Missed cleavage handling always enabled now

.github/workflows/publish_macos.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   release_macos:
-    runs-on: macos-latest
+    runs-on: macos-12
 
     steps:
       - uses: actions/checkout@v1

.github/workflows/publish_windows.yml

@@ -23,5 +23,3 @@ jobs:
         run: yarn run electron:publish
         env:
           GH_TOKEN: ${{ secrets.GH_TOKEN }}
-          CSC_LINK: ${{ secrets.windows_certs }}
-          CSC_KEY_PASSWORD: ${{ secrets.windows_certs_password }}

package.json

@@ -1,6 +1,6 @@
 {
     "name": "unipept-desktop",
-    "version": "2.0.1",
+    "version": "2.0.2",
     "productName": "Unipept Desktop",
     "private": false,
     "author": "Unipept Team (Ghent University)",

src/components/analysis/AnalysisSummary.vue

@@ -76,7 +76,7 @@
                             :horizontal="true"
                             :equate-il.sync="equateIl"
                             :filter-duplicates.sync="filterDuplicates"
-                            :missing-cleavage.sync="missedCleavage">
+                            :missing-cleavage="true">
                         </search-settings-form>
 
                         <div class="d-flex justify-center align-center mt-4">
@@ -120,7 +120,6 @@ import {
     ProteomicsAssay,
     CountTable,
     Peptide,
-    SearchSettingsForm,
     SearchConfiguration,
     PeptideTrust,
     Pept2DataCommunicator,
@@ -139,6 +138,7 @@ import AnalysisSourceSelect from "@/components/assay/AnalysisSourceSelect.vue";
 import ConfigurationManager from "@/logic/configuration/ConfigurationManager";
 import CustomDatabase from "@/logic/custom_database/CustomDatabase";
 import ExportResultsButton from "@/components/analysis/ExportResultsButton.vue";
+import SearchSettingsForm from "@/components/analysis/SearchSettingsForm.vue";
 
 @Component({
     components: { PeptideSummaryTable, SearchSettingsForm, ExportResultsButton, Tooltip, AnalysisSourceSelect }
@@ -323,7 +323,7 @@ export default class AnalysisSummary extends Vue {
     }
 
     private update() {
-        const config = new SearchConfiguration(this.equateIl, this.filterDuplicates, this.missedCleavage);
+        const config = new SearchConfiguration(this.equateIl, this.filterDuplicates, true);
         this.assay.setSearchConfiguration(config);
 
         this.assay.setAnalysisSource(this.analysisSource);

