From 1914a801141ad55bd2363b2643cce915ed5ec255 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Thu, 8 Aug 2024 12:50:42 -0400
Subject: [PATCH] Add slider for allowed gappyness

---
 lib/src/components/dialogs/SettingsDialog.tsx | 19 +++++++++++++++
 lib/src/model.ts                              | 23 ++++++++++++++++++-
 yarn.lock                                     | 18 +++++++--------
 3 files changed, 50 insertions(+), 10 deletions(-)

diff --git a/lib/src/components/dialogs/SettingsDialog.tsx b/lib/src/components/dialogs/SettingsDialog.tsx
index 758f1a48..a2b1fdb1 100644
--- a/lib/src/components/dialogs/SettingsDialog.tsx
+++ b/lib/src/components/dialogs/SettingsDialog.tsx
@@ -119,8 +119,10 @@ const MSASettings = observer(function MSASettings({
     bgColor,
     contrastLettering,
     colWidth,
+    allowedGappyness,
     drawMsaLetters,
     colorSchemeName,
+    hideGaps,
     rowHeight,
   } = model
 
@@ -142,6 +144,11 @@ const MSASettings = observer(function MSASettings({
         onChange={() => model.setContrastLettering(!contrastLettering)}
         label="Use contrast lettering"
       />
+      <Checkbox2
+        checked={hideGaps}
+        onChange={() => model.setHideGaps(!hideGaps)}
+        label={`Hide columns that are ${100 - allowedGappyness}% gaps`}
+      />
 
       <div className={classes.flex}>
         <Typography>Column width ({colWidth}px)</Typography>
@@ -163,6 +170,18 @@ const MSASettings = observer(function MSASettings({
           onChange={(_, val) => model.setRowHeight(val as number)}
         />
       </div>
+      {hideGaps ? (
+        <div className={classes.flex}>
+          <Typography>Allowed gappyness ({100 - allowedGappyness}%)</Typography>
+          <Slider
+            className={classes.field}
+            min={1}
+            max={100}
+            value={allowedGappyness}
+            onChange={(_, val) => model.setAllowedGappyness(val as number)}
+          />
+        </div>
+      ) : null}
 
       <TextField
         select
diff --git a/lib/src/model.ts b/lib/src/model.ts
index d465fa6b..7cc19eea 100644
--- a/lib/src/model.ts
+++ b/lib/src/model.ts
@@ -103,6 +103,10 @@ function stateModelFactory() {
          * #property
          */
         showDomains: false,
+        /**
+         * #property
+         */
+        allowedGappyness: 100,
         /**
          * #property
          */
@@ -123,6 +127,10 @@ function stateModelFactory() {
          * #property
          */
         drawMsaLetters: true,
+        /**
+         * #property
+         */
+        hideGaps: true,
 
         /**
          * #property
@@ -320,6 +328,18 @@ function stateModelFactory() {
         | Record<string, InterProScanResults>,
     }))
     .actions(self => ({
+      /**
+       * #action
+       */
+      setHideGaps(arg: boolean) {
+        self.hideGaps = arg
+      },
+      /**
+       * #action
+       */
+      setAllowedGappyness(arg: number) {
+        self.allowedGappyness = arg
+      },
       /**
        * #action
        */
@@ -669,6 +689,7 @@ function stateModelFactory() {
        * #getter
        */
       get blanks() {
+        const { allowedGappyness } = self
         const blanks = []
         const strs = this.leaves
           .map(leaf => this.MSA?.getRow(leaf.data.name))
@@ -681,7 +702,7 @@ function stateModelFactory() {
               counter++
             }
           }
-          if (counter === strs.length) {
+          if (counter / strs.length >= allowedGappyness / 100) {
             blanks.push(i)
           }
         }
diff --git a/yarn.lock b/yarn.lock
index cb005be1..a0bc79f2 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -1535,9 +1535,9 @@ callsites@^3.0.0:
   integrity sha512-P8BjAsXvZS+VIDUI11hHCQEv74YT67YUi5JJFNWIqL235sBmjX4+qx9Muvls5ivyNENctx46xQLQ3aTuE7ssaQ==
 
 caniuse-lite@^1.0.30001646:
-  version "1.0.30001650"
-  resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001650.tgz#dd1eba0938e39536d184c3c99b2569a13788bc16"
-  integrity sha512-fgEc7hP/LB7iicdXHUI9VsBsMZmUmlVJeQP2qqQW+3lkqVhbmjEU8zp+h5stWeilX+G7uXuIUIIlWlDw9jdt8g==
+  version "1.0.30001651"
+  resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001651.tgz#52de59529e8b02b1aedcaaf5c05d9e23c0c28138"
+  integrity sha512-9Cf+Xv1jJNe1xPZLGuUXLNkE1BoDkqRqYyFJ9TDYSqhduqA4hu4oR9HluGoWYQC/aj8WHjsGVV+bwkh0+tegRg==
 
 canvas-sequencer@^3.1.0:
   version "3.1.0"
@@ -2291,9 +2291,9 @@ for-each@^0.3.3:
     is-callable "^1.1.3"
 
 foreground-child@^3.1.0:
-  version "3.2.1"
-  resolved "https://registry.yarnpkg.com/foreground-child/-/foreground-child-3.2.1.tgz#767004ccf3a5b30df39bed90718bab43fe0a59f7"
-  integrity sha512-PXUUyLqrR2XCWICfv6ukppP96sdFwWbNEnfEMt7jNsISjMsvaLNinAHNDYyvkyU+SZG2BTSbT5NjG+vZslfGTA==
+  version "3.3.0"
+  resolved "https://registry.yarnpkg.com/foreground-child/-/foreground-child-3.3.0.tgz#0ac8644c06e431439f8561db8ecf29a7b5519c77"
+  integrity sha512-Ld2g8rrAyMYFXBhEqMz8ZAHBi4J4uS1i/CxGMDnjyFWddMXLVcDp051DZfu+t7+ab7Wv6SMqpWmyFIj5UbfFvg==
   dependencies:
     cross-spawn "^7.0.0"
     signal-exit "^4.0.1"
@@ -3909,9 +3909,9 @@ synckit@^0.9.1:
     tslib "^2.6.2"
 
 terser@^5.17.4:
-  version "5.31.4"
-  resolved "https://registry.yarnpkg.com/terser/-/terser-5.31.4.tgz#60274c4d3e20eb9a6468526a8878aba8e8428c5f"
-  integrity sha512-3OU03GgblDgu0g+sdnsVzhBPxnjV+WJuMmocN1qBBZDQ3ia7jZQSAkePeKbPlYAejGXUTYe1CmSaUeV51mvaIw==
+  version "5.31.5"
+  resolved "https://registry.yarnpkg.com/terser/-/terser-5.31.5.tgz#e48b7c65f32d2808e7dad803e4586a0bc3829b87"
+  integrity sha512-YPmas0L0rE1UyLL/llTWA0SiDOqIcAQYLeUj7cJYzXHlRTAnMSg9pPe4VJ5PlKvTrPQsdVFuiRiwyeNlYgwh2Q==
   dependencies:
     "@jridgewell/source-map" "^0.3.3"
     acorn "^8.8.2"