void drawWrappedText(RenderingContext* rc, SkCanvas* cv, TextDrawInfo* text, float textSize, SkPaint& paintText) {
if(text->textWrap == 0) {
// set maximum for all text
text->textWrap = 40;
}
if(text->text.length() > text->textWrap) {
const char* c_str = text->text.c_str();
int end = text->text.length();
int line = 0;
int pos = 0;
int start = 0;
while(start < end) {
const char* p_str = c_str;
int lastSpace = -1;
int prevPos = -1;
int charRead = 0;
do {
int lastSpace = nextWord((uint8_t*)p_str, &charRead);
if (lastSpace == -1) {
pos = end;
} else {
p_str += lastSpace;
if(pos != start && charRead >= text->textWrap){
break;
}
pos += lastSpace;
}
} while(pos < end && charRead < text->textWrap);
PROFILE_NATIVE_OPERATION(rc, drawTextOnCanvas(cv, c_str, pos - start , text->centerX, text->centerY + line * (textSize + 2), paintText, text->textShadow));
c_str += (pos - start);
start = pos;
line++;
}
} else {
PROFILE_NATIVE_OPERATION(rc, drawTextOnCanvas(cv, text->text.data(), text->text.length(), text->centerX, text->centerY, paintText, text->textShadow));
}
}
boolean lineToGffFields(struct lineFile *lf, char *line, char *fields[9])
/* Convert first eight space-separated fields to first 8
* gff items, and stick rest of line in last item. */
{
char *s, *word;
int i;
/* Pretty much ignore comments and blank lines. */
s = skipLeadingSpaces(line);
if (s[0] == '#' || s[0] == '0')
return FALSE;
for (i=0; i<8; ++i)
{
word = nextWord(&s);
if (word == NULL)
errAbort("Expecting at least 8 words line %d of %s", lf->lineIx, lf->fileName);
fields[i] = word;
}
fields[8] = skipLeadingSpaces(s);
return TRUE;
}
XP_S16
dict_findStartsWith( DictIter* iter, const XP_UCHAR* prefix )
{
ASSERT_INITED( iter );
array_edge* edge = dict_getTopEdge( iter->dict );
XP_S16 offset = findStartsWithChars( iter, prefix, 0, edge, 0 );
if ( 0 > offset ) {
/* not found; do nothing */
} else if ( 0 == offset ) {
if ( !firstWord( iter ) ) {
offset = -1;
}
} else {
if ( ACCEPT_ITER( iter, iter->nEdges ) || nextWord( iter ) ) {
DictPosition result = figurePosition( iter );
iter->position = result;
} else {
offset = -1;
}
}
return offset;
}
static int countWordsUsedInPhrase(char *phrase, struct slName *wordList)
/* Count the number of words in wordList that are used in phrase.
* The words are in order and space-separated in phrase. */
{
int count = 0;
struct slName *word;
char *dupe = cloneString(phrase);
char *s = dupe, *w;
for (word = wordList; word != NULL; word = word->next)
{
w = nextWord(&s);
if (w == NULL)
break;
if (sameWord(w, word->name))
count += 1;
else
break;
}
freeMem(dupe);
return count;
}
char *nextQuotedWord(char **pLine)
/* Generalization of nextWord. Returns next quoted
* string or if no quotes next word. Updates *pLine
* to point past word that is returned. Does not return
* quotes. */
{
char *line, c;
line = skipLeadingSpaces(*pLine);
if (line == NULL || line[0] == 0)
return NULL;
c = *line;
if (c == '"' || c == '\'')
{
if (!parseQuotedString(line, line, pLine))
return NULL;
return line;
}
else
{
return nextWord(pLine);
}
}
struct htmlCookie *htmlCookieFileRead(char *fileName)
/* Read cookies from a line oriented file. First word in line
* is the cookie name, the rest of the line the cookie value. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct htmlCookie *list = NULL, *cookie;
char *line, *word;
while (lineFileNextReal(lf, &line))
{
word = nextWord(&line);
line = skipLeadingSpaces(line);
if (line == NULL)
errAbort("Missing cookie value line %d of %s", lf->lineIx, lf->fileName);
AllocVar(cookie);
cookie->name = cloneString(word);
cookie->value = cloneString(line);
slAddHead(&list, cookie);
}
lineFileClose(&lf);
slReverse(&list);
return list;
}
struct segFile *segMayOpen(char *fileName)
/* Open up a segment file for reading. Read header and verify. Prepare
* for subsequent calls to segNext(). Return NULL if file does not exist. */
{
struct segFile *sf;
struct lineFile *lf;
char *line, *name, *val, *word;
char *sig = "##seg";
/* Open fileName. */
if ((lf = lineFileMayOpen(fileName, TRUE)) == NULL)
return NULL;
AllocVar(sf);
sf->lf = lf;
/* Check for a valid signature. */
lineFileNeedNext(lf, &line, NULL);
if (!startsWith(sig, line))
errAbort("%s does not start with %s", fileName, sig);
line += strlen(sig);
/* parse name=val. */
while ((word = nextWord(&line)) != NULL)
{
name = word;
val = strchr(word, '=');
if (val == NULL)
errAbort("Missing = after %s line 1 of %s", name, fileName);
*val++ = 0;
if (sameString(name, "version"))
sf->version = atoi(val);
}
if (sf->version == 0)
errAbort("No version line 1 of %s", fileName);
return sf;
}
static boolean isDescriptionMatch(struct track *track, char **words, int wordCount)
// We parse str and look for every word at the start of any word in track description (i.e. google style).
{
if(words)
{
// We do NOT lookup up parent hierarchy for html descriptions.
char *html = track->tdb->html;
if(!isEmpty(html))
{
/* This probably could be made more efficient by parsing the html into some kind of b-tree, but I am assuming
that the inner html loop while only happen for 1-2 words for vast majority of the tracks. */
int i, numMatches = 0;
html = stripRegEx(html, "<[^>]*>", REG_ICASE);
for(i = 0; i < wordCount; i++)
{
char *needle = words[i];
char *haystack, *tmp = cloneString(html);
boolean found = FALSE;
while((haystack = nextWord(&tmp)))
{
char *ptr = strstrNoCase(haystack, needle);
if(ptr != NULL && ptr == haystack)
{
found = TRUE;
break;
}
}
if(found)
numMatches++;
else
break;
}
if(numMatches == wordCount)
return TRUE;
}
}
return FALSE;
}
XP_U32
dict_countWords( const DictIter* iter, LengthsArray* lens )
{
DictIter counter;
dict_initIterFrom( &counter, iter );
if ( NULL != lens ) {
XP_MEMSET( lens, 0, sizeof(*lens) );
}
XP_U32 count;
XP_Bool ok;
for ( count = 0, ok = firstWord( &counter );
ok; ok = nextWord( &counter) ) {
++count;
if ( NULL != lens ) {
++lens->lens[counter.nEdges];
}
}
return count;
}
struct mafFile *mafMayOpen(char *fileName)
/* Open up a maf file and verify header. */
{
struct mafFile *mf;
struct lineFile *lf;
char *line, *word;
char *sig = "##maf";
if ((lf = lineFileMayOpen(fileName, TRUE)) == NULL)
return NULL;
AllocVar(mf);
mf->lf = lf;
lineFileNeedNext(lf, &line, NULL);
if (!startsWith(sig, line))
{
errAbort("%s does not start with %s", fileName, sig);
}
line += strlen(sig);
while ((word = nextWord(&line)) != NULL)
{
/* Parse name=val. */
char *name = word;
char *val = strchr(word, '=');
if (val == NULL)
errAbort("Missing = after %s line 1 of %s\n", name, fileName);
*val++ = 0;
if (sameString(name, "version"))
mf->version = atoi(val);
else if (sameString(name, "scoring"))
mf->scoring = cloneString(val);
}
if (mf->version == 0)
errAbort("No version line 1 of %s\n", fileName);
return mf;
}
static void
indexOne( XP_U16 depth, Tile* tiles, IndexData* data, DictIter* prevIter,
DictPosition* prevIndex )
{
DictIter curIter;
dict_initIterFrom( &curIter, prevIter );
if ( findWordStartsWith( &curIter, tiles, depth ) ) {
while ( !wordsEqual( &curIter, prevIter ) ) {
++*prevIndex;
if ( !nextWord( prevIter ) ) {
XP_ASSERT( 0 );
}
}
XP_ASSERT( data->count == 0 ||
data->indices[data->count-1] < *prevIndex );
data->indices[data->count] = *prevIndex;
if ( NULL != data->prefixes ) {
XP_MEMCPY( data->prefixes + (data->count * depth), tiles, depth );
}
++data->count;
}
}
void addFa(char *file, struct hash *fileHash, struct hash *seqHash)
/* Add a fa file to hashes. */
{
struct lineFile *lf = lineFileOpen(file, TRUE);
char *line, *name;
char *rFile = hashStoreName(fileHash, file);
while (lineFileNext(lf, &line, NULL))
{
if (line[0] == '>')
{
struct seqFilePos *sfp;
