+    bits32 itemStep;	/* For some section types, the # of bases between items. */
85 
+    bits32 itemSpan;	/* For some section types, the # of bases in each item. */
86 
+    UBYTE type;		/* Type byte. */
87 
+    UBYTE reserved;	/* Always zero for now. */
88 
+    bits16 itemCount;	/* Number of items in block. */
89 
+    };
90 
+
91 
+void bwgSectionHeadFromMem(char **pPt, struct bwgSectionHead *head, boolean isSwapped);
92 
+/* Read section header. */
93 
+
94 
+
95 
+int bwgSectionCmp(const void *va, const void *vb);
96 
+/* Compare to sort based on chrom,start,end.  */
97 
+
98 
+struct bwgSection *bwgParseWig(
99 
+	char *fileName,       /* Name of ascii wig file. */
100 
+	boolean clipDontDie,  /* Skip items outside chromosome rather than aborting. */
101 
+	struct hash *chromSizeHash,  /* If non-NULL items checked to be inside chromosome. */
102 
+	int maxSectionSize,   /* Biggest size of a section.  100 - 100,000 is usual range. */
103 
+	struct lm *lm);	      /* Memory pool to allocate from. */
19 104 
 /* Parse out ascii wig file - allocating memory in lm. */
20 105
21 106 
 int bwgAverageResolution(struct bwgSection *sectionList);
src/ucsc/bwgQuery.c
History View file @ f470dd1f
... ... 
@@ -20,7 +20,7 @@
20 20 
 #include "bigWig.h"
21 21 
 #include "bigBed.h"
22 22
23 
-static char const rcsid[] = "$Id: bwgQuery.c,v 1.23 2009/11/12 23:15:52 kent Exp $";
23 
+static char const rcsid[] = "$Id: bwgQuery.c,v 1.24 2010/06/03 18:08:37 kent Exp $";
24 24
25 25 
 struct bbiFile *bigWigFileOpen(char *fileName)
26 26 
 /* Open up big wig file. */
... ... 
@@ -28,17 +28,11 @@ struct bbiFile *bigWigFileOpen(char *fileName)
28 28 
 return bbiFileOpen(fileName, bigWigSig, "big wig");
29 29 
 }
30 30
31 
-struct bwgSectionHead
32 
-/* A header from a bigWig file section */
33 
-    {
34 
-    bits32 chromId;	/* Chromosome short identifier. */
35 
-    bits32 start,end;	/* Range covered. */
36 
-    bits32 itemStep;	/* For some section types, the # of bases between items. */
37 
-    bits32 itemSpan;	/* For some section types, the # of bases in each item. */
38 
-    UBYTE type;		/* Type byte. */
39 
-    UBYTE reserved;	/* Always zero for now. */
40 
-    bits16 itemCount;	/* Number of items in block. */
41 
-    };
31 
+boolean bigWigFileCheckSigs(char *fileName)
32 
+/* check file signatures at beginning and end of file */
33 
+{
34 
+return bbiFileCheckSigs(fileName, bigWigSig, "big wig");
35 
+}
42 36
43 37 
 #ifdef OLD
44 38 
 static void bwgSectionHeadRead(struct bbiFile *bwf, struct bwgSectionHead *head)
... ... 
@@ -57,7 +51,7 @@ head->itemCount = udcReadBits16(udc, isSwapped);
57 51 
 }
58 52 
 #endif /* OLD */
59 53
60 
-static void bwgSectionHeadFromMem(char **pPt, struct bwgSectionHead *head, boolean isSwapped)
54 
+void bwgSectionHeadFromMem(char **pPt, struct bwgSectionHead *head, boolean isSwapped)
61 55 
 /* Read section header. */
62 56 
 {
63 57 
 char *pt = *pPt;
... ... 
@@ -388,3 +382,16 @@ bigWigSummaryArray(bwf, chrom, start, end, summaryType, 1, &arrayOfOne);
388 382 
 return arrayOfOne;
389 383 
 }
390 384
385 
+boolean isBigWig(char *fileName)
386 
+/* Peak at a file to see if it's bigWig */
387 
+{
388 
+FILE *f = mustOpen(fileName, "rb");
389 
+bits32 sig;
390 
+mustReadOne(f, sig);
391 
+fclose(f);
392 
+if (sig == bigWigSig)
393 
+    return TRUE;
394 
+sig = byteSwap32(sig);
395 
+return sig == bigWigSig;
396 
+}
397 
+
src/ucsc/cheapcgi.h
History View file @ f470dd1f
... ... 
