From 723747fa9f295da308d7ba5c93ce848d682cd4c7 Mon Sep 17 00:00:00 2001
From: Cameron Gilchrist <clmgilchrist@gmail.com>
Date: Thu, 31 Aug 2023 16:27:29 +0900
Subject: [PATCH] fix chain res map index

---
 frontend/AlignmentPanel.vue  |  4 +---
 frontend/StructureViewer.vue | 12 +++++-------
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/frontend/AlignmentPanel.vue b/frontend/AlignmentPanel.vue
index 4819b58..54660e7 100644
--- a/frontend/AlignmentPanel.vue
+++ b/frontend/AlignmentPanel.vue
@@ -30,11 +30,9 @@
 <script>
 import Alignment from './Alignment.vue'
 
-// Map indices in the alignment to the corresponding indices in the structure
-// realStart will be 1-based
+// Map 0-based indices in the alignment to corresponding 1-based indices in the structure
 function makePositionMap(realStart, alnString) {
     let map = Array(alnString.length);
-    // let map = new Map()
     for (let i = 0, gaps = 0; i < alnString.length; i++) {
         if (alnString[i] === '-') {
             map[i] = null;
diff --git a/frontend/StructureViewer.vue b/frontend/StructureViewer.vue
index 189be12..50d3a2b 100644
--- a/frontend/StructureViewer.vue
+++ b/frontend/StructureViewer.vue
@@ -215,11 +215,9 @@ const atomToPDBRow = (ap) => {
 
 // Map 1-based indices in a selection to residue index/resno
 const makeChainMap = (structure, sele) => {
-    // let idx = 1
     let map = new Map()
     structure.eachResidue(rp => {
-        map.set(rp.resno, { index: rp.index, resno: rp.resno });
-        // idx++;
+        map.set(rp.index + 1, { index: rp.index, resno: rp.resno });
     }, new Selection(sele));
     return map
 }
@@ -416,9 +414,9 @@ END
             if (!this.qChainResMap) {
                 return '';
             }
-            let start = this.alignment.qStartPos;
-            let end   = this.alignment.qEndPos;
-            let sele  = `${start}-${end}`;
+            let start = this.qChainResMap.get(this.alignment.qStartPos);
+            let end   = this.qChainResMap.get(this.alignment.qEndPos);
+            let sele  = `${start.resno}-${end.resno}`;
             if (this.queryChain) {
                 sele = `${sele} AND ${this.queryChainSele}`;
             }
@@ -472,7 +470,7 @@ END
             })
         
         Promise.all([
-            (__LOCAL__)
+            (this.$LOCAL)
                 ? pulchra(mockPDB(this.hits.query.qCa, this.hits.query.sequence))
                 : this.$axios.get("api/result/" + this.$route.params.ticket + '/query'),
             pulchra(mockPDB(this.alignment.tCa, this.alignment.tSeq))