line += 1;
name = nextWord(&line);
if (name == NULL)
errAbort("bad line %d of %s", lf->lineIx, lf->fileName);
AllocVar(sfp);
hashAddSaveName(seqHash, name, sfp, &sfp->name);
sfp->file = rFile;
sfp->pos = lineFileTell(lf);
}
}
lineFileClose(&lf);
}
void doCheck(char *line, struct sockaddr_in *hubIp)
/* Send back check result - either a check in message or
* jobDone. */
{
char *jobIdString = nextWord(&line);
if (jobIdString != NULL)
{
int jobId = atoi(jobIdString);
struct job *job = findRunningJob(jobId);
struct paraMessage pm;
pmInit(&pm, ntohl(hubIp->sin_addr.s_addr), paraHubPort);
if (job != NULL)
pmPrintf(&pm, "checkIn %s %s running", hostName, jobIdString);
else
{
struct job *job = findFinishedJob(jobId);
if (job == NULL)
pmPrintf(&pm, "checkIn %s %s free", hostName, jobIdString);
else
pmPrintf(&pm, "jobDone %s %s", jobIdString, job->doneMessage);
}
pmSend(&pm, mainRudp);
}
}
void wigToBedGraph(char *wigIn, char *bedOut)
/* wigToBedGraph - Convert wig files to bedGraph, merging adjacent items with identical values
* when possible.. */
{
struct lineFile *lf = lineFileOpen(wigIn, TRUE);
FILE *f = mustOpen(bedOut, "w");
struct bgOut *out = bgOutNew(f);
char *line;
while (lineFileNextReal(lf, &line))
{
char *firstWord = nextWord(&line);
struct hash *vars = hashVarLine(line, lf->lineIx);
if (sameString("fixedStep", firstWord))
convertFixedStepSection(lf, vars, out);
else if (sameString("variableStep", firstWord))
convertVariableStepSection(lf, vars, out);
else
errAbort("Expecting fixedStep or variableStep line %d of %s, got:\n\t%s", lf->lineIx,
lf->fileName, line);
freeHashAndVals(&vars);
}
bgOutFree(&out);
carefulClose(&f);
}
static struct hash *readDictionary(char *fileName, int *retMaxSize)
/* Read in dictionary table and put it in hash that is
* keyed by numeric version of string. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line, *word;
struct hash *hash = hashNew(18);
int maxSize = 0, size;
while (lineFileNext(lf, &line, NULL))
{
while ((word = nextWord(&line)) != NULL)
{
char numBuf[MAXWORDSIZE];
toNum(word, numBuf, sizeof(numBuf));
hashAdd(hash, numBuf, cloneString(word));
size = strlen(numBuf);
if (size > maxSize)
maxSize = size;
}
}
lineFileClose(&lf);
*retMaxSize = maxSize;
return hash;
}
struct hgFindSpec *hgFindSpecFromRa(char *db, char *raFile, char *releaseTag)
/* Load track info from ra file into list. */
{
static boolean reEntered = FALSE;
struct lineFile *lf = lineFileOpen(raFile, TRUE);
char *line, *word;
struct hgFindSpec *hfsList = NULL, *hfs;
boolean done = FALSE;
char *incFile;
for (;;)
{
/* Seek to next line that starts with 'searchName' or 'searchTable' */
for (;;)
{
char *subRelease;
if (!lineFileNext(lf, &line, NULL))
{
done = TRUE;
break;
}
if (startsWith("searchName", line) || startsWith("searchTable", line))
{
lineFileReuse(lf);
break;
}
else if ((incFile = trackDbInclude(raFile, line, &subRelease)) != NULL)
{
if (subRelease)
trackDbCheckValidRelease(subRelease);
if (releaseTag && subRelease && !sameString(subRelease, releaseTag))
errAbort("Include with release %s inside include with release %s line %d of %s", subRelease, releaseTag, lf->lineIx, lf->fileName);
/* Set reEntered=TRUE whenever we recurse, so we don't polish
* multiple times and get too many backslash-escapes. */
boolean reBak = reEntered;
reEntered = TRUE;
struct hgFindSpec *incHfs = hgFindSpecFromRa(db, incFile, subRelease);
reEntered = reBak;
hfsList = slCat(hfsList, incHfs);
}
}
if (done)
break;
/* Allocate track structure and fill it in until next blank line. */
AllocVar(hfs);
slAddHead(&hfsList, hfs);
for (;;)
{
/* Break at blank line or EOF. */
if (!lineFileNext(lf, &line, NULL))
break;
line = skipLeadingSpaces(line);
if (line == NULL || line[0] == 0)
break;
/* Skip comments. */
if (line[0] == '#')
continue;
/* Parse out first word and decide what to do. */
word = nextWord(&line);
if (line == NULL)
errAbort("No value for %s line %d of %s",
word, lf->lineIx, lf->fileName);
line = trimSpaces(line);
hgFindSpecAddInfo(hfs, word, line);
}
if (releaseTag)
hgFindSpecAddRelease(hfs, releaseTag);
}
lineFileClose(&lf);
if (! reEntered)
{
for (hfs = hfsList; hfs != NULL; hfs = hfs->next)
{
hgFindSpecPolish(db, hfs);
}
}
slReverse(&hfsList);
return hfsList;
}
void hgGnfMicroarray(char *expTable, char *dataTable, char *atlasFile)
/** Main function that does all the work for new-style*/
{
struct lineFile *lf = lineFileOpen(atlasFile, TRUE);
char *line;
int i, wordCount, expCount;
char **row;
float *data;
char *affyId;
struct hash *hash = newHash(17);
FILE *f = NULL;
int dataCount = 0;
/* Open Atlas file and use first line to create experiment table. */
if (!lineFileNextReal(lf, &line))
errAbort("%s is empty", lf->fileName);
if (startsWith("Affy", line))
line += 4;
if (startsWith("Gene Name", line))
line += 9;
if (line[0] != '\t')
errAbort("%s doesn't seem to be a new format atlas file", lf->fileName);
expCount = lineToExpTable(line+1, expTable);
if (expCount <= 0)
errAbort("No experiments in %s it seems", lf->fileName);
warn("%d experiments\n", expCount);
f = hgCreateTabFile(tabDir, dataTable);
AllocArray(row, expCount);
AllocArray(data, expCount);
while (lineFileNextReal(lf, &line))
{
affyId = nextWord(&line);
wordCount = chopByWhite(line, row, expCount);
if (wordCount != expCount)
errAbort("Expecting %d data points, got %d line %d of %s",
expCount, wordCount, lf->lineIx, lf->fileName);
if (chopName != NULL)
{
char *e = stringIn(chopName, affyId);
if (e != NULL)
*e = 0;
}
if (hashLookup(hash, affyId))
{
warn("Duplicate %s, skipping all but first.", affyId);
continue;
}
for (i=0; i<expCount; ++i)
{
data[i] = sqlFloat(row[i]);
}
shortDataOut(f, affyId, expCount, data);
++dataCount;
if (limit != 0 && dataCount >= limit)
break;
}
lineFileClose(&lf);
if (doLoad)
{
struct sqlConnection *conn = sqlConnect(database);
expDataCreateTable(conn, dataTable);
hgLoadTabFile(conn, tabDir, dataTable, &f);
hgRemoveTabFile(tabDir, dataTable);
sqlDisconnect(&conn);
}
}
void doSearchTracks(struct group *groupList)
{
if (!advancedJavascriptFeaturesEnabled(cart))
{
warn("Requires advanced javascript features.");
return;
}
struct group *group;
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
#ifdef TRACK_SEARCH_ON_TYPE
char *typeSearch = cartOptionalString(cart, TRACK_SEARCH_ON_TYPE);
#else///ifndef TRACK_SEARCH_ON_TYPE
char *typeSearch = NULL;
#endif///def TRACK_SEARCH_ON_TYPE
char *descSearch;
char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP);
boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search") || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0;
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
int numMetadataSelects, tracksFound = 0;
int numMetadataNonEmpty = 0;
char **mdbVar = NULL;
char **mdbVal = NULL;
#ifdef ONE_FUNC
struct hash *parents = newHash(4);
#endif///def ONE_FUNC
boolean simpleSearch;
struct trix *trix;
char trixFile[HDB_MAX_PATH_STRING];
char **descWords = NULL;
int descWordCount = 0;
boolean searchTermsExist = FALSE;
int cols;
char buf[512];
if(sameString(currentTab, "simpleTab"))
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
simpleSearch = TRUE;
freez(&nameSearch);
#ifdef TRACK_SEARCH_ON_TYPE
freez(&typeSearch);
#endif///def TRACK_SEARCH_ON_TYPE
freez(&groupSearch);
}
else
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
simpleSearch = FALSE;
}
if(descSearch)
stripChar(descSearch, '"');
trackList = getTrackList(&groupList, -2); // global
makeGlobalTrackHash(trackList);
// NOTE: This is necessary when container cfg by '*' results in vis changes
// This will handle composite/view override when subtrack specific vis exists, AND superTrack reshaping.
parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated
getSearchTrixFile(database, trixFile, sizeof(trixFile));
trix = trixOpen(trixFile);
slSort(&groupList, gCmpGroup);
for (group = groupList; group != NULL; group = group->next)
{
groupTrackListAddSuper(cart, group);
if (group->trackList != NULL)
{
groups[numGroups] = cloneString(group->name);
labels[numGroups] = cloneString(group->label);
numGroups++;
if (numGroups >= ArraySize(groups))
internalErr();
}
}
safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly", organism, hFreezeFromDb(database));
webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE);
hPrintf("<div style='max-width:1080px;'>");
hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n", hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
safef(buf, sizeof(buf), "%lu", clock1());
cgiMakeHiddenVar("hgt_", buf); // timestamps page to avoid browser cache
hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n", TRACK_SEARCH_CURRENT_TAB, currentTab);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER);
hPrintf("<div id='tabs' style='display:none; %s'>\n"
"<ul>\n"
"<li><a href='#simpleTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B></a></li>\n"
"<li><a href='#advancedTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B></a></li>\n"
"</ul>\n"
"<div id='simpleTab' style='max-width:inherit;'>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
hPrintf("<table style='width:100%%; font-size:.9em;'><tr><td colspan='2'>");
hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' style='max-width:1000px; width:100%%;' onkeyup='findTracksSearchButtonsEnable(true);'>\n",
TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : descSearch);
if (simpleSearch && descSearch)
searchTermsExist = TRUE;
hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>");
//hPrintf("</td></tr></table>");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
hPrintf("</div>\n");
// Advanced tab
hPrintf("<div id='advancedTab' style='width:inherit;'>\n"
"<table cellSpacing=0 style='width:inherit; font-size:.9em;'>\n");
cols = 8;
// Track Name contains
hPrintf("<tr><td colspan=3></td>");
hPrintf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
hPrintf("</td></tr>\n");
// Description contains
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>");
hPrintf("<td><b style='max-width:100px;'>Description:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' onkeyup='findTracksSearchButtonsEnable(true);' style='max-width:536px; width:536px; font-size:.9em;'>",
TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
hPrintf("</td></tr>\n");
if (!simpleSearch && descSearch)
searchTermsExist = TRUE;
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td><b style='max-width:100px;'>Group:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (!simpleSearch && groupSearch)
searchTermsExist = TRUE;
#ifdef TRACK_SEARCH_ON_TYPE
// Track Type is (drop down)
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
char **formatTypes = NULL;
char **formatLabels = NULL;
int formatCount = getFormatTypes(&formatLabels, &formatTypes);
cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch, "class='typeSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (!simpleSearch && typeSearch)
searchTermsExist = TRUE;
#endif///def TRACK_SEARCH_ON_TYPE
// Metadata selects require careful accounting
if(metaDbExists)
numMetadataSelects = printMdbSelects(conn, cart, simpleSearch, &mdbVar, &mdbVal, &numMetadataNonEmpty, cols);
else
numMetadataSelects = 0;
hPrintf("</table>\n");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
//hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n");
hPrintf("</div>\n</div>\n");
hPrintf("</form>\n");
hPrintf("</div>"); // Restricts to max-width:1000px;
if(descSearch != NULL && !strlen(descSearch))
descSearch = NULL;
if(groupSearch != NULL && sameString(groupSearch, ANYLABEL))
groupSearch = NULL;
if(typeSearch != NULL && sameString(typeSearch, ANYLABEL))
typeSearch = NULL;
if(!isEmpty(descSearch))
{
char *tmp = cloneString(descSearch);
char *val = nextWord(&tmp);
struct slName *el, *descList = NULL;
int i;
while (val != NULL)
{
slNameAddTail(&descList, val);
descWordCount++;
val = nextWord(&tmp);
}
descWords = needMem(sizeof(char *) * descWordCount);
for(i = 0, el = descList; el != NULL; i++, el = el->next)
descWords[i] = strLower(el->name);
}
if (doSearch && simpleSearch && descWordCount <= 0)
doSearch = FALSE;
if(doSearch)
{
// Now search
struct slRef *tracks = NULL;
if(simpleSearch)
tracks = simpleSearchForTracksstruct(trix,descWords,descWordCount);
else
tracks = advancedSearchForTracks(conn,groupList,descWords,descWordCount,nameSearch,typeSearch,descSearch,groupSearch,numMetadataNonEmpty,numMetadataSelects,mdbVar,mdbVal);
// Sort and Print results
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
tracksFound = slCount(tracks);
if(tracksFound > 1)
findTracksSort(&tracks,simpleSearch,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
}
hFreeConn(&conn);
webNewSection("About Track Search");
if(metaDbExists)
hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE "
"metadata. If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
else
hPrintf("<p>Search for terms in track descriptions, groups, and names. "
"If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n");
webEndSectionTables();
}
static struct joiner *joinerParsePassOne(char *fileName)
/* Do first pass parsing of joiner file and return list of
* joinerSets. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line, *word;
struct dyString *dyBuf = dyStringNew(0);
struct joiner *joiner;
struct joinerSet *js;
AllocVar(joiner);
joiner->fileName = cloneString(fileName);
joiner->symHash = newHash(9);
joiner->databasesChecked = newHash(8);
joiner->databasesIgnored = newHash(8);
while ((line = nextSubbedLine(lf, joiner->symHash, dyBuf)) != NULL)
{
if ((word = nextWord(&line)) != NULL)
{
if (sameString("set", word))
{
char *var, *val;
var = nextWord(&line);
if (var == NULL)