@@ -17,17 +17,27 @@
17 17 
 #include "hash.h"
18 18 
 #endif
19 19
20 
-#define COLOR_BG_DEFAULT        "#FFFEE8"
21 
-#define COLOR_BG_ALTDEFAULT     "#FFF9D2"
22 
-#define COLOR_BG_GHOST          "#EEEEEE"
23 
-#define COLOR_BG_PALE           "#F8F8F8"
24 
-#define COLOR_DARKGREEN         "#008800"
25 
-#define COLOR_DARKBLUE          "#000088"
26 
-#define COLOR_LTGREY            "#CCCCCC"
27 
-#define COLOR_YELLOW            "#FFFF00"
28 
-#define COLOR_LTYELLOW          "#FFF380"
29 
-#define COLOR_WHITE             "#FFFFFF"
30 
-#define COLOR_RED               "#AA0000"
20 
+#define COLOR_BG_DEFAULT         "#FFFEE8"
21 
+#define COLOR_BG_ALTDEFAULT      "#FFF9D2"
22 
+#define COLOR_BG_DEFAULT_DARKER  "#FCECC0"
23 
+#define COLOR_BG_DEFAULT_DARKEST "#EED5B7"
24 
+#define COLOR_BG_GHOST           "#EEEEEE"
25 
+#define COLOR_BG_PALE            "#F8F8F8"
26 
+#define COLOR_BG_HEADER_LTBLUE   "#D9E4F8"
27 
+#define COLOR_DARKGREEN          "#008800"
28 
+#define COLOR_LTGREEN            "#CCFFCC"
29 
+#define COLOR_DARKBLUE           "#000088"
30 
+#define COLOR_BLUE_BUTTON        "#91B3E6"
31 
+#define COLOR_DARKGREY           "#666666"
32 
+#define COLOR_LTGREY             "#CCCCCC"
33 
+#define COLOR_YELLOW             "#FFFF00"
34 
+#define COLOR_LTYELLOW           "#FFF380"
35 
+#define COLOR_WHITE              "#FFFFFF"
36 
+#define COLOR_RED                "#AA0000"
37 
+#define COLOR_TRACKLIST_LEVEL1   COLOR_BG_DEFAULT
38 
+#define COLOR_TRACKLIST_LEVEL2   COLOR_BG_ALTDEFAULT
39 
+#define COLOR_TRACKLIST_LEVEL3   COLOR_BG_DEFAULT_DARKER
40 
+#define COLOR_TRACKLIST_LEVEL4   COLOR_BG_DEFAULT_DARKEST
31 41
32 42 
 void initSigHandlers(boolean dumpStack);
33 43 
 /* set handler for various terminal signals for logging purposes.
... ... 
@@ -67,7 +77,14 @@ char *cgiScriptName();
67 77 
 /* Return name of script so libs can do context-sensitive stuff. */
68 78
69 79 
 char *cgiServerName();
70 
-/* Return name of server */
80 
+/* Return name of server, better to use cgiServerNamePort() for
81 
+   actual URL construction */
82 
+
83 
+char *cgiServerPort();
84 
+/* Return port number of server */
85 
+
86 
+char *cgiServerNamePort();
87 
+/* Return name of server with port if different than 80 */
71 88
72 89 
 char *cgiRemoteAddr();
73 90 
 /* Return IP address of client (or "unknown"). */
... ... 
