3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 braney Mon Feb 17 10:41:18 2020 -0800 delete long unused code for HIV, Cancer browser. RIP Fan. diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index 3e4c3c4..39ea344 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -4421,54 +4421,50 @@ char *thisOrg = hOrganism(database); cartWebStart(cart, database, "Get DNA in Window (%s/%s)", database, thisOrg); printf("<H2>Get DNA for </H2>\n"); printf("<FORM ACTION=\"%s\">\n\n", hgcName()); cartSaveSession(cart); cgiMakeHiddenVar("g", "htcGetDna2"); cgiMakeHiddenVar("table", tbl); cgiContinueHiddenVar("i"); cgiContinueHiddenVar("o"); cgiContinueHiddenVar("t"); cgiContinueHiddenVar("l"); cgiContinueHiddenVar("r"); puts("Position "); savePosInTextBox(seqName, winStart+1, winEnd); -/* bypass message about Table Browser for GSID server, since we haven't offered TB for GSID */ -if (!hIsGsidServer()) - { if (tbl[0] == 0) { puts("<P>" "Note: This page retrieves genomic DNA for a single region. " "If you would prefer to get DNA for many items in a particular track, " "or get DNA with formatting options based on gene structure (introns, exons, UTRs, etc.), try using the "); printf("<A HREF=\"%s\" TARGET=_blank>", hgTablesUrl(TRUE, NULL)); puts("Table Browser</A> with the \"sequence\" output format. You can also use the "); printf("<A HREF=\"../goldenPath/help/api.html\" TARGET=_blank>"); puts("REST API</A> with the <b>/getData/sequence</b> endpoint function " "to extract sequence data with coordinates."); } else { puts("<P>" "Note: if you would prefer to get DNA for more than one feature of " "this track at a time, try the "); printf("<A HREF=\"%s\" TARGET=_blank>", hgTablesUrl(FALSE, tbl)); puts("Table Browser</A> using the output format sequence."); } - } hgSeqOptionsHtiCart(hti,cart); puts("<P>"); cgiMakeButton("submit", "get DNA"); if (dbIsFound) cgiMakeButton("submit", EXTENDED_DNA_BUTTON); puts("</FORM><P>"); if (dbIsFound) puts("Note: The \"Mask repeats\" option applies only to \"get DNA\", not to \"extended case/color options\". <P>"); } boolean dnaIgnoreTrack(char *track) /* Return TRUE if this is one of the tracks too boring * to put DNA on. */ { @@ -4770,71 +4766,30 @@ printf("</TD>"); printf("<TD>"); safef(buf, sizeof buf, "%s_green", tdb->track); cgiMakeIntVar(buf, cartUsualInt(cart, buf, 0), 3); printf("</TD>"); printf("<TD>"); safef(buf, sizeof buf, "%s_blue", tdb->track); cgiMakeIntVar(buf, cartUsualInt(cart, buf, 0), 3); printf("</TD>"); printf("</TR>\n"); } } } printf("</TABLE>\n"); printf("</FORM>\n"); -if (hIsGsidServer()) - { - printf("<H3>Coloring Information and Examples</H3>\n"); - puts("The color values range from 0 (darkest) to 255 (lightest) and are additive.\n"); - puts("The examples below show a few ways to highlight individual tracks, " - "and their interplay. It's good to keep it simple at first. It's easy " - "to make pretty, but completely cryptic, displays with this feature."); - puts( - "<UL>" - "<LI>To put Genes in upper case red text, check the " - "appropriate box in the Toggle Case column and set the color to pure " - "red, RGB (255,0,0). Upon submitting, any Gene within the " - "designated chromosomal interval will now appear in red capital letters.\n" - "<LI>To see the overlap between Genes and InterPro Domains try " - "setting the Genes/Regions to red (255,0,0) and InterPro to green (0,255,0). " - "Places where the Genes and InterPro Domains overlap will be painted yellow " - "(255,255,0).\n" - "<LI>To get a level-of-coverage effect for tracks like Genes with " - "multiple overlapping items, initially select a darker color such as deep " - "green, RGB (0,64,0). Nucleotides covered by a single Gene will appear dark " - "green, while regions covered with more Genes get progressively brighter — " - "saturating at 4 Genes." - "<LI>Another track can be used to mask unwanted features. Setting the " - "InterPro track to RGB (255,255,255) will white-out Genes within InterPro " - "domains. " - "</UL>"); - puts("<H3>Further Details and Ideas</H3>"); - puts("<P>Copying and pasting the web page output to a text editor such as Word " - "will retain upper case but lose colors and other formatting. That is still " - "useful because other web tools such as " - "<A HREF=\"https://www.ncbi.nlm.nih.gov/blast\" TARGET=_BLANK>NCBI Blast</A> " - "can be set to ignore lower case. To fully capture formatting such as color " - "and underlining, view the output as \"source\" in your web browser, or download " - "it, or copy the output page into an html editor.