errAbort("set what line %d of %s", lf->lineIx, lf->fileName);
val = trimSpaces(line);
if (isEmpty(val))
errAbort("Set with no value line %d of %s",
lf->lineIx, lf->fileName);
hashAdd(joiner->symHash, var, cloneString(val));
}
else if (sameString("identifier", word))
{
js = parseIdentifierSet(lf, line, joiner->symHash, dyBuf);
if (js != NULL)
slAddHead(&joiner->jsList, js);
}
else if (sameString("exclusiveSet", word))
{
struct hash *exHash = newHash(8);
addDatabasesToHash(exHash, line, lf);
slAddHead(&joiner->exclusiveSets, exHash);
}
else if (sameString("databasesChecked", word))
{
addDatabasesToHash(joiner->databasesChecked, line, lf);
}
else if (sameString("databasesIgnored", word))
{
addDatabasesToHash(joiner->databasesIgnored, line, lf);
}
else if (sameString("tablesIgnored", word))
{
struct joinerIgnore *ig;
ig = parseTablesIgnored(lf, line, joiner->symHash, dyBuf);
slAddHead(&joiner->tablesIgnored, ig);
}
else if (sameString("dependency", word))
{
struct joinerDependency *dep;
dep = parseDependency(lf, line);
slAddHead(&joiner->dependencyList, dep);
}
else if (sameString("type", word))
{
struct joinerType *type;
type = parseType(lf, line, joiner->symHash, dyBuf);
slAddHead(&joiner->typeList, type);
}
else
{
errAbort("unrecognized '%s' line %d of %s",
word, lf->lineIx, lf->fileName);
}
}
}
lineFileClose(&lf);
dyStringFree(&dyBuf);
slReverse(&joiner->jsList);
slReverse(&joiner->tablesIgnored);
slReverse(&joiner->typeList);
return joiner;
}
static int
dimensionsChanged (BrailleDisplay *brl) {
int ok = 1;
const char *word;
int columns1;
int rows1;
int columns2 = 0;
int rows2 = 0;
if ((word = nextWord())) {
if (isInteger(&columns1, word) && (columns1 > 0)) {
rows1 = 1;
if ((word = nextWord())) {
if (isInteger(&rows1, word) && (rows1 > 0)) {
if ((word = nextWord())) {
if (isInteger(&columns2, word) && (columns2 > 0)) {
rows2 = 0;
if ((word = nextWord())) {
if (isInteger(&rows2, word) && (rows2 > 0)) {
} else {
logMessage(LOG_WARNING, "invalid status row count: %s", word);
ok = 0;
}
}
} else {
logMessage(LOG_WARNING, "invalid status column count: %s", word);
ok = 0;
}
}
} else {
logMessage(LOG_WARNING, "invalid text row count: %s", word);
ok = 0;
}
}
} else {
logMessage(LOG_WARNING, "invalid text column count: %s", word);
ok = 0;
}
} else {
logMessage(LOG_WARNING, "missing text column count");
ok = 0;
}
if (ok) {
int count1 = columns1 * rows1;
int count2 = columns2 * rows2;
unsigned char *braille;
wchar_t *text;
unsigned char *status;
if ((braille = calloc(count1, sizeof(*braille)))) {
if ((text = calloc(count1, sizeof(*text)))) {
if ((status = calloc(count2, sizeof(*status)))) {
brailleColumns = columns1;
brailleRows = rows1;
brailleCount = count1;
statusColumns = columns2;
statusRows = rows2;
statusCount = count2;
if (brailleCells) free(brailleCells);
brailleCells = braille;
memset(brailleCells, 0, count1);
if (textCharacters) free(textCharacters);
textCharacters = text;
wmemset(textCharacters, WC_C(' '), count1);
if (statusCells) free(statusCells);
statusCells = status;
memset(statusCells, 0, count2);
memset(genericCells, 0, GSC_COUNT);
brl->textColumns = brailleColumns;
brl->textRows = brailleRows;
brl->statusColumns = statusColumns;
brl->statusRows = statusRows;
return 1;
}
free(text);
}
free(braille);
}
}
return 0;
}
struct commit* getCommits()
/* Get all commits from startTag to endTag */
{
int numCommits = 0;
safef(gitCmd,sizeof(gitCmd), ""
"git log %s..%s --name-status > commits.tmp"
, startTag, endTag);
runShell(gitCmd);
struct lineFile *lf = lineFileOpen("commits.tmp", TRUE);
int lineSize;
char *line;
struct commit *commits = NULL, *commit = NULL;
struct files *files = NULL, *f = NULL;
char *sep = "";
while (lineFileNext(lf, &line, &lineSize))
{
boolean isMerge = FALSE;
char *w = nextWord(&line);
AllocVar(commit);
if (!sameString("commit", w))
errAbort("expected keyword commit parsing commits.tmp\n");
commit->commitId = cloneString(nextWord(&line));
commit->commitNumber = ++numCommits;
lineFileNext(lf, &line, &lineSize);
w = nextWord(&line);
if (sameString("Merge:", w))
{
isMerge = TRUE;
lineFileNext(lf, &line, &lineSize);
w = nextWord(&line);
}
if (!sameString("Author:", w))
errAbort("expected keyword Author: parsing commits.tmp\n");
/* by request, keep just the email account name */
char *lc = strchr(line, '<');
if (!lc)
errAbort("expected '<' char in email address in Author: parsing commits.tmp\n");
++lc;
char *rc = strchr(lc, '>');
if (!rc)
errAbort("expected '>' char in email address in Author: parsing commits.tmp\n");
char *ac = strchr(lc, '@');
if (ac)
rc = ac;
commit->author = cloneStringZ(lc, rc-lc);
lineFileNext(lf, &line, &lineSize);
w = nextWord(&line);
if (!sameString("Date:", w))
errAbort("expected keyword Date: parsing commits.tmp\n");
commit->date = cloneString(line);
lineFileNext(lf, &line, &lineSize);
if (!sameString("", line))
errAbort("expected blank line parsing commits.tmp\n");
/* collect the comment-lines */
struct dyString *dy = NULL;
dy = dyStringNew(0);
sep = "";
files = NULL;
while (lineFileNext(lf, &line, &lineSize))
{
if (sameString("", line))
break;
w = skipLeadingSpaces(line);
dyStringPrintf(dy, "%s%s", w, sep);
sep = "\n";
}
commit->comment = cloneString(dy->string);
freeDyString(&dy);
if (!isMerge)
{
/* collect the files-list */
while (lineFileNext(lf, &line, &lineSize))
{
if (sameString("", line))
break;
AllocVar(f);
w = nextWord(&line);
f->type = w[0];
f->path = cloneString(line);
slAddHead(&files, f);
}
slReverse(&files);
}
commit->files = files;
if (!isMerge /* for now, default to filtering out the records for automatic-merges */
&& !endsWith(commit->comment, "elease log update")) /* filter out automatic release log commits */
slAddHead(&commits, commit);
verbose(2,
"commitId: %s\n"
"author: %s\n"
"date: %s\n"
"comment: [%s]\n"
"file(s): \n"
, commit->commitId
, commit->author
, commit->date
, commit->comment);
for (f=commit->files; f; f = f->next)
{
verbose(2, "%c %s\n", f->type, f->path);
// anything other than M or A?
