From bfee6975a6276b546d497c571781e0bc9710731f Mon Sep 17 00:00:00 2001
From: Nick Rosenau <nickrosenau@Nicks-MacBook-Pro.local>
Date: Wed, 22 Nov 2023 17:16:20 -0500
Subject: [PATCH 1/6] Added shift select for amino acids, added copy feature
 for amino acid selection.

---
 src/EventHandler.tsx     |  4 +++-
 src/SelectionHandler.tsx | 19 ++++++++++++++++++-
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/src/EventHandler.tsx b/src/EventHandler.tsx
index aff47a38f..8f258f2b1 100644
--- a/src/EventHandler.tsx
+++ b/src/EventHandler.tsx
@@ -223,7 +223,9 @@ export class EventHandler extends React.PureComponent<EventsHandlerProps> {
    */
   handleMouseEvent = (e: React.MouseEvent<HTMLDivElement>) => {
     const { handleMouseEvent } = this.props;
-
+    if(e.shiftKey){
+      this.handleCopy();
+    }
     if (e.type === "mouseup") {
       this.resetClicked();
       if (this.clickedOnce === e.target && this.clickedTwice === e.target) {
diff --git a/src/SelectionHandler.tsx b/src/SelectionHandler.tsx
index 938d0210c..2621f1e50 100644
--- a/src/SelectionHandler.tsx
+++ b/src/SelectionHandler.tsx
@@ -39,7 +39,7 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
   declare context: React.ContextType<typeof SelectionContext>;
 
   /** Only state is the selection range */
-  state = { ...defaultSelection };
+  state = { ...defaultSelection, aminoAcidShiftStart: null };
 
   /* previous base cursor is over, used in circular drag select */
   previousBase: null | number = null;
@@ -65,6 +65,7 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
   /** a map between the id of child elements and their associated SelectRanges */
   idToRange = new Map<string, Selection>();
 
+
   componentDidMount = () => {
     if (!document) return;
     document.addEventListener("mouseup", this.stopDrag);
@@ -173,6 +174,20 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
           selectionEnd = clockwise ? knownRange.end : knownRange.start;
         }
 
+        if(e.shiftKey){
+          if(this.state.aminoAcidShiftStart){
+            selectionStart = this.state.aminoAcidShiftStart
+            selectionEnd = selectionEnd
+          }
+          else{
+            this.setState({aminoAcidShiftStart: selectionStart})
+          }
+          
+        }
+        else{
+          this.setState({aminoAcidShiftStart: null})
+        }
+
         this.setSelection({
           ...knownRange,
           clockwise: clockwise,
@@ -194,6 +209,8 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
           this.handleCircularSeqEvent(e);
         }
 
+        this.setState({aminoAcidShiftStart: null})
+
         break;
       }
       default:

From e57b55cfd4aa921611e6298b797add0a4034e4cb Mon Sep 17 00:00:00 2001
From: Nick Rosenau <nickrosenau@Nicks-MacBook-Pro.local>
Date: Wed, 22 Nov 2023 17:20:58 -0500
Subject: [PATCH 2/6] formatting.

---
 src/EventHandler.tsx     |  2 +-
 src/SelectionHandler.tsx | 22 +++++++++-------------
 2 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/src/EventHandler.tsx b/src/EventHandler.tsx
index 8f258f2b1..e7afeca59 100644
--- a/src/EventHandler.tsx
+++ b/src/EventHandler.tsx
@@ -223,7 +223,7 @@ export class EventHandler extends React.PureComponent<EventsHandlerProps> {
    */
   handleMouseEvent = (e: React.MouseEvent<HTMLDivElement>) => {
     const { handleMouseEvent } = this.props;
-    if(e.shiftKey){
+    if (e.shiftKey) {
       this.handleCopy();
     }
     if (e.type === "mouseup") {
diff --git a/src/SelectionHandler.tsx b/src/SelectionHandler.tsx
index 2621f1e50..9e40369ea 100644
--- a/src/SelectionHandler.tsx
+++ b/src/SelectionHandler.tsx
@@ -65,7 +65,6 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
   /** a map between the id of child elements and their associated SelectRanges */
   idToRange = new Map<string, Selection>();
 
-
   componentDidMount = () => {
     if (!document) return;
     document.addEventListener("mouseup", this.stopDrag);
@@ -174,18 +173,15 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
           selectionEnd = clockwise ? knownRange.end : knownRange.start;
         }
 
-        if(e.shiftKey){
-          if(this.state.aminoAcidShiftStart){
-            selectionStart = this.state.aminoAcidShiftStart
-            selectionEnd = selectionEnd
-          }
-          else{
-            this.setState({aminoAcidShiftStart: selectionStart})
+        if (e.shiftKey) {
+          if (this.state.aminoAcidShiftStart) {
+            selectionStart = this.state.aminoAcidShiftStart;
+            selectionEnd = selectionEnd;
+          } else {
+            this.setState({ aminoAcidShiftStart: selectionStart });
           }
-          
-        }
-        else{
-          this.setState({aminoAcidShiftStart: null})
+        } else {
+          this.setState({ aminoAcidShiftStart: null });
         }
 
         this.setSelection({
@@ -209,7 +205,7 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
           this.handleCircularSeqEvent(e);
         }
 
-        this.setState({aminoAcidShiftStart: null})
+        this.setState({ aminoAcidShiftStart: null });
 
         break;
       }

From 45263a027d5daf06d8967428c5afe62b69349b9c Mon Sep 17 00:00:00 2001
From: Nick Rosenau <nickrosenau@Nicks-MacBook-Pro.local>
Date: Wed, 22 Nov 2023 17:24:39 -0500
Subject: [PATCH 3/6] remove var.