@@ -75,8 +92,33 @@ char *cgiRemoteAddr();
75 92 
 char *cgiUserAgent();
76 93 
 /* Return remote user agent (HTTP_USER_AGENT) or NULL if remote user agent is not known */
77 94
95 
+enum browserType
96 
+/* How to look at a track. */
97 
+    {
98 
+    btUnknown=0, // Not yet known
99 
+    btOpera=1,   // Opera
100 
+    btIE=2,      // MS Internet Explorer
101 
+    btFF=3,      // Firefox
102 
+    btChrome=4,  // Google Chrome
103 
+    btSafari=5,  // Safari
104 
+    btOther=6    // Anything else
105 
+    };
106 
+
107 
+enum osType
108 
+/* How to look at a track. */
109 
+    {
110 
+    osUnknown=0, // Not yet known
111 
+    osWindows=1, // The evil empire
112 
+    osLinux=2,   // Workhorse
113 
+    osMac=3,     // ashion or Religion
114 
+    osOther=4    // Anything else
115 
+    };
116 
+
117 
+enum browserType cgiClientBrowser(char **browserQualifier, enum osType *clientOs, char **clientOsQualifier);
78 118 
 /* These routines abort the html output if the input isn't
79 119 
  * there or is misformatted. */
120 
+#define cgiBrowser() cgiClientBrowser(NULL,NULL,NULL)
121 
+
80 122 
 char *cgiString(char *varName);
81 123 
 int cgiInt(char *varName);
82 124 
 double cgiDouble(char *varName);
... ... 
@@ -213,9 +255,9 @@ void cgiMakeCheckBoxJS(char *name, boolean checked, char *javascript);
213 255 
 void cgiMakeCheckBoxIdAndJS(char *name, boolean checked, char *id, char *javascript);
214 256 
 /* Make check box with ID and javascript. */
215 257
216 
-void cgiMakeCheckBox2BoolWithIdAndJS(char *name, boolean checked, boolean enabled,char *id, char *javascript);
217 
-/* Make check box supporting 2 boolean state: checke/unchecked and enabled/disabled
218 
-   Also support ID and javascript.*/
258 
+void cgiMakeCheckBoxFourWay(char *name, boolean checked, boolean enabled, char *id, char *classes, char *moreHtml);
259 
+/* Make check box - with fourWay functionality (checked/unchecked by enabled/disabled
260 
+ * Also makes a shadow hidden variable that supports the 2 boolean states. */
219 261
220 262 
 void cgiMakeTextArea(char *varName, char *initialVal, int rowCount, int columnCount);
221 263 
 /* Make a text area with area rowCount X columnCount and with text: intialVal. */
... ... 
@@ -287,6 +329,19 @@ void cgiMakeDropListWithVals(char *name, char *menu[], char *values[],
287 329 
 void cgiMakeDropListFull(char *name, char *menu[], char *values[], int menuSize, char *checked, char *extraAttribs);
288 330 
 /* Make a drop-down list with names and values. */
289 331
332 
+void cgiDropDownWithTextValsAndExtra(char *name, char *text[], char *values[],
333 
+    int count, char *selected, char *extra);
334 
+/* Make a drop-down list with both text and values. */
335 
+
336 
+char *cgiMakeSelectDropList(boolean multiple, char *name, struct slPair *valsAndLabels,char *selected, char *anyAll,char *extraClasses, char *extraHtml);
337 
+// Returns allocated string of HTML defining a drop-down select (if multiple, REQUIRES ui-dropdownchecklist.js)
338 
+// In valsAndLabels, val (pair->name) must be filled in but label (pair->val) may be NULL.
339 
+// selected, if not NULL is a val found in the valsAndLabels (multiple then comma delimited list).  If null and anyAll not NULL, that will be selected
340 
+// anyAll, if not NULL is the string for an initial option.  It can contain val and label, delimited by a comma
341 
+// extraHtml, if not NULL contains id, javascript calls and style.  It does NOT contain class definitions
342 
+#define cgiMakeMultiSelectDropList(name, valsAndLabels, selected, anyAll, extraClasses, extraHtml)  cgiMakeSelectDropList(TRUE, (name), (valsAndLabels), (selected), (anyAll), (extraClasses), (extraHtml))
343 
+#define cgiMakeSingleSelectDropList(name, valsAndLabels, selected, anyAll, extraClasses, extraHtml) cgiMakeSelectDropList(FALSE,(name), (valsAndLabels), (selected), (anyAll), (extraClasses), (extraHtml))
344 
+
290 345 
 void cgiMakeMultList(char *name, char *menu[], int menuSize, struct slName *checked, int length);
291 346 
 /* Make a list of names which can have multiple selections.