if (f->type != 'M' && f->type != 'A' )
verbose(2, "special type: %c %s\n", f->type, f->path);
}
verbose(2, "------------\n");
}
lineFileClose(&lf);
/* We want to keep them chronological order,
so do not need slReverse since the addHead reversed git log's rev chron order already */
unlink("commits.tmp");
return commits;
}
void queryResponse(int sd, struct bzp *bzp, struct blatzIndex *indexList)
/* Respond to query message - read options and dna from socket,
* and do alignment. */
{
struct bzp lbzp = *bzp;
struct dnaSeq *seq = NULL;
char buf[256], *line, *word;
char *out = NULL, *mafT = NULL, *mafQ = NULL;
/* First get options - overriding what got set at startup. */
for (;;)
{
if ((line = netGetString(sd, buf)) == NULL)
{
truncatedQuery(1);
return;
}
word = nextWord(&line);
line = skipLeadingSpaces(line);
if (sameString(word, "seq"))
break;
else if (sameString(word, "rna"))
lbzp.rna = TRUE;
else if (sameString(word, "minScore"))
lbzp.minScore = atoi(line);
else if (sameString(word, "minGapless"))
lbzp.minGapless = atoi(line);
else if (sameString(word, "multiHits"))
lbzp.multiHits = atoi(line);
else if (sameString(word, "minChain"))
lbzp.minChain = atoi(line);
else if (sameString(word, "maxExtend"))
lbzp.maxExtend = atoi(line);
else if (sameString(word, "maxBandGap"))
lbzp.maxBandGap = atoi(line);
else if (sameString(word, "minExpand"))
lbzp.minExpand = atoi(line);
else if (sameString(word, "expandWindow"))
lbzp.expandWindow = atoi(line);
else if (sameString(word, "out"))
lbzp.out = out = cloneString(line);
else if (sameString(word, "mafQ"))
lbzp.mafQ = mafQ = cloneString(line);
else if (sameString(word, "mafT"))
lbzp.mafT = mafT = cloneString(line);
}
/* Get DNA into seq*/
{
char *name = netGetString(sd, buf);
char *dna;
if (name == NULL)
{
truncatedQuery(2);
return;
}
dna = netGetHugeString(sd);
if (dna == NULL)
{
truncatedQuery(3);
return;
}
AllocVar(seq);
seq->dna = dna;
seq->size = strlen(dna);
seq->name = cloneString(name);
bzpTime("Received %d bases in %s", seq->size, seq->name);
if (lbzp.rna)
maskTailPolyA(seq->dna, seq->size);
}
/* Create alignments into chainList and write results. */
{
FILE *f = netFileFromSocket(sd);
struct chain *chainList = blatzAlign(&lbzp, indexList, seq);
blatzWriteChains(&lbzp, &chainList, seq, 0, seq->size, seq->size, indexList, f);
bzpTime("sent result - %d chains", slCount(chainList));
carefulClose(&f);
}
dnaSeqFree(&seq);
freez(&out);
freez(&mafQ);
freez(&mafT);
}
void CBatchCounter::LSLOC(results* result, string line, size_t lineNumber, string lineBak, string &strLSLOC, string &strLSLOCBak,
bool &data_continue, unsigned int &temp_lines, unsigned int &phys_exec_lines,
unsigned int &phys_data_lines/*, StringVector &loopLevel*/)// warning fix
{
size_t start, end;
size_t strSize;
bool trunc_flag = false;
string exclude = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789_$";
string str, spc;
unsigned int cnt = 0;
string tmp = CUtil::TrimString(line);
string tmpBak = CUtil::TrimString(lineBak);
start = 0;
end = tmp.length();
// skip whole line '(' or ')'
if (tmp == "(" || tmp == ")")
{
strLSLOC = strLSLOCBak = "";
phys_exec_lines++;
temp_lines = 0;
return;
}
// there may be more than 1 logical SLOC in this line
#ifdef _MSC_VER
char * context = NULL; // used for strtok_s( ) below
#else
//
#endif
bool has_for = false;
bool has_for_in = false;
while (start < tmp.length())
{
end = tmp.length();
if (start == 0) {
has_for = false;
has_for_in = false;
}
//std::cout << start <<"start\n";
// check if is a label
bool isLabel = false;
for (unsigned int i = 0; tmp[i] != '\0'; i++) {
if (tmp[i] == ' ') {
continue;
} else if (tmp[i] == ':') {
isLabel = true;
break;
} else {
break;
}
}
if(isLabel) {
strLSLOC = strLSLOCBak = "";
phys_exec_lines++;
temp_lines = 0;
return;
}
char * token = NULL;
// Allocate a char array that must be deleted later.
char* line = new char[end - start + 1];
#ifdef _MSC_VER
// Use more Secure C library API
strcpy_s( line, (end - start + 1) * sizeof(char), tmp.substr(start).c_str() );
#else
// Use older less Secure C library API
strcpy( line, tmp.substr(start).c_str() );
#endif
// check |, &
bool hasPipe = false;
size_t pipePos = 0;
bool hasAmp = false;
size_t ampPos = 0;
for (int i = 0; line[i] != '\0'; i++) {
if (line[i] == '|') {
if (!hasPipe) {
pipePos = (size_t)i;
}
hasPipe = true;
line[i] = ' ';
}
if (line[i] == '&') {
if (!hasAmp) {
ampPos = (size_t)i;
}
hasAmp = true;
line[i] = ' ';
}
}
#ifdef _MSC_VER
// Use more Secure C library API
token = strtok_s( line, " .@:", &context );
#else
// Use older less Secure C library API
token = strtok( line, " .@:" );
#endif
for (int i = 0; token[i] != '\0'; i++) {
token[i] = (char)lowerChars[ TL_ARR( token[i] ) ];
}
if (strcmp(token, "else") == 0)
{
#ifdef _MSC_VER
// Use more Secure C library API
token = strtok_s( NULL, " .@:", &context );
#else
// Use older less Secure C library API
token = strtok( NULL, " .@:" );
#endif
}
if (token == NULL) {
strLSLOC = strLSLOCBak = "";
phys_exec_lines++;
temp_lines = 0;
delete line;
return;
}
//first keyword
//std::cout << token << "TOKEN\n";
string firstWord(token);
firstWord = CUtil::ToLower(firstWord);
bool checkFirstWord = false;
for(std::vector<string>::iterator it = exec_name_list.begin(); it != exec_name_list.end(); ++it) {
if (*it == firstWord) {
checkFirstWord = true;
break;
}
}
if(!checkFirstWord) {
strLSLOC = strLSLOCBak = "";
phys_exec_lines++;
temp_lines = 0;
delete line;
return;
}
//if, for, choice as first word
bool isComplexWord = false;
bool isCall = false;
size_t nextKeyWordStart = (size_t)(-1);
bool isKeyWord = false;
bool hasElse = false;
char * nextToken = NULL;
size_t tmpNextKeyWordStart = (size_t)(-1);
size_t tmpEnd = (size_t)(-1);
for(std::vector<string>::iterator it = cmplx_cond_list.begin(); it != cmplx_cond_list.end(); ++it) {
if (*it == firstWord) {
isComplexWord = true;
break;
}
}
//for as first word
if (firstWord.compare("for") == 0) {
has_for = true;
}
//call as first word
if (firstWord.compare("call") == 0) {
isCall = true;
}
// go through the rest of words
#ifdef _MSC_VER
// Use more Secure C library API
nextToken = strtok_s( NULL, " .@:", &context );
#else
// Use older less Secure C library API
nextToken = strtok( NULL, " .@:" );
#endif
while (nextToken != NULL)
{
string nextWord(nextToken);
nextWord = CUtil::ToLower(nextWord);
if (has_for && nextWord.compare("in") == 0)
has_for_in = true;
if (nextWord.compare("else") == 0)
hasElse = true;
if (!isKeyWord)
{
for(std::vector<string>::iterator it2 = exec_name_list.begin(); it2 != exec_name_list.end(); ++it2)
{
if (*it2 == nextWord)
{
isKeyWord = true;
tmpNextKeyWordStart = CUtil::FindKeyword(CUtil::ToLower(tmp), nextWord, start + firstWord.length(), end);
//std::cout << tmpNextKeyWordStart << "NEXT_START\n";
tmpEnd = tmpNextKeyWordStart; // !!!!!
