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/lib/jalview.c src/hg/lib/jalview.c
index afcf32b..ba1a1d1 100644
--- src/hg/lib/jalview.c
+++ src/hg/lib/jalview.c
@@ -1,57 +1,60 @@
 /* display multiple alignment using jalview */
+
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "portable.h"
 
 void displayJalView(char *inUrl, char *type, char *optional)
 {
 //char *host = getenv("HTTP_HOST"); 
 printf("<applet code=\"jalview.bin.JalviewLite\"\n");
 printf(" width=\"140\"");
 printf(" height=\"35\"");
 printf(" archive=\"/pseudogene/jalviewApplet.jar\">\n");
 printf("<param name=\"file\" value=\"%s\">\n", inUrl);
 //printf("<param name=\"file\" value=\"http://%s/%s\">\n", host, inUrl);
 printf("<param name=\"defaultColour\" value=\"%% Identity\">\n");
 printf("<param name=\"showAnnotation\" value=\"false\">\n");
 printf("<param name=\"wrap\" value=\"true\">\n");
 printf("<param name=\"sortBy\" value=\"Pairwise Identity\">\n");
 printf("<param name=\"type\" value=\"URL\">\n");
 printf("<param name=\"format\" value=\"%s\">\n", type);
 if (optional != NULL)
     printf("%s\n",optional);
 #ifdef GROUP
 printf("<param name=\"groups\" value=\"1\">");
 printf("<param name=\"group1\" value=\"1-99:PID:false:false:false\">");
 printf("jalview");
 #endif
 printf("</APPLET>\n");
 
 #ifdef samplejalview
 <applet code="jalview.bin.JalviewLite" width="140" height="35" archive="jalviewApplet.jar">
 <param name="file" value="uniref50.fa">
 <param name="defaultColour" value="Blosum62">
 <param name="RGB"  value="F2F2FF">
 <param name="linkLabel_1" value="SRS">
 <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
 <param name="linkLabel_2" value="Uniprot">
 <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 </applet>
 #endif
 #ifdef OBJECT
 printf("\n<OBJECT ");
 printf(" classid=\"jalview.ButtonAlignApplet.class\"\n");
 printf(" codetype=\"application/java\"\n");
 printf(" codebase=\"pseudogene/\"\n");
 printf(" code=\"jalview.ButtonAlignApplet.class\"\n");
 printf(" width=\"100\"");
 printf(" height=\"35\"");
 printf(">\n");
 printf("<param name=\"input\" value=\"http://%s/%s\">\n", host, inUrl);
 printf("<param name=\"type\" value=\"URL\">\n");
 printf("<param name=\"format\" value=\"%s\">\n", type);
 printf("<PARAM name=fontsize value=\"14\">\n");
 if (optional != NULL)
     printf("%s\n",optional);
 printf("</OBJECT>\n");
 #endif
 }