292 347 
  * Same as drop-down list except "multiple" is added to select tag */
... ... 
@@ -301,7 +356,10 @@ void cgiMakeCheckboxGroupWithVals(char *name, char *menu[], char *values[], int
301 356 
 /* Make a table of checkboxes that have the same variable name but different
302 357 
  * values (same behavior as a multi-select input), with nice labels in menu[]. */
303 358
304 
-void cgiMakeHiddenVar(char *varName, char *string);
359 
+void cgiMakeHiddenVarWithExtra(char *varName, char *string, char *extra);
360 
+/* Store string in hidden input for next time around. */
361 
+
362 
+#define cgiMakeHiddenVar(name,val) cgiMakeHiddenVarWithExtra((name),(val),NULL)
305 363 
 /* Store string in hidden input for next time around. */
306 364
307 365 
 void cgiContinueHiddenVar(char *varName);
... ... 
@@ -414,14 +472,17 @@ void cgiResetState();
414 472 
 /* This is for reloading CGI settings multiple times in the same program
415 473 
  * execution.  No effect if state has not yet been initialized. */
416 474
417 
-void commonCssStyles();
418 
-/* Defines a few common styles to use through CSS */
475 
+void cgiDown(float lines);
476 
+// Drop down a certain number of lines (may be fractional)
477 
+
478 
+char *commonCssStyles();
479 
+/* Returns a string of common CSS styles */
419 480
420 481 
 char *javaScriptLiteralEncode(char *inString);
421 
-/* Use backslash escaping on newline
422 
- * and quote chars, backslash and others.
423 
- * Intended that the encoded string will be
424 
- * put between quotes at a higher level and
482 
+/* Use backslash escaping on newline
483 
+ * and quote chars, backslash and others.
484 
+ * Intended that the encoded string will be
485 
+ * put between quotes at a higher level and
425 486 
  * then interpreted by Javascript. */
426 487
427 488 
 #endif /* CHEAPCGI_H */
src/ucsc/cirTree.c
History View file @ f470dd1f
... ... 
@@ -451,7 +451,7 @@ if (crt != NULL)
451 451 
     }
452 452 
 }
453 453
454 
-static inline int cmpTwoBits32(bits32 aHi, bits32 aLo, bits32 bHi, bits32 bLo)
454 
+inline int cmpTwoBits32(bits32 aHi, bits32 aLo, bits32 bHi, bits32 bLo)
455 455 
 /* Return - if b is less than a , 0 if equal, else +*/
456 456 
 {
457 457 
 if (aHi < bHi)
src/ucsc/common.c
History View file @ f470dd1f
... ... 
@@ -8,8 +8,9 @@
8 8 
 #include "errabort.h"
9 9 
 #include "portable.h"
10 10 
 #include "linefile.h"
11 
+#include "hash.h"
11 12
12 
-static char const rcsid[] = "$Id: common.c,v 1.140 2009/11/24 15:36:59 kent Exp $";
13 
+static char const rcsid[] = "$Id: common.c,v 1.151 2010/06/02 19:06:41 tdreszer Exp $";
13 14
14 15 
 void *cloneMem(void *pt, size_t size)
15 16 
 /* Allocate a new buffer of given size, and copy pt to it. */
... ... 
@@ -19,7 +20,7 @@ memcpy(newPt, pt, size);
19 20 
 return newPt;
20 21 
 }
21 22
22 
-static char *cloneStringZExt(char *s, int size, int copySize)
23 
+static char *cloneStringZExt(const char *s, int size, int copySize)
23 24 
 /* Make a zero terminated copy of string in memory */
24 25 
 {
25 26 
 char *d = needMem(copySize+1);
... ... 
@@ -29,13 +30,13 @@ d[copySize] = 0;
29 30 
 return d;
30 31 
 }
31 32
32 
-char *cloneStringZ(char *s, int size)
33 
+char *cloneStringZ(const char *s, int size)
33 34 
 /* Make a zero terminated copy of string in memory */
34 35 
 {
35 36 
 return cloneStringZExt(s, strlen(s), size);
36 37 
 }
37 38
38 
-char *cloneString(char *s)
39 
+char *cloneString(const char *s)
39 40 
 /* Make copy of string in dynamic memory */
40 41 
 {
41 42 
 int size = 0;
... ... 