src/components/analysis/CustomTooltip.vue

@@ -0,0 +1,110 @@
+<template>
+  <div
+      class="tooltip-wrapper"
+      @mouseenter="startShowTooltipTimer"
+      @mouseleave="cancelShowTooltipTimer"
+  >
+    <slot></slot>
+    <div
+        v-if="visible"
+        class="custom-tooltip"
+        ref="tooltip"
+        @mouseenter="cancelHideTooltipTimer"
+        @mouseleave="startHideTooltipTimer"
+    >
+      Missed cleavage handling is now always enabled. Because of a change in
+      Unipept's underlying search engine, enabling missed cleavage handling no
+      longer results in a performance penalty. As a result, this configuration
+      option will be removed in a future release. See
+      <a
+          href="https://github.com/unipept/unipept/wiki/Unipept-Next"
+          target="_blank"
+          rel="noopener noreferrer"
+          class="text-white"
+      >this page</a>
+      for more information.
+    </div>
+  </div>
+</template>
+
+<script lang="ts">
+import { Vue, Component } from 'vue-property-decorator';
+
+@Component
+export default class CustomTooltip extends Vue {
+  visible = false;
+  showTooltipTimer: number | null = null;
+  hideTooltipTimer: number | null = null;
+
+  startShowTooltipTimer() {
+    this.cancelHideTooltipTimer();
+    if (this.showTooltipTimer !== null) {
+      clearTimeout(this.showTooltipTimer);
+      this.showTooltipTimer = null;
+    }
+    this.showTooltipTimer = window.setTimeout(() => {
+      this.visible = true;
+    }, 300);
+  }
+
+  cancelShowTooltipTimer() {
+    if (this.showTooltipTimer !== null) {
+      clearTimeout(this.showTooltipTimer);
+      this.showTooltipTimer = null;
+    }
+    this.startHideTooltipTimer();
+  }
+
+  startHideTooltipTimer() {
+    this.cancelHideTooltipTimer();
+    this.hideTooltipTimer = window.setTimeout(() => {
+      this.visible = false;
+    }, 1000);
+  }
+
+  cancelHideTooltipTimer() {
+    if (this.hideTooltipTimer !== null) {
+      clearTimeout(this.hideTooltipTimer);
+      this.hideTooltipTimer = null;
+    }
+  }
+}
+</script>
+
+<style scoped>
+.tooltip-wrapper {
+  position: relative;
+  display: inline-block;
+  overflow: visible;
+}
+
+.custom-tooltip {
+  position: absolute;
+  bottom: 100%;
+  left: 50%;
+  transform: translateX(-50%);
+  background-color: #323232;
+  color: #fff;
+  padding: 8px;
+  border-radius: 4px;
+  box-shadow: 0 2px 10px rgba(0, 0, 0, 0.2);
+  z-index: 1000;
+  margin-bottom: 8px;
+  transition: opacity 0.2s ease-in-out;
+  pointer-events: auto;
+  max-width: 400px;
+  width: max-content;
+  overflow: hidden;
+  white-space: normal;
+  line-height: 1.4;
+}
+
+.custom-tooltip a {
+  color: #1e88e5;
+  text-decoration: underline;
+}
+
+.custom-tooltip a:hover {
+  color: #1565c0;
+}
+</style>

src/components/analysis/SearchSettingsForm.vue

@@ -0,0 +1,98 @@
+<template>
+  <div
+      :class="{
+            'search-settings-form': true,
+            'd-flex': true,
+            'flex-column': !horizontal,
+            'flex-row': horizontal,
+            'justify-space-between': horizontal
+    }">
+    <tooltip message="Equate isoleucine (I) and leucine (L) when matching peptides to UniProt entries.">
+      <v-checkbox :disabled="disabled" v-model="equateIlModel" label="Equate I and L" hide-details class="mt-0">
+        <span slot="label">Equate I and L</span>
+      </v-checkbox>
+    </tooltip>
+    <tooltip message="Remove duplicate peptides from the input before searching.">
+      <v-checkbox :disabled="disabled" v-model="filterDuplicatesModel" hide-details class="mt-0">
+        <span slot="label">Filter duplicate peptides</span>
+      </v-checkbox>
+    </tooltip>
+    <custom-tooltip message="Recombine subpeptides of miscleavages. Enabling this has a serious performance impact!">
+      <v-checkbox disabled input-value="true" hide-details class="mt-0">
+        <span slot="label">Advanced missed cleavage handling</span>
+      </v-checkbox>
+    </custom-tooltip>
+  </div>
+</template>
+
+<script lang="ts">
+import Vue from "vue";
+import Component from "vue-class-component";
+import { Prop, Watch } from "vue-property-decorator";
+import CustomTooltip from "@/components/analysis/CustomTooltip.vue";
+import { Tooltip } from "unipept-web-components"
+
+@Component({
+  components: {
+    CustomTooltip,
+    Tooltip
+  },
+  computed: {
+    equateIlModel: {
+      get() {
+        return this.equateIl;
+      },
+      set(val) {
+        this.equateIlData = val;
+        this.$emit("update:equate-il", val);
+      }
+    },
+    filterDuplicatesModel: {
+      get(): boolean {
+        return this.filterDuplicates;
+      },
+      set(val: boolean) {
+        this.filterDuplicatesData = val;
+        this.$emit("update:filter-duplicates", val);
+      }
+    },
+    missingCleavageModel: {
+      get() {
+        return this.missingCleavage;
+      },
+      set(val) {
+        this.missingCleavageData = val;
+        this.$emit("update:missing-cleavage", val);
+      }
+    }
+  }
+})
+export default class SearchSetingsForm extends Vue {
+  @Prop({ default: false }) disabled!: boolean;
+  @Prop({ default: true }) equateIl!: boolean;
+  @Prop({ default: true }) filterDuplicates!: boolean;
+  @Prop({ default: false }) missingCleavage!: boolean;
+  /**
+   * Show the component in a horizontal or vertical fashion? Set to true to show the different checkboxes on one line.
+   */
+  @Prop({ required: false, default: true })
+  private horizontal: boolean;
+
+  private equateIlData: boolean = this.equateIl;
+  private filterDuplicatesData: boolean = this.filterDuplicates;
+  private missingCleavageData: boolean = this.missingCleavage;
+
+  @Watch("equateIl") onEquateIlChanged() {
+    this.equateIlData = this.equateIl;
+  }
+
+  @Watch("filterDuplicates") onFilterDuplicatesChanged() {
+
+    this.filterDuplicatesData = this.filterDuplicates;
+  }
+
+  @Watch("missingCleavage") onMissingCleavageChanged() {
+    this.missingCleavageData = this.missingCleavage;
+  }
+}
+</script>