</P>"); - puts("<P>The default line width of 60 characters is standard, but if you have " - "a reasonable sized monitor it's useful to set this higher - to 125 characters " - "or more. You can see more DNA at once this way, and fewer line breaks help " - "in finding DNA strings using the web browser search function.</P>"); - } -else - { printf("<H3>Coloring Information and Examples</H3>\n"); puts("The color values range from 0 (darkest) to 255 (lightest) and are additive.\n"); puts("The examples below show a few ways to highlight individual tracks, " "and their interplay. It's good to keep it simple at first. It's easy " "to make pretty, but completely cryptic, displays with this feature."); puts( "<UL>" "<LI>To put exons from RefSeq Genes in upper case red text, check the " "appropriate box in the Toggle Case column and set the color to pure " "red, RGB (255,0,0). Upon submitting, any RefSeq Gene within the " "designated chromosomal interval will now appear in red capital letters.\n" "<LI>To see the overlap between RefSeq Genes and Genscan predictions try " "setting the RefSeq Genes to red (255,0,0) and Genscan to green (0,255,0). " "Places where the RefSeq Genes and Genscan overlap will be painted yellow " "(255,255,0).\n" @@ -4852,31 +4807,30 @@ puts("<P>Copying and pasting the web page output to a text editor such as Word " "will retain upper case but lose colors and other formatting. That is still " "useful because other web tools such as " "<A HREF=\"https://www.ncbi.nlm.nih.gov/blast\" TARGET=_BLANK>NCBI Blast</A> " "can be set to ignore lower case. To fully capture formatting such as color " "and underlining, view the output as \"source\" in your web browser, or download " "it, or copy the output page into an html editor.</P>"); puts("<P>The default line width of 60 characters is standard, but if you have " "a reasonable sized monitor it's useful to set this higher - to 125 characters " "or more. You can see more DNA at once this way, and fewer line breaks help " "in finding DNA strings using the web browser search function.</P>"); puts("<P>Be careful about requesting complex formatting for a very large " "chromosomal region. After all the html tags are added to the output page, " "the file size may exceed size limits that your browser, clipboard, and " "other software can safely display. The tool will format 10 Mb and more, however.</P>"); - } trackDbFreeList(&tdbList); } void doGetBlastPep(char *readName, char *table) /* get predicted protein */ { int qStart; struct psl *psl; int start, end; struct sqlResult *sr; struct sqlConnection *conn = hAllocConn(database); struct dnaSeq *tSeq; char query[256], **row; char fullTable[HDB_MAX_TABLE_STRING]; boolean hasBin; @@ -25443,35 +25397,30 @@ cartSetString(cart, "i", "PrintAllSequences"); hgCustom(newCts->tdb->track, NULL); } void doMiddle() /* Generate body of HTML. */ { char *track = cartString(cart, "g"); char *item = cloneString(cartOptionalString(cart, "i")); char *parentWigMaf = cartOptionalString(cart, "parentWigMaf"); struct trackDb *tdb = NULL; hgBotDelayFrac(0.5); -if (hIsGisaidServer()) - { - validateGisaidUser(cart); - } - /* database and organism are global variables used in many places */ getDbAndGenome(cart, &database, &genome, NULL); organism = hOrganism(database); scientificName = hScientificName(database); initGenbankTableNames(database); dbIsFound = trackHubDatabase(database) || sqlDatabaseExists(database); // Try to deal with virt chrom position used by hgTracks. // Hack the cart vars to set to a non virtual chrom mode position if (sameString("virt", cartString(cart, "c")) || sameString("getDna", cartUsualString(cart, "g", "")) ) { char *nvPos = cartUsualString(cart, "nonVirtPosition", NULL); @@ -26433,38 +26382,30 @@ { doJaxAliasGenePred(tdb, item); } else if (sameWord(table, "wgRna")) { doWgRna(tdb, item); } else if (sameWord(table, "ncRna")) { doNcRna(tdb, item); } else if (sameWord(table, "gbProtAnn")) { doGbProtAnn(tdb, item); } -else if (sameWord(table, "h1n1Gene")) - { - doH1n1Gene(tdb, item); - } -else if (startsWith("h1n1_", table) || startsWith("h1n1b_", table)) - { - doH1n1Seq(tdb, item); - } else if (sameWord(table, "bdgpGene") || sameWord(table, "bdgpNonCoding")) { doBDGPGene(tdb, item); } else if (sameWord(table, "flyBaseGene") || sameWord(table, "flyBaseNoncoding")) { doFlyBaseGene(tdb, item); } else if (sameWord(table, "bgiGene")) { doBGIGene(tdb, item); } else if (sameWord(table, "bgiSnp")) { doBGISnp(tdb, item);