@@ -52,13 +53,16 @@ size_t size = strlen(s);
52 53 
 return cloneMem(s, size+1);
53 54 
 }
54 55
55 
-
56 
-/* fill a specified area of memory with zeroes */
57 
-void zeroBytes(void *vpt, int count)
56 
+char *catTwoStrings(char *a, char *b)
57 
+/* Allocate new string that is a concatenation of two strings. */
58 58 
 {
59 
-char *pt = (char*)vpt;
60 
-while (--count>=0)
61 
-    *pt++=0;
59 
+int aLen = strlen(a), bLen = strlen(b);
60 
+int len = aLen + bLen;
61 
+char *newBuf = needLargeMem(len+1);
62 
+memcpy(newBuf, a, aLen);
63 
+memcpy(newBuf+aLen, b, bLen);
64 
+newBuf[len] = 0;
65 
+return newBuf;
62 66 
 }
63 67
64 68 
 /* Reverse the order of the bytes. */
... ... 
@@ -149,7 +153,7 @@ for (i=0; i<length; ++i)
149 153 
 /** List managing routines. */
150 154
151 155 
 /* Count up elements in list. */
152 
-int slCount(void *list)
156 
+int slCount(const void *list)
153 157 
 {
154 158 
 struct slList *pt = (struct slList *)list;
155 159 
 int len = 0;
... ... 
@@ -457,6 +461,24 @@ else
457 461 
 return median;
458 462 
 }
459 463
464 
+void doubleBoxWhiskerCalc(int count, double *array, double *retMin,
465 
+	double *retQ1, double *retMedian, double *retQ3, double *retMax)
466 
+/* Calculate what you need to draw a box and whiskers plot from an array of doubles. */
467 
+{
468 
+doubleSort(count, array);
469 
+*retMin = array[0];
470 
+*retQ1 = array[(count+2)/4];
471 
+int halfCount = count>>1;
472 
+if ((count&1) == 1)
473 
+    *retMedian = array[halfCount];
474 
+else
475 
+    {
476 
+    *retMedian = (array[halfCount] + array[halfCount-1]) * 0.5;
477 
+    }
478 
+*retQ3 = array[(3*count+2)/4];
479 
+*retMax = array[count-1];
480 
+}
481 
+
460 482 
 struct slDouble *slDoubleNew(double x)
461 483 
 /* Return a new double. */
462 484 
 {
... ... 
@@ -496,6 +518,22 @@ freeMem(array);
496 518 
 return median;
497 519 
 }
498 520
521 
+void slDoubleBoxWhiskerCalc(struct slDouble *list, double *retMin,
522 
+	double *retQ1, double *retMedian, double *retQ3, double *retMax)
523 
+/* Calculate what you need to draw a box and whiskers plot from a list of slDoubles. */
524 
+{
525 
+int i,count = slCount(list);
526 
+struct slDouble *el;
527 
+double *array;
528 
+if (count == 0)
529 
+    errAbort("Can't take do slDoubleBoxWhiskerCalc of empty list");
530 
+AllocArray(array,count);
531 
+for (i=0, el=list; i<count; ++i, el=el->next)
532 
+    array[i] = el->val;
533 
+doubleBoxWhiskerCalc(count, array, retMin, retQ1, retMedian, retQ3, retMax);
534 
+freeMem(array);
535 
+}
536 
+
499 537 
 static int intCmp(const void *va, const void *vb)
500 538 
 /* Compare function to sort array of ints. */
501 539 
 {
... ... 