//std::cout << tmpEnd << "CURR_END\n";
break;
}
}
}
#ifdef _MSC_VER
// Use more Secure C library API
nextToken = strtok_s( NULL, " .@:", &context );
#else
// Use older less Secure C library API
nextToken = strtok( NULL, " .@:" );
#endif
}
if (isKeyWord)
{
//std::cout << pipePos << "pipePos\n";
if (hasPipe && pipePos >= tmpEnd)
hasPipe = false;
//std::cout << ampPos << "ampPos\n";
if (hasAmp && ampPos >= tmpEnd)
hasAmp = false;
}
else
{
hasPipe = false;
hasAmp = false;
}
if ((isComplexWord || isCall || hasElse || has_for_in || hasPipe || hasAmp) && isKeyWord) { // REMEMBER TO CHANGE THE SAME CODE BELOW
nextKeyWordStart = tmpNextKeyWordStart;
end = tmpEnd;
}
if (tmp[0] != '^') {
//std::cout << "2\n";
strSize = CUtil::TruncateLine(end - start + 1, strLSLOC.length(), this->lsloc_truncate, trunc_flag);
if (strSize > 0) {
strLSLOC += CUtil::TrimString(tmp.substr(start, strSize));
strLSLOCBak += CUtil::TrimString(tmpBak.substr(start, strSize));
}
start = end + 1;
if ((isComplexWord || isCall || hasElse || has_for_in || hasPipe || hasAmp) && isKeyWord) { // REMEMBER TO CHANGE THE SAME CODE ABOVE
start = nextKeyWordStart;
}
if (strLSLOCBak.length() > 0) { //add physical SLOC
if (result->addSLOC(strLSLOCBak, lineNumber, trunc_flag)) { //add a logical SLOC
cnt = 0;
CUtil::CountTally(strLSLOC, data_name_list, cnt, 1, exclude, "", "", &result->data_name_count);
temp_lines++;
if (data_continue == true || cnt > 0) {
result->data_lines[LOG]++;
phys_data_lines = temp_lines;
}
else {
result->exec_lines[LOG]++;
phys_exec_lines = temp_lines;
}
}
else if (data_continue == true)
phys_data_lines = temp_lines;
else
phys_exec_lines = temp_lines;
}
data_continue = false;
temp_lines = 0;
strLSLOC = strLSLOCBak = "";
}
delete line;
line = NULL;
}
}
void TEditor::handleEvent( TEvent& event )
{
TView::handleEvent( event );
convertEvent( event );
Boolean centerCursor = Boolean(!cursorVisible());
uchar selectMode = 0;
if( selecting == True || (getShiftState() & 0x03) != 0 )
selectMode = smExtend;
switch( event.what )
{
case evMouseDown:
if( event.mouse.doubleClick == True )
selectMode |= smDouble;
do {
lock();
if( event.what == evMouseAuto )
{
TPoint mouse = makeLocal( event.mouse.where );
TPoint d = delta;
if( mouse.x < 0 )
d.x--;
if( mouse.x >= size.x )
d.x++;
if( mouse.y < 0 )
d.y--;
if( mouse.y >= size.y )
d.y++;
scrollTo(d.x, d.y);
}
setCurPtr(getMousePtr(event.mouse.where), selectMode);
selectMode |= smExtend;
unlock();
} while( mouseEvent(event, evMouseMove + evMouseAuto) );
break;
case evKeyDown:
if( event.keyDown.charScan.charCode == 9 ||
( event.keyDown.charScan.charCode >= 32 && event.keyDown.charScan.charCode < 255 ) )
{
lock();
if( overwrite == True && hasSelection() == False )
if( curPtr != lineEnd(curPtr) )
selEnd = nextChar(curPtr);
insertText( &event.keyDown.charScan.charCode, 1, False);
trackCursor(centerCursor);
unlock();
}
else
return;
break;
case evCommand:
switch( event.message.command )
{
case cmFind:
find();
break;
case cmReplace:
replace();
break;
case cmSearchAgain:
doSearchReplace();
break;
default:
lock();
switch( event.message.command )
{
case cmCut:
clipCut();
break;
case cmCopy:
clipCopy();
// hideSelect(); // JS 12.4.94
break;
case cmPaste:
clipPaste();
break;
case cmUndo:
undo();
break;
case cmClear:
deleteSelect();
break;
case cmCharLeft:
setCurPtr(prevChar(curPtr), selectMode);
break;
case cmCharRight:
setCurPtr(nextChar(curPtr), selectMode);
break;
case cmWordLeft:
setCurPtr(prevWord(curPtr), selectMode);
break;
case cmWordRight:
setCurPtr(nextWord(curPtr), selectMode);
break;
case cmLineStart:
setCurPtr(lineStart(curPtr), selectMode);
break;
case cmLineEnd:
setCurPtr(lineEnd(curPtr), selectMode);
break;
case cmLineUp:
setCurPtr(lineMove(curPtr, -1), selectMode);
break;
case cmLineDown:
setCurPtr(lineMove(curPtr, 1), selectMode);
break;
case cmPageUp:
setCurPtr(lineMove(curPtr, -(size.y-1)), selectMode);
break;
case cmPageDown:
setCurPtr(lineMove(curPtr, size.y-1), selectMode);
break;
case cmTextStart:
setCurPtr(0, selectMode);
break;
case cmTextEnd:
setCurPtr(bufLen, selectMode);
break;
case cmNewLine:
newLine();
break;
case cmBackSpace:
deleteRange(prevChar(curPtr), curPtr, True);
break;
case cmDelChar:
deleteRange(curPtr, nextChar(curPtr), True);
break;
case cmDelWord:
deleteRange(curPtr, nextWord(curPtr), False);
break;
case cmDelStart:
deleteRange(lineStart(curPtr), curPtr, False);
break;
case cmDelEnd:
deleteRange(curPtr, lineEnd(curPtr), False);
break;
case cmDelLine:
deleteRange(lineStart(curPtr), nextLine(curPtr), False);
break;
case cmInsMode:
toggleInsMode();
break;
case cmStartSelect:
startSelect();
break;
case cmHideSelect:
hideSelect();
break;
case cmIndentMode:
autoIndent = Boolean(!autoIndent);
break;
default:
unlock();
return;
}
trackCursor(centerCursor);
unlock();
break;
}
case evBroadcast:
switch( event.message.command )
{
case cmScrollBarChanged:
checkScrollBar( event, hScrollBar, delta.x );
checkScrollBar( event, vScrollBar, delta.y );
break;
default:
return;
}
}
clearEvent(event);
}
static void parseSteppedSection(struct lineFile *lf, char *initialLine, struct pos *pos)
/* Parse out stepped section, adding info about it to pos. */
{
/* Parse out first word of initial line and make sure it is something we recognize. */
char *typeWord = nextWord(&initialLine);
enum bwgSectionType type = bwgTypeFixedStep;
if (sameString(typeWord, "variableStep"))
type = bwgTypeVariableStep;
else if (sameString(typeWord, "fixedStep"))
type = bwgTypeFixedStep;
else
errAbort("Unknown type %s\n", typeWord);
/* Set up defaults for values we hope to parse out of rest of line. */
bits32 start = 0;
char *chrom = NULL;
/* Parse out var=val pairs. */
char *varEqVal;
while ((varEqVal = nextWord(&initialLine)) != NULL)
{
char *wordPairs[2];
int wc = chopByChar(varEqVal, '=', wordPairs, 2);
if (wc != 2)
errAbort("strange var=val pair line %d of %s", lf->lineIx, lf->fileName);
char *var = wordPairs[0];
char *val = wordPairs[1];
if (sameString(var, "chrom"))
chrom = cloneString(val);
else if (sameString(var, "start"))
start = parseUnsignedVal(lf, var, val);
}
/* Check that we have all that are required and no more, and call type-specific routine to parse
* rest of section. */
if (chrom == NULL)
errAbort("Missing chrom= setting line %d of %s\n", lf->lineIx, lf->fileName);
pos->chrom = chrom;
if (type == bwgTypeFixedStep)
{
if (start == 0)
errAbort("Missing start= setting line %d of %s\n", lf->lineIx, lf->fileName);
for (;;)
{
char *line;
if (!lineFileNextReal(lf, &line))
break;
if (steppedSectionEnd(line, 1))
{
lineFileReuse(lf);
break;
}
}
}
else
{
for (;;)
{
char *line;
if (!lineFileNextReal(lf, &line))