src/components/assay/CreateAssayDialog.vue

@@ -110,8 +110,10 @@
                         </v-simple-checkbox>
                     </template>
                     <template v-slot:item.missedCleavage="{ item }">
-                        <v-simple-checkbox v-model="item.searchConfiguration.enableMissingCleavageHandling" color="primary">
-                        </v-simple-checkbox>
+                        <custom-tooltip>
+                            <v-simple-checkbox disabled :value="true" color="primary">
+                            </v-simple-checkbox>
+                        </custom-tooltip>
                     </template>
                     <template v-slot:item.actions="{ item }">
                         <v-tooltip bottom open-delay="500">
@@ -231,6 +233,7 @@ import ConfigurationManager from "@/logic/configuration/ConfigurationManager";
 import AssayFileSystemDataWriter from "@/logic/filesystem/assay/AssayFileSystemDataWriter";
 import CustomDatabase from "@/logic/custom_database/CustomDatabase";
 import ConfirmDeletionDialog from "@/components/dialogs/ConfirmDeletionDialog.vue";
+import CustomTooltip from "@/components/analysis/CustomTooltip.vue";
 
 
 const { dialog } = require("@electron/remote");
@@ -250,7 +253,7 @@ type ProteomicsAssayPlaceholder = {
 }
 
 @Component({
-    components: { ConfirmDeletionDialog, AnalysisSourceSelect }
+    components: { ConfirmDeletionDialog, AnalysisSourceSelect, CustomTooltip }
 })
 export default class CreateAssayDialog extends Vue {
     @Prop({ required: true })
@@ -345,14 +348,12 @@ export default class CreateAssayDialog extends Vue {
     }
 
     get areAllMissedCleavage(): boolean {
-        return this.assayPlaceholders.every(
-            (item: ProteomicsAssayPlaceholder) => item.searchConfiguration.enableMissingCleavageHandling
-        );
+        return true;
     }
 
     set areAllMissedCleavage(value: boolean) {
         for (const item of this.assayPlaceholders) {
-            item.searchConfiguration.enableMissingCleavageHandling = value;
+            item.searchConfiguration.enableMissingCleavageHandling = true;
         }
     }
 
@@ -550,7 +551,7 @@ export default class CreateAssayDialog extends Vue {
             name: this.generateUniqueAssayName("New assay"),
             nameError: "",
             peptides: "",
-            searchConfiguration: new SearchConfiguration(),
+            searchConfiguration: new SearchConfiguration(true, true, true),
             analysisSource: this.renderableSources[0],
             analysisSourceError: "",
             inProgress: false
@@ -577,7 +578,7 @@ export default class CreateAssayDialog extends Vue {
                     name: assayName,
                     nameError: "",
                     peptides: "",
-                    searchConfiguration: new SearchConfiguration(),
+                    searchConfiguration: new SearchConfiguration(true, true, true),
                     analysisSource: this.renderableSources[0],
                     analysisSourceError: "",
                     inProgress: true