@@ -582,6 +620,17 @@ const struct slName *b = *((struct slName **)vb);
582 620 
 return strcmp(a->name, b->name);
583 621 
 }
584 622
623 
+int slNameCmpStringsWithEmbeddedNumbers(const void *va, const void *vb)
624 
+/* Compare strings such as gene names that may have embedded numbers,
625 
+ * so that bmp4a comes before bmp14a */
626 
+{
627 
+const struct slName *a = *((struct slName **)va);
628 
+const struct slName *b = *((struct slName **)vb);
629 
+return cmpStringsWithEmbeddedNumbers(a->name, b->name);
630 
+}
631 
+
632 
+
633 
+
585 634 
 void slNameSort(struct slName **pList)
586 635 
 /* Sort slName list. */
587 636 
 {
... ... 
@@ -702,6 +751,37 @@ slReverse(&list);
702 751 
 return list;
703 752 
 }
704 753
754 
+struct slName *slNameListOfUniqueWords(char *text,boolean respectQuotes)
755 
+// Return list of unique words found by parsing string delimited by whitespace.
756 
+// If respectQuotes then ["Lucy and Ricky" 'Fred and Ethyl'] will yield 2 slNames no quotes
757 
+{
758 
+struct slName *list = NULL;
759 
+char *word = NULL;
760 
+while (text != NULL)
761 
+    {
762 
+    if (respectQuotes)
763 
+        {
764 
+        word = nextWordRespectingQuotes(&text);
765 
+        if (word != NULL)
766 
+            {
767 
+            if (word[0] == '"')
768 
+                stripChar(word, '"');
769 
+            else if (word[0] == '\'')
770 
+                stripChar(word, '\'');
771 
+            }
772 
+        }
773 
+    else
774 
+        word = nextWord(&text);
775 
+    if (word)
776 
+        slNameStore(&list, word);
777 
+    else
778 
+        break;
779 
+    }
780 
+
781 
+slReverse(&list);
782 
+return list;
783 
+}
784 
+
705 785 
 struct slName *slNameListFromStringArray(char *stringArray[], int arraySize)
706 786 
 /* Return list of slNames from an array of strings of length arraySize.
707 787 
  * If a string in the array is NULL, the array will be treated as
... ... 
@@ -765,6 +845,21 @@ slReverse(&lines);
765 845 
 return lines;
766 846 
 }
767 847
848 
+struct slName *slNameIntersection(struct slName *a, struct slName *b)
849 
+/* return intersection of two slName lists.  */
850 
+{
851 
+struct hash *hashA = newHash(0);
852 
+struct slName *el, *retval = NULL;
853 
+
854 
+for (el = a; el != NULL; el = el->next)
855 
+    hashAddInt(hashA, el->name, 1);
856 
+for (el = b; el != NULL; el = el->next)
857 
+    if(hashLookup(hashA, el->name) != NULL)
858 
+        slNameAddHead(&retval, el->name);
859 
+hashFree(&hashA);
860 
+return retval;
861 
+}
862 
+
768 863 
 struct slRef *refOnList(struct slRef *refList, void *val)
769 864 
 /* Return ref if val is already on list, otherwise NULL. */
770 865 
 {
... ... 
@@ -892,31 +987,294 @@ if (el == NULL)
892 987 
 return el->val;
893 988 
 }
894 989
895 
-struct slPair *slPairFromString(char *s)
896 
-/* Return slPair list parsed from list in string s
897 
- * name1=val1 name2=val2 ...
898 
- * Returns NULL if parse error */
990 
+struct slPair *slPairListFromString(char *str,boolean respectQuotes)
991 
+// Return slPair list parsed from list in string like:  [name1=val1 name2=val2 ...]
992 
+// if respectQuotes then string can have double quotes: [name1="val 1" "name 2"=val2 ...]
993 
+//    resulting pair strips quotes: {name1}={val 1},{name 2}={val2}
994 
+// Returns NULL if parse error.  Free this up with slPairFreeValsAndList.
899 995 
 {
996 
+char *s = skipLeadingSpaces(str);  // Would like to remove this and tighten up the standard someday.
