From b0efd5c8afb9698a6ebfc20797c0891efc30c195 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Wed, 27 Sep 2023 10:40:16 -0700
Subject: [PATCH 1/2] adding help text for seq details. UNTESTED!

---
 .../sequencePanel/sequencePanelSectionHelp.js | 44 +++++++++++++++++++
 .../main-app/src/containers/genePage/index.js |  3 +-
 2 files changed, 46 insertions(+), 1 deletion(-)
 create mode 100644 apps/main-app/src/components/sequencePanel/sequencePanelSectionHelp.js

diff --git a/apps/main-app/src/components/sequencePanel/sequencePanelSectionHelp.js b/apps/main-app/src/components/sequencePanel/sequencePanelSectionHelp.js
new file mode 100644
index 000000000..7e44ec4bc
--- /dev/null
+++ b/apps/main-app/src/components/sequencePanel/sequencePanelSectionHelp.js
@@ -0,0 +1,44 @@
+import React from 'react';
+
+const SequencePanelSectionHelp = () => (
+  <div>
+    <p>
+      The set of genome features contributed by each MOD is used by this
+      section to obtain the sequence of the gene and a list of transcripts.
+      When a transcript is selected, Sequence Details will highlight it
+      according to the scheme selected in the “Mode” menu. The options are:
+    </p>
+    <ul>
+      <li>gene - The genomic sequence from start to end with portions that
+          are UTR and coding highlighted</li>
+      <li>CDS - The coding sequence of the mRNA that is the result of in
+          silico splicing</li>
+      <li>cDNA - The CDS with UTRs added</li>
+      <li>protein - The amino acid sequence that results from the CDS in
+          silico transcription</li>
+      <li>genomic - The stretch of sequence from start to end with no
+          special highlighting</li>
+      <li>genomic +500bp up and down stream - The stretch of sequence from
+          start to end with 500 base pairs of padding on both ends</li>
+      <li>gene with collapsed introns - same as gene, but the introns are
+          compressed to 10 base pairs at the splice junction and the remainder
+          replaced with ellipses</li>
+      <li>gene with 500bp up and down stream - same as “gene” but with 500bp
+          of up and down stream sequence added</li>
+      <li>gene with 500bp up and down stream and collapsed introns - same as
+          “gene with collapsed introns” but with up and downstream padding
+          added</li>
+    </ul>
+    <p>
+      After selecting the mode, you can copy either the “plain text” of the
+      sequence (that is, without any color highlighting) or copy the
+      highlighted text with the provided buttons. The plain text option is
+      provided for copying into web forms (such as BLAST) and text editors that
+      don’t allow formatting. The copy with highlights button will allow you to
+      paste into a “rich” text editor that will preserve the highlighting from
+      the web page.
+    </p>
+  </div>
+);
+
+export default SequencePanelSectionHelp;
diff --git a/apps/main-app/src/containers/genePage/index.js b/apps/main-app/src/containers/genePage/index.js
index f3739a796..49aa2c9d8 100644
--- a/apps/main-app/src/containers/genePage/index.js
+++ b/apps/main-app/src/containers/genePage/index.js
@@ -45,6 +45,7 @@ import GeneSymbol from '../../components/GeneSymbol';
 import PhenotypeCrossRefs from './PhenotypeCrossRefs';
 import SpeciesName from '../../components/SpeciesName';
 import SequenceFeatureViewerSectionHelp from '../../components/sequenceFeatureViewer/sequenceFeatureViewerSectionHelp';
+import SequencePanelSectionHelp from '../../components/sequencePanel/sequencePanelSectionHelp';
 import TransgenicAlleleSectionHelp from '../../components/transgenicAlleles/transgenicAllelesSectionHelp';
 import DiseaseSectionHelp from '../../components/disease/diseaseSectionHelp';
 
@@ -212,7 +213,7 @@ const GenePage = ({geneId}) => {
           />
         </Subsection>
 
-        <Subsection title={SEQUENCE_DETAILS}>
+        <Subsection title={SEQUENCE_DETAILS}> help={<SequencePanelSectionHelp />}
 	  <SequencePanel
             refseq={genomeLocation.chromosome}
             start={genomeLocation.start}

From 520e4b43a82d5fc131ee0d181540108eb759c631 Mon Sep 17 00:00:00 2001
From: Scott Cain <scott+git@scottcain.net>
Date: Wed, 27 Sep 2023 12:21:36 -0700
Subject: [PATCH 2/2] fixed formatting/syntax

---
 apps/main-app/src/containers/genePage/index.js | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/apps/main-app/src/containers/genePage/index.js b/apps/main-app/src/containers/genePage/index.js
index 49aa2c9d8..9faef3115 100644
--- a/apps/main-app/src/containers/genePage/index.js
+++ b/apps/main-app/src/containers/genePage/index.js
@@ -213,7 +213,10 @@ const GenePage = ({geneId}) => {
           />
         </Subsection>
 
-        <Subsection title={SEQUENCE_DETAILS}> help={<SequencePanelSectionHelp />}
+        <Subsection 
+          help={<SequencePanelSectionHelp />}
+          title={SEQUENCE_DETAILS}
+        >
 	  <SequencePanel
             refseq={genomeLocation.chromosome}
             start={genomeLocation.start}