2c4c813bcb91cf575584d868a1d145f3a3bc6416
kate
  Mon Nov 17 00:28:14 2014 -0800
Add peptide table with sequence and other info for details page.  refs #25054
diff --git src/hg/lib/peptideAtlasPeptide.c src/hg/lib/peptideAtlasPeptide.c
new file mode 100644
index 0000000..029bf01
--- /dev/null
+++ src/hg/lib/peptideAtlasPeptide.c
@@ -0,0 +1,141 @@
+/* peptideAtlasPeptide.c was originally generated by the autoSql program, which also 
+ * generated peptideAtlasPeptide.h and peptideAtlasPeptide.sql.  This module links the database and
+ * the RAM representation of objects. */
+
+#include "common.h"
+#include "linefile.h"
+#include "dystring.h"
+#include "jksql.h"
+#include "peptideAtlasPeptide.h"
+
+
+
+char *peptideAtlasPeptideCommaSepFieldNames = "accession,sequence,sampleCount,hydrophobicity,proteotypicScore";
+
+void peptideAtlasPeptideStaticLoad(char **row, struct peptideAtlasPeptide *ret)
+/* Load a row from peptideAtlasPeptide table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->accession = row[0];
+ret->sequence = row[1];
+ret->sampleCount = sqlSigned(row[2]);
+ret->hydrophobicity = sqlFloat(row[3]);
+ret->proteotypicScore = sqlFloat(row[4]);
+}
+
+struct peptideAtlasPeptide *peptideAtlasPeptideLoad(char **row)
+/* Load a peptideAtlasPeptide from row fetched with select * from peptideAtlasPeptide
+ * from database.  Dispose of this with peptideAtlasPeptideFree(). */
+{
+struct peptideAtlasPeptide *ret;
+
+AllocVar(ret);
+ret->accession = cloneString(row[0]);
+ret->sequence = cloneString(row[1]);
+ret->sampleCount = sqlSigned(row[2]);
+ret->hydrophobicity = sqlFloat(row[3]);
+ret->proteotypicScore = sqlFloat(row[4]);
+return ret;
+}
+
+struct peptideAtlasPeptide *peptideAtlasPeptideLoadAll(char *fileName) 
+/* Load all peptideAtlasPeptide from a whitespace-separated file.
+ * Dispose of this with peptideAtlasPeptideFreeList(). */
+{
+struct peptideAtlasPeptide *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[5];
+
+while (lineFileRow(lf, row))
+    {
+    el = peptideAtlasPeptideLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct peptideAtlasPeptide *peptideAtlasPeptideLoadAllByChar(char *fileName, char chopper) 
+/* Load all peptideAtlasPeptide from a chopper separated file.
+ * Dispose of this with peptideAtlasPeptideFreeList(). */
+{
+struct peptideAtlasPeptide *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[5];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = peptideAtlasPeptideLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct peptideAtlasPeptide *peptideAtlasPeptideCommaIn(char **pS, struct peptideAtlasPeptide *ret)
+/* Create a peptideAtlasPeptide out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new peptideAtlasPeptide */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->accession = sqlStringComma(&s);
+ret->sequence = sqlStringComma(&s);
+ret->sampleCount = sqlSignedComma(&s);
+ret->hydrophobicity = sqlFloatComma(&s);
+ret->proteotypicScore = sqlFloatComma(&s);
+*pS = s;
+return ret;
+}
+
+void peptideAtlasPeptideFree(struct peptideAtlasPeptide **pEl)
+/* Free a single dynamically allocated peptideAtlasPeptide such as created
+ * with peptideAtlasPeptideLoad(). */
+{
+struct peptideAtlasPeptide *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->accession);
+freeMem(el->sequence);
+freez(pEl);
+}
+
+void peptideAtlasPeptideFreeList(struct peptideAtlasPeptide **pList)
+/* Free a list of dynamically allocated peptideAtlasPeptide's */
+{
+struct peptideAtlasPeptide *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    peptideAtlasPeptideFree(&el);
+    }
+*pList = NULL;
+}
+
+void peptideAtlasPeptideOutput(struct peptideAtlasPeptide *el, FILE *f, char sep, char lastSep) 
+/* Print out peptideAtlasPeptide.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->accession);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->sequence);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->sampleCount);
+fputc(sep,f);
+fprintf(f, "%g", el->hydrophobicity);
+fputc(sep,f);
+fprintf(f, "%g", el->proteotypicScore);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+