From 619cc880371f3228e6a1fb33c6bfb6e7a7e2622c Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 10 Sep 2015 04:40:52 +0100
Subject: [PATCH 1/1] JAL-1684 updated example to just a fragment of the
 estrogen sequences

---
 examples/applets.html                    |    8 ++++----
 examples/estrogenReceptorCdna_frag.fa    |   12 ++++++++++++
 examples/estrogenReceptorProtein_frag.fa |   14 ++++++++++++++
 3 files changed, 30 insertions(+), 4 deletions(-)
 create mode 100644 examples/estrogenReceptorCdna_frag.fa
 create mode 100644 examples/estrogenReceptorProtein_frag.fa

diff --git a/examples/applets.html b/examples/applets.html
index 8d32d5f..3dfa83a 100644
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -178,8 +178,8 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
    code="jalview.bin.JalviewLite" width="140" height="35"
    archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
 <param name="permissions" value="sandbox"/>
-<param name="file2" value="estrogenReceptorCdna.fa"/>
-<param name="file" value="estrogenReceptorProtein.aln"/>
+<param name="file2" value="estrogenReceptorCdna_frag.fa"/>
+<param name="file" value="estrogenReceptorProtein_frag.fa"/>
 <param name="enableSplitFrame" value="true"/>
 <param name="scaleProteinAsCdna" value="true"/>
 <param name="showFullId" value="false"/>
@@ -192,8 +192,8 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
      value="http://www.jalview.org/services/launchApp"/>
 </applet>
 </td>
-      <td valign="center">Displays a split window view of protein
-        and its related cDNA.<br />Proteins were aligned with <a
+      <td valign="center">Displays a split window view showing aligned protein
+        and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
         href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
         via the Jalvew Desktop).<br />Data retrieved from Uniprot and
         ENA, after Thornton, Need and Crews, <a
diff --git a/examples/estrogenReceptorCdna_frag.fa b/examples/estrogenReceptorCdna_frag.fa
new file mode 100644
index 0000000..da5f5c8
--- /dev/null
+++ b/examples/estrogenReceptorCdna_frag.fa
@@ -0,0 +1,12 @@
+>EMBLCDS|BAA89539/1111-1224 Anguilla japonica (Japanese eel) progesterone receptor
+gaaggccatcataactacttgtgtgctggacggaatgactgcatcgtggacaagatccgtaggaaaaactgt
+cctgcttgtcgcctcagaaagtgctaccaggcgggaatgata---
+>EMBLCDS|BAA75464/1564-1677 Anguilla japonica (Japanese eel) androgen receptor alpha
+gaagggaaacagaagtacctgtgcgccagcatcaatgattgcaccattgataaacttcgaaggaagaactgc
+ccctcttgccgtctcaaaaggtgctttgctgccggaatgacc---
+>EMBLCDS|AAA17402/70-183 Serinus canaria (common canary) partial androgen receptor
+gaaggtaaacagaagtacctctgtgccagccgcaacgactgcaccatcgacaagttccggcggaaaaactgc
+ccctcctgccgcctgcgcaagtgctacgaggccgggatgacg---
+>EMBLCDS|AAK20929/592-708 Petromyzon marinus (sea lamprey) partial estrogen receptor
+caaggccacaatgactacatgtgcccggccaccaaccagtgcaccatcgacaggaaccgtcgcaagagctgt
+caggcttgccgcctgcgtaagtgctacgaagtgggcatggtcaaa
diff --git a/examples/estrogenReceptorProtein_frag.fa b/examples/estrogenReceptorProtein_frag.fa
new file mode 100644
index 0000000..cb3c37e
--- /dev/null
+++ b/examples/estrogenReceptorProtein_frag.fa
@@ -0,0 +1,14 @@
+>UNIPROT|Q7LCB3/249-274
+---SLEHTLPVNRETLKRKVSGNRCASPV----------
+>UNIPROT|Q9VSE9/175-200
+---GSGTSGGNGGGGGGGTSGGNATNASA----------
+>UNIPROT|Q9IBD5/371-408
+EGHHNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMI-
+>UNIPROT|Q9YGV9/522-559
+EGKQKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMT-
+>UNIPROT|Q90ZM7/97-134
+EGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCIQAGMT-
+>UNIPROT|Q91445/24-61
+EGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMT-
+>UNIPROT|Q90ZM8/198-236
+QGHNDYMCPATNQCTIDRNRRKSCQACRLRKCYEVGMVK
-- 
1.7.10.2