e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/hgGene/swissProtComments.c src/hg/hgGene/swissProtComments.c
index 042f0cb..5a89388 100644
--- src/hg/hgGene/swissProtComments.c
+++ src/hg/hgGene/swissProtComments.c
@@ -1,162 +1,165 @@
 /* SwissProt comments - print out SwissProt comments if any. */
 
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "spDb.h"
 #include "hgGene.h"
 
 
 struct spComment
 /* Swiss prot comment. */
     {
     struct spComment *next;
     int typeId;		/* Comment type. */
     int valId;		/* Comment value. */
     };
 
 static boolean swissProtCommentsExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if swissProt database exists and there are comments
  * on this gene.  This does first part of database lookup and
  * stores it in section->items as a spComment list. */
 {
 char query[512], **row;
 struct sqlResult *sr;
 boolean commentFound = FALSE;
 
 struct spComment *list = NULL, *com;
 char *acc = swissProtAcc;
 if (acc != NULL)
     {
     sqlSafef(query, sizeof(query),
 	"select commentType,commentVal from comment where acc='%s'" , acc);
     sr = sqlGetResult(spConn, query);
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	commentFound = TRUE;
 	AllocVar(com);
 	com->typeId = atoi(row[0]);
 	com->valId = atoi(row[1]);
 	slAddHead(&list, com);
 	}
     slReverse(&list);
     section->items = list;
     if (!commentFound)
 	{
 	/* check if the acc has become a secondary ID */
 	sqlSafef(query, sizeof(query),
 	    "select accession from proteome.spSecondaryID where accession2='%s'" , acc);
 	sr = sqlGetResult(spConn, query);
 	row = sqlNextRow(sr);
 	if (row != NULL)
 	    {
 	    acc = cloneString(row[0]);
 	    sqlFreeResult(&sr);
 	    sqlSafef(query, sizeof(query),
 		  "select commentType,commentVal from comment where acc='%s'" , acc);
 	    sr = sqlGetResult(spConn, query);
 	    while ((row = sqlNextRow(sr)) != NULL)
 		{
 		AllocVar(com);
 		com->typeId = atoi(row[0]);
 		com->valId = atoi(row[1]);
 		slAddHead(&list, com);
 		}
 	    slReverse(&list);
 	    section->items = list;
 	    }
 	}
     }
 
 return list != NULL;
 }
 
 static char *omimUrl = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=OMIM&term=%d&doptcmdl=Detailed&tool=genome.ucsc.edu";
 
 static void mimSubPrint(char *s)
 /* Print out putting in hyperlinks for OMIM. */
 {
 char *e, *f, *g;
 while (s != NULL && s[0] != 0)
     {
     boolean gotOmim = FALSE;
     e = stringIn("[MIM:", s);
     if (e != NULL)
         {
 	f = e + strlen("[MIM:");
 	if (isdigit(f[0]))
 	    {
 	    g = strchr(f, ']');
 	    if (g != 0 && g - f < 8)
 	        {
 		int omimId = atoi(f);
 		int skipSize = g - e + 1;
 		mustWrite(stdout, s, e-s);
 		hPrintf("<A HREF=\"");
 		hPrintf(omimUrl, omimId);
 		hPrintf("\" TARGET=_blank>");
 		mustWrite(stdout, e, skipSize);
 		hPrintf("</A>");
 		s = e + skipSize;
 		gotOmim = TRUE;
 		}
 	    }
 	}
     if (!gotOmim)
         {
 	hPrintf("%s", s);
 	s = NULL;
 	}
     }
 }
 
 static void swissProtCommentsPrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out SwissProt comments - looking up typeId/commentVal. */
 {
 struct spComment *com;
 char *acc = swissProtAcc;
 char *description;
 char *id = spAnyAccToId(spConn, acc);
 if (id == NULL)
     {
     errAbort("<br>%s seems to no longer be a valid protein ID in our latest UniProtKB DB", acc);
     }
     
 /* the new logic below is to handle the situation that an accession may have
    become a secondary accession number in a newer UniProt DB release */
 description = spDescription(spConn, spFindAcc(spConn, acc));
 			    
 hPrintf("<B>ID:</B> ");
 hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" TARGET=_blank>", acc);
 hPrintf("%s</A><BR>\n", id);
 if (description != NULL)
     hPrintf("<B>DESCRIPTION:</B> %s<BR>\n", description);
 for (com = section->items; com != NULL; com = com->next)
     {
     char *type = spCommentType(spConn, com->typeId);
     if (!sameWord(type, "ALTERNATIVE PRODUCTS"))
 	{
 	char *val = spCommentVal(spConn, com->valId);
 	hPrintf("<B>%s:</B> ", type);
 	mimSubPrint(val);
 	hPrintf("<BR>");
 	freeMem(type);
 	freeMem(val);
 	}
     }
 slFreeList(&section->items);
 freeMem(description);
 }
 
 struct section *swissProtCommentsSection(struct sqlConnection *conn,
 	struct hash *sectionRa)
 /* Create SwissProt comments section. */
 {
 struct section *section = sectionNew(sectionRa, "swissProtComments");
 section->exists = swissProtCommentsExists;
 section->print = swissProtCommentsPrint;
 return section;
 }