break;
if (steppedSectionEnd(line, 2))
{
lineFileReuse(lf);
break;
}
bits32 s = atoi(line);
if (start == 0 || s < start)
start = s;
}
}
pos->start = start-1;
}
void gensatFtpImages(char *checkMd5, char *outDir)
/* gensatFtpImages - Download images guided by output of gensatFtpList. */
{
int err;
char source[PATH_LEN], nativeImage[PATH_LEN], jpgImage[PATH_LEN];
char dir[PATH_LEN], file[PATH_LEN], ext[PATH_LEN];
struct lineFile *lf = lineFileOpen(checkMd5, TRUE);
char *line, *md5, *relativePath;
struct dyString *command = dyStringNew(0);
while(lineFileNext(lf, &line, NULL))
{
/* Parse out two columns of checkMd5 file. */
md5 = nextWord(&line);
relativePath = skipLeadingSpaces(line);
/* Figure out output path, and if file already exists skip it. */
safef(nativeImage, sizeof(nativeImage), "%s/%s", outDir, relativePath);
strcpy(jpgImage, nativeImage);
if (endsWith(jpgImage, ".bz2"))
chopSuffix(jpgImage);
if (endsWith(jpgImage, ".png") || endsWith(jpgImage, ".tif") ||
endsWith(jpgImage, ".tiff") || endsWith(jpgImage, ".jpeg") ||
endsWith(jpgImage, ".jpg") || endsWith(jpgImage, ".JPG") )
{
chopSuffix(jpgImage);
strcat(jpgImage, ".jpg");
}
else if (endsWith(jpgImage, ".txt") || endsWith(jpgImage, ".zip")
|| endsWith(jpgImage, ".doc"))
continue;
else
errAbort("Unrecognized image type in file %s", jpgImage);
if (!fileExists(jpgImage))
{
/* Create any directories needed. */
splitPath(relativePath, dir, file, ext);
dyStringClear(command);
dyStringPrintf(command, "mkdir -p '%s/%s'", outDir, dir);
system(command->string);
/* wget the file. */
safef(source, sizeof(source), "%s/%s", uri, relativePath);
if (safeGetOne(source, md5, nativeImage))
{
if (endsWith(nativeImage, ".bz2"))
{
dyStringClear(command);
dyStringPrintf(command, "bunzip2 '%s'", nativeImage);
verbose(1, "%s\n", command->string);
err = system(command->string);
if (err != 0)
errAbort("err %d on %s", err, command->string);
chopSuffix(nativeImage);
}
if (!endsWith(nativeImage, ".jpg") )
{
dyStringClear(command);
dyStringPrintf(command, "convert '%s' '%s'", nativeImage, jpgImage);
verbose(1, "%s\n", command->string);
err = system(command->string);
if (err != 0)
errAbort("err %d on %s", err, command->string);
remove(nativeImage);
}
}
else
{
if (++errCount > maxErrs)
errAbort("Aborting after %d errors", errCount);
}
}
else
{
verbose(1, "Already have %s\n", jpgImage);
}
}
}
void affyPslAndAtlasToBedNew(char *pslFile, char *atlasFile, char *bedOut,
char *expRecOut)
/** Main function that does all the work for new-style*/
{
struct lineFile *lf = lineFileOpen(atlasFile, TRUE);
char *line, *name;
int i, wordCount, expCount;
char **row;
double *data, median;
double invMedian, ratio, logRatio;
char *affyId;
struct hash *hash = newHash(17);
struct psl *psl;
struct bed *bed;
FILE *f = NULL;
int dataCount = 0, pslCount = 0, bedCount = 0;
int minExpVal = 20;
/* Open Atlas file and use first line to create experiment table. */
if (!lineFileNextReal(lf, &line))
errAbort("%s is empty", lf->fileName);
if (startsWith("Affy", line))
line += 4;
if (line[0] != '\t')
errAbort("%s doesn't seem to be a new format atlas file", lf->fileName);
expCount = lineToExp(line+1, expRecOut);
if (expCount <= 0)
errAbort("No experiments in %s it seems", lf->fileName);
warn("%d experiments\n", expCount);
f = mustOpen(bedOut, "w");
/* Build up a hash keyed by affyID with an int array of data
* for value. Do output in short case. */
AllocArray(row, expCount);
while (lineFileNextReal(lf, &line))
{
affyId = nextWord(&line);
wordCount = chopByWhite(line, row, expCount);
if (wordCount != expCount)
errAbort("Expecting %d data points, got %d line %d of %s",
expCount, wordCount, lf->lineIx, lf->fileName);
if (hashLookup(hash, affyId))
{
warn("Duplicate %s, skipping all but first.", affyId);
continue;
}
AllocArray(data, expCount);
for (i=0; i<expCount; ++i)
{
data[i] = atof(row[i]);
if (data[i] < minExpVal)
data[i] = minExpVal;
}
median = findPositiveMedian(data, expCount, minExpVal);
if (median >= 0)
{
invMedian = 1.0/median;
for (i=0; i<expCount; ++i)
{
double val = data[i];
val = safeLog2(invMedian*val);
data[i] = val;
}
if (shortOut)
shortDataOut(f, affyId, expCount, data);
else
hashAdd(hash, affyId, data);
}
data = NULL;
++dataCount;
}
lineFileClose(&lf);
warn("%d rows of expression data\n", dataCount);
/* Stream through psl file, converting it to bed with expression data. */
if (!shortOut)
{
lf = pslFileOpen(pslFile);
while ((psl = pslNext(lf)) != NULL)
{
++pslCount;
/* get probe id from sequence name */
name=parseNameFromHgc(psl->qName);
data = hashFindVal(hash, name);
if (data != NULL)
{
struct bed *bed = bedFromPsl(psl);
bed->expCount = expCount;
AllocArray(bed->expIds, expCount);
AllocArray(bed->expScores, expCount);
for (i=0; i<expCount; ++i)
{
bed->expScores[i] = data[i];
bed->expIds[i] = i;
}
bedTabOutN(bed, 15, f);
++bedCount;
bedFree(&bed);
}
pslFree(&psl);
}
warn("%d records in %s", pslCount, pslFile);
warn("%d records written to %s", bedCount, bedOut);
}
lineFileClose(&lf);
carefulClose(&f);
}
void hgLoadRnaFold(char *database, char *table, char *foldDir)
/* hgLoadRnaFold - Load a directory full of RNA fold files into database. */
{
char path[PATH_LEN];
struct slName *dirList, *dirEl;
struct lineFile *lf;
char *line, *word, *s, c;
FILE *f = hgCreateTabFile(tabDir, table);
int count = 0;
dirList = listDir(foldDir, "*");
for (dirEl = dirList; dirEl != NULL; dirEl = dirEl->next)
{
char *name = dirEl->name;
if (sameString(name, "CVS"))
continue;
safef(path, sizeof(path), "%s/%s", foldDir, name);
lf = lineFileOpen(path, TRUE);
if (!lineFileNext(lf, &line, NULL))
{
if (warnEmpty)
{
warn("%s is empty, skipping\n", name);
lineFileClose(&lf);
continue;
}
else
errAbort("%s is empty\n", name);
}
if (!isupper(line[0]))
notFold(path, 1);
fprintf(f, "%s\t", name); /* Save name */
fprintf(f, "%s\t", line); /* Save sequence */
lineFileNeedNext(lf, &line, NULL);
c = line[0];
if (c != '.' && c != '(')
notFold(path, 2);
word = nextWord(&line);
fprintf(f, "%s\t", word); /* Save nested parenthesis */
/* Parse out (energy) term at end of line. */
s = strchr(line, '(');
if (s == NULL)
notFold(path, 3);
word = skipLeadingSpaces(s+1);
if (word == NULL || (!word[0] == '-' && !isdigit(word[0])))
notFold(path, 4);
if ((s = strchr(word, ')')) == NULL)
notFold(path, 5);
*s = 0;
fprintf(f, "%s\n", word);
lineFileClose(&lf);
++count;
}
printf("Parsed %d files\n", count);
if (doLoad)
{
struct sqlConnection *conn = sqlConnect(database);
rnaFoldCreateTable(conn, table);
hgLoadTabFile(conn, tabDir, table, &f);
hgRemoveTabFile(tabDir, table);
sqlDisconnect(&conn);
}
}