997 
+if (isEmpty(s))
998 
+    return NULL;
999 
+
900 1000 
 struct slPair *list = NULL;
901 
-char *name;
902 
-char *ss = cloneString(s);
903 
-char *word = ss;
904 
-while((name = nextWord(&word)))
905 
-    {
906 
-    char *val = strchr(name,'=');
907 
-    if (!val)
1001 
+char name[1024];
1002 
+char val[1024];
1003 
+char buf[1024];
1004 
+bool inQuote = FALSE;
1005 
+char *b = buf;
1006 
+char sep = '=';
1007 
+char c = ' ';
1008 
+int mode = 0;
1009 
+while(1)
1010 
+    {
1011 
+    c = *s++;
1012 
+    if (mode == 0 || mode == 2) // reading name or val
908 1013 
 	{
909 
-	warn("missing equals sign in name=value pair: name=[%s] in string=[%s]\n", name, s);
910 
-	return NULL;
1014 
+	boolean term = FALSE;
1015 
+	if (respectQuotes && b == buf && !inQuote && c == '"')
1016 
+	    inQuote = TRUE;
1017 
+	else if (inQuote && c == '"')
1018 
+	    term = TRUE;
1019 
+	else if ((c == sep || c == 0) && !inQuote)
1020 
+	    {
1021 
+	    term = TRUE;
1022 
+	    --s;  // rewind
1023 
+	    }
1024 
+	else if (c == ' ' && !inQuote)
1025 
+	    {
1026 
+	    warn("slPairListFromString: Unexpected whitespace in %s", str);
1027 
+	    return NULL;
1028 
+	    }
1029 
+	else if (c == 0 && inQuote)
1030 
+	    {
1031 
+	    warn("slPairListFromString: Unterminated quote in %s", str);
1032 
+	    return NULL;
1033 
+	    }
1034 
+	else
1035 
+	    {
1036 
+	    *b++ = c;
1037 
+	    if ((b - buf) > sizeof buf)
1038 
+		{
1039 
+		warn("slPairListFromString: pair name or value too long in %s", str);
1040 
+		return NULL;
1041 
+		}
1042 
+	    }
1043 
+	if (term)
1044 
+	    {
1045 
+	    inQuote = FALSE;
1046 
+	    *b = 0;
1047 
+	    if (mode == 0)
1048 
+		{
1049 
+		safecpy(name, sizeof name, buf);
1050 
+		if (strlen(name)<1)
1051 
+		    {
1052 
+		    warn("slPairListFromString: Pair name cannot be empty in %s", str);
1053 
+		    return NULL;
1054 
+		    }
1055 
+		// Shall we check for name being alphanumeric, at least for the respectQuotes=FALSE case?
1056 
+		}
1057 
+	    else // mode == 2
1058 
+		{
1059 
+		safecpy(val, sizeof val, buf);
1060 
+		if (!respectQuotes && (hasWhiteSpace(name) || hasWhiteSpace(val))) // should never happen
1061 
+		    {
1062 
+		    warn("slPairListFromString() Unexpected white space in name=value pair: [%s]=[%s] in string=[%s]\n", name, val, str);
1063 
+		    break;
1064 
+		    }
1065 
+		slPairAdd(&list, name, cloneString(val));
1066 
+		}
1067 
+	    ++mode;
1068 
+	    }
1069 
+	}
1070 
+    else if (mode == 1) // read required "=" sign
1071 
+	{
1072 
+	if (c != '=')
1073 
+	    {
1074 
+	    warn("slPairListFromString: Expected character = after name in %s", str);
1075 
+	    return NULL;
1076 
+	    }
1077 
+	++mode;
1078 
+	sep = ' ';
1079 
+	b = buf;
1080 
+	}
1081 
+    else // (mode == 3) reading optional separating space
1082 
+	{
1083 
+	if (c == 0)
1084 
+	    break;
1085 
+	if (c != ' ')
1086 
+	    {
1087 
+	    mode = 0;
1088 
+	    --s;
1089 
+	    b = buf;
1090 
+	    sep = '=';
1091 
+	    }
911 1092 
 	}
912 
-    *val++ = 0;
913 
-    slPairAdd(&list, name, cloneString(val));
914 1093 
     }
915 
-freez(&ss);
916 1094 
 slReverse(&list);
917 1095 
 return list;
918 1096 
 }
919 1097
1098 
+char *slPairListToString(struct slPair *list,boolean quoteIfSpaces)
1099 
+// Returns an allocated string of pairs in form of [name1=val1 name2=val2 ...]
1100 
+// If requested, will wrap