---
 src/SelectionHandler.tsx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/SelectionHandler.tsx b/src/SelectionHandler.tsx
index 9e40369ea..6af882233 100644
--- a/src/SelectionHandler.tsx
+++ b/src/SelectionHandler.tsx
@@ -176,7 +176,6 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
         if (e.shiftKey) {
           if (this.state.aminoAcidShiftStart) {
             selectionStart = this.state.aminoAcidShiftStart;
-            selectionEnd = selectionEnd;
           } else {
             this.setState({ aminoAcidShiftStart: selectionStart });
           }

From ea0d3ed1bbf392f60a2838368e79448c7e721898 Mon Sep 17 00:00:00 2001
From: Nick Rosenau <nickrosenau@Nicks-MBP.lan>
Date: Fri, 1 Dec 2023 18:24:48 -0500
Subject: [PATCH 4/6] click then shift to highlight aa.

---
 src/SelectionHandler.tsx | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/src/SelectionHandler.tsx b/src/SelectionHandler.tsx
index 6af882233..0e49a7e48 100644
--- a/src/SelectionHandler.tsx
+++ b/src/SelectionHandler.tsx
@@ -39,7 +39,7 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
   declare context: React.ContextType<typeof SelectionContext>;
 
   /** Only state is the selection range */
-  state = { ...defaultSelection, aminoAcidShiftStart: null };
+  state = { ...defaultSelection, aminoAcidShiftStart: null, prevAA: null };
 
   /* previous base cursor is over, used in circular drag select */
   previousBase: null | number = null;
@@ -128,7 +128,7 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
       return; // there isn't a known range with the id of the element
     }
     knownRange = { ...knownRange, end: knownRange.end || 0, start: knownRange.start || 0 };
-
+    
     const { direction, end, start, viewer } = knownRange;
     switch (knownRange.type) {
       case "ANNOTATION":
@@ -173,14 +173,24 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
           selectionEnd = clockwise ? knownRange.end : knownRange.start;
         }
 
+        
+        
         if (e.shiftKey) {
-          if (this.state.aminoAcidShiftStart) {
-            selectionStart = this.state.aminoAcidShiftStart;
-          } else {
-            this.setState({ aminoAcidShiftStart: selectionStart });
+          if(this.state.prevAA && selectionStart){
+            selectionStart = this.state.prevAA 
+            this.setState({ aminoAcidShiftStart: selectionStart});
+          }
+          else{
+            if (this.state.aminoAcidShiftStart) {
+              console.log(this.state.aminoAcidShiftStart)
+              selectionStart = this.state.aminoAcidShiftStart;
+            } else {
+              this.setState({ aminoAcidShiftStart: selectionStart });
+            }
           }
+          
         } else {
-          this.setState({ aminoAcidShiftStart: null });
+          this.setState({ aminoAcidShiftStart: null, prevAA: selectionStart });
         }
 
         this.setSelection({

From 997bb4c50150b65b80f231305be40859cd8e8127 Mon Sep 17 00:00:00 2001
From: Nick Rosenau <nickrosenau@Nicks-MBP.lan>
Date: Fri, 1 Dec 2023 18:33:11 -0500
Subject: [PATCH 5/6] format.

---
 src/SelectionHandler.tsx | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/src/SelectionHandler.tsx b/src/SelectionHandler.tsx
index 0e49a7e48..db7a2a6e3 100644
--- a/src/SelectionHandler.tsx
+++ b/src/SelectionHandler.tsx
@@ -128,7 +128,7 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
       return; // there isn't a known range with the id of the element
     }
     knownRange = { ...knownRange, end: knownRange.end || 0, start: knownRange.start || 0 };
-    
+
     const { direction, end, start, viewer } = knownRange;
     switch (knownRange.type) {
       case "ANNOTATION":
@@ -173,22 +173,18 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
           selectionEnd = clockwise ? knownRange.end : knownRange.start;
         }
 
-        
-        
         if (e.shiftKey) {
-          if(this.state.prevAA && selectionStart){
-            selectionStart = this.state.prevAA 
-            this.setState({ aminoAcidShiftStart: selectionStart});
-          }
-          else{
+          if (this.state.prevAA && selectionStart) {
+            selectionStart = this.state.prevAA;
+            this.setState({ aminoAcidShiftStart: selectionStart });
+          } else {
             if (this.state.aminoAcidShiftStart) {
-              console.log(this.state.aminoAcidShiftStart)
+              console.log(this.state.aminoAcidShiftStart);
               selectionStart = this.state.aminoAcidShiftStart;
             } else {
               this.setState({ aminoAcidShiftStart: selectionStart });
             }
           }
-          
         } else {
           this.setState({ aminoAcidShiftStart: null, prevAA: selectionStart });
         }

From 851b1ae2c2a58265cdbab35877df9b0b2cb31c77 Mon Sep 17 00:00:00 2001
From: Nick Rosenau <nickrosenau@Nicks-MBP.lan>
Date: Fri, 1 Dec 2023 18:34:56 -0500
Subject: [PATCH 6/6] format.

---
 src/SelectionHandler.tsx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/SelectionHandler.tsx b/src/SelectionHandler.tsx
index db7a2a6e3..2c33269e9 100644
--- a/src/SelectionHandler.tsx
+++ b/src/SelectionHandler.tsx
@@ -179,7 +179,6 @@ export default class SelectionHandler extends React.PureComponent<SelectionHandl
             this.setState({ aminoAcidShiftStart: selectionStart });
           } else {
             if (this.state.aminoAcidShiftStart) {
-              console.log(this.state.aminoAcidShiftStart);
               selectionStart = this.state.aminoAcidShiftStart;
             } else {
               this.setState({ aminoAcidShiftStart: selectionStart });