static void parseSteppedSection(struct lineFile *lf, boolean clipDontDie,
struct hash *chromSizeHash, char *initialLine,
struct lm *lm, int itemsPerSlot, struct bwgSection **pSectionList)
/* Parse out a variableStep or fixedStep section and add it to list, breaking it up as need be. */
{
/* Parse out first word of initial line and make sure it is something we recognize. */
char *typeWord = nextWord(&initialLine);
enum bwgSectionType type = bwgTypeFixedStep;
if (sameString(typeWord, "variableStep"))
type = bwgTypeVariableStep;
else if (sameString(typeWord, "fixedStep"))
type = bwgTypeFixedStep;
else
errAbort("Unknown type %s\n", typeWord);
/* Set up defaults for values we hope to parse out of rest of line. */
int span = 0;
bits32 step = 0;
bits32 start = 0;
char *chrom = NULL;
/* Parse out var=val pairs. */
char *varEqVal;
while ((varEqVal = nextWord(&initialLine)) != NULL)
{
char *wordPairs[2];
int wc = chopByChar(varEqVal, '=', wordPairs, 2);
if (wc != 2)
errAbort("strange var=val pair line %d of %s", lf->lineIx, lf->fileName);
char *var = wordPairs[0];
char *val = wordPairs[1];
if (sameString(var, "chrom"))
chrom = cloneString(val);
else if (sameString(var, "span"))
span = parseUnsignedVal(lf, var, val);
else if (sameString(var, "step"))
step = parseUnsignedVal(lf, var, val);
else if (sameString(var, "start"))
{
start = parseUnsignedVal(lf, var, val);
}
else
errAbort("Unknown setting %s=%s line %d of %s", var, val, lf->lineIx, lf->fileName);
}
/* Check that we have all that are required and no more, and call type-specific routine to parse
* rest of section. */
if (chrom == NULL)
errAbort("Missing chrom= setting line %d of %s\n", lf->lineIx, lf->fileName);
bits32 chromSize = (chromSizeHash ? hashIntVal(chromSizeHash, chrom) : BIGNUM);
if (start > chromSize)
{
warn("line %d of %s: chromosome %s has %u bases, but item starts at %u",
lf->lineIx, lf->fileName, chrom, chromSize, start);
if (!clipDontDie)
noWarnAbort();
}
if (type == bwgTypeFixedStep)
{
if (start == 0)
errAbort("Missing start= setting line %d of %s\n", lf->lineIx, lf->fileName);
if (step == 0)
errAbort("Missing step= setting line %d of %s\n", lf->lineIx, lf->fileName);
if (span == 0)
span = step;
parseFixedStepSection(lf, clipDontDie, lm, itemsPerSlot,
chrom, chromSize, span, start-1, step, pSectionList);
}
else
{
if (start != 0)
errAbort("Extra start= setting line %d of %s\n", lf->lineIx, lf->fileName);
if (step != 0)
errAbort("Extra step= setting line %d of %s\n", lf->lineIx, lf->fileName);
if (span == 0)
span = 1;
parseVariableStepSection(lf, clipDontDie, lm, itemsPerSlot,
chrom, chromSize, span, pSectionList);
}
}
static struct joinerSet *parseIdentifierSet(struct lineFile *lf,
char *line, struct hash *symHash, struct dyString *dyBuf)
/* Parse out one joiner record - keep going until blank line or
* end of file. */
{
struct joinerSet *js;
struct joinerField *jf;
char *word, *e;
char *parts[3];
int partCount;
/* Parse through first line - first word is name. */
word = nextWord(&line);
if (word == NULL || strchr(word, '=') != NULL)
errAbort("joiner without name line %d of %s\n", lf->lineIx, lf->fileName);
AllocVar(js);
js->name = cloneString(word);
js->lineIx = lf->lineIx;
while ((word = nextWord(&line)) != NULL)
{
char *e = strchr(word, '=');
if (e != NULL)
*e++ = 0;
if (sameString(word, "typeOf"))
{
js->typeOf = cloneSpecified(lf, word, e);
}
else if (sameString(word, "external"))
{
js->external = cloneSpecified(lf, word, e);
}
else if (sameString(word, "fuzzy"))
{
js->isFuzzy = TRUE;
}
else if (sameString(word, "dependency"))
{
js->isDependency = TRUE;
}
else
{
errAbort("Unknown attribute %s line %d of %s", word,
lf->lineIx, lf->fileName);
}
}
/* Parse second line, make sure it is quoted, and save as description. */
line = nextSubbedLine(lf, symHash, dyBuf);
if (line == NULL)
lineFileUnexpectedEnd(lf);
line = trimSpaces(line);
if (line[0] != '"' || lastChar(line) != '"')
errAbort("Expecting quoted line, line %d of %s\n",
lf->lineIx, lf->fileName);
line[strlen(line)-1] = 0;
js->description = cloneString(line+1);
/* Go through subsequent lines. */
while ((line = nextSubbedLine(lf, symHash, dyBuf)) != NULL)
{
/* Keep grabbing until we get a blank line. */
line = skipLeadingSpaces(line);
if (line[0] == 0)
break;
/* First word in line should be database.tabe.field. */
word = nextWord(&line);
partCount = chopString(word, ".", parts, ArraySize(parts));
if (partCount != 3)
errAbort("Expecting database.table.field line %d of %s",
lf->lineIx, lf->fileName);
/* Allocate struct and save table and field. */
AllocVar(jf);
jf->lineIx = lf->lineIx;
jf->table = cloneString(parts[1]);
jf->field = cloneString(parts[2]);
if (js->fieldList == NULL && !js->isFuzzy)
{
jf->isPrimary = TRUE;
jf->unique = TRUE;
jf->full = TRUE;
}
jf->minCheck = 1.0;
slAddHead(&js->fieldList, jf);
/* Database may be a comma-separated list. Parse it here. */
jf->dbList = parseDatabaseList(lf, parts[0]);
/* Look for other fields in subsequent space-separated words. */
while ((word = nextWord(&line)) != NULL)
{
if ((e = strchr(word, '=')) != NULL)
*e++ = 0;
if (sameString("comma", word))
{
jf->separator = cloneString(",");
}
else if (sameString("separator", word))
{
jf->separator = cloneSpecified(lf, word, e);
}
else if (sameString("chopBefore", word))
{
if (e == NULL)
unspecifiedVar(lf, word);
slNameStore(&jf->chopBefore, e);
}
else if (sameString("chopAfter", word))
{
if (e == NULL)
unspecifiedVar(lf, word);
slNameStore(&jf->chopAfter, e);
}
else if (sameString("indexOf", word))
{
jf->indexOf = TRUE;
}
else if (sameString("dupeOk", word))
{
if (!jf->isPrimary)
warn("dupeOk outsite primary key line %d of %s",
lf->lineIx, lf->fileName);
jf->unique = FALSE;
}
else if (sameString("minCheck", word))
{
if (e == NULL)
unspecifiedVar(lf, word);
jf->minCheck = atof(e);
}
else if (sameString("unique", word))
{
jf->unique = TRUE;
}
else if (sameString("full", word))
{
jf->full = TRUE;
}
else if (sameString("splitPrefix", word))
{
jf->splitPrefix = cloneSpecified(lf, word, e);
}
else if (sameString("splitSuffix", word))
{
jf->splitSuffix = cloneSpecified(lf, word, e);
}
else if (sameString("exclude", word))
{
if (e == NULL)
unspecifiedVar(lf, word);
slNameStore(&jf->exclude, e);
}
else
{
errAbort("Unrecognized attribute %s line %d of %s",
word, lf->lineIx, lf->fileName);
}
}
if (jf->indexOf && jf->separator == NULL)
errAbort("indexOf without comma or separator line %d of %s",
lf->lineIx, lf->fileName);
if (jf->isPrimary && jf->separator != NULL)
errAbort("Error line %d of %s\n"
"Primary key can't be a list (comma or separator)."
, lf->lineIx, lf->fileName);
}
slReverse(&js->fieldList);
return js;
}
