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/hgTables/pal.c src/hg/hgTables/pal.c
index 6128b88..d6599a9 100644
--- src/hg/hgTables/pal.c
+++ src/hg/hgTables/pal.c
@@ -1,89 +1,92 @@
+/* Copyright (C) 2011 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "trackDb.h"
 #include "cart.h"
 #include "hgTables.h"
 #include "pal.h"
 
 
 boolean isPalCompatible(struct sqlConnection *conn,
     struct trackDb *track, char *table)
 /* Return TRUE if table is genePred and there is a maf. */
 {
 char setting[128], *p = setting;
 
 if (track == NULL)
     return FALSE;
 if (isEmpty(track->type))
     return FALSE;
 safecpy(setting, sizeof setting, track->type);
 char *type = nextWord(&p);
 
 if (!sameString(type, "genePred"))
     return FALSE;
 
 if (!sameString(track->table, table))
     return FALSE;
 
 /* we also check for a maf table */
 struct slName *list = hTrackTablesOfType(conn, "wigMaf%%");
 
 if (list != NULL)
     {
     slFreeList(&list);
     return TRUE;
     }
 
 return FALSE;
 }
 
 void doGenePredPal(struct sqlConnection *conn)
 /* Output genePred protein alignment. */
 {
 if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
     {
     sendParamsToGalaxy(hgtaDoPalOut, "submit");
     return;
     }
 
 /* get rid of pesky cookies that would bring us back here */
 cartRemove(cart, hgtaDoPal);
 cartRemove(cart, hgtaDoPalOut);
 
 if (anyIntersection() && intersectionIsBpWise())
     errAbort("Can't do CDS FASTA output when bit-wise intersection is on. "
     "Please go back and select another output type, or clear the intersection.");
 
 struct lm *lm = lmInit(64*1024);
 int fieldCount;
 struct bed *bedList = cookedBedsOnRegions(conn, curTable, getRegions(),
 	lm, &fieldCount);
 
 //lmCleanup(&lm);
 
 textOpen();
 
 int outCount = palOutPredsInBeds(conn, cart, bedList, curTable);
 
 /* Do some error diagnostics for user. */
 if (outCount == 0)
     explainWhyNoResults(NULL);
 }
 
 void addOurButtons()
 /* callback from options dialog to add navigation buttons */
 {
 printf("For information about output data format see the "
   "<A HREF=\"../goldenPath/help/hgTablesHelp.html#FASTA\">User's Guide</A>.<BR>");
 cgiMakeButton(hgtaDoPalOut, "get output");
 hPrintf(" ");
 cgiMakeButton(hgtaDoMainPage, "cancel");
 hPrintf("<input type=\"hidden\" name=\"%s\" value=\"\">\n", hgtaDoPal);
 }
 
 void doOutPalOptions(struct sqlConnection *conn)
 /* Output pal page. */
 {
 htmlOpen("Select multiple alignment and options for %s", curTrack->shortLabel);
 palOptions(cart, conn, addOurButtons, hgtaDoPal);
 htmlClose();
 }