Add iterative searcher to Foldseek #97
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| @@ -168,14 +213,16 @@ export default { | |||
| return { | |||
| inSearch: false, | |||
| errorMessage: "", | |||
| mode: storage.getItem('mode') || this.$STRINGS.MODE_DEFAULT_KEY, | |||
| showCurl: false, | |||
| mode: this.$STRINGS.MODE_DEFAULT_KEY, | |||
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| </v-flex> | ||
| </v-layout> | ||
| <reference :reference="$STRINGS.CITATION"></reference> |
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| ({{ | ||
| databases.filter(db => database.includes(db.path)).map(db => db.name).sort().join(", ") | ||
| }}) | ||
| </template> with {{ $STRINGS.APP_NAME }} in <strong>{{ modes[mode] }}</strong> mode<span v-if="iterativeSearch"><strong> iterative</strong></span>. |
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Please add iterative to beginning of sentence
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| <v-item-group class="v-btn-toggle"> | ||
| <v-btn color="primary" :block="false" x-large v-on:click="search" :disabled="searchDisabled"><v-icon>{{ $MDI.Magnify }}</v-icon> Search</v-btn> | ||
| <v-btn v-if="isMultimer" color="secondary" :block="false" x-large v-on:click="goToMultimer"><v-icon>{{ $MDI.Multimer }}</v-icon> Go to Multimer</v-btn> | ||
| </v-item-group> | ||
| <div :style="!$vuetify.breakpoint.xsOnly ? 'margin-left: 1em;' : 'margin-top: 1em;'"> | ||
| <span><strong>Summary</strong></span><br> | ||
| Search <template v-if="taxFilter"> | ||
| <strong>{{ taxFilter.text }}</strong> in | ||
| </template> | ||
| <template v-if="database.length == databases.length"> | ||
| <strong>all available</strong> databases | ||
| <v-divider class="my-2"></v-divider> | ||
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| <v-radio-group v-model="iterativeSearch"> | ||
| <v-tooltip open-delay="300" top> | ||
| <template v-slot:activator="{ on }"> | ||
| <label v-on="on"> | ||
| Iterative search | ||
| <v-icon color="#FFFFFFB3" style="margin-top:-3px" small v-on="on">{{ $MDI.HelpCircleOutline }}</v-icon> | ||
| </label> | ||
| </template> | ||
| <span>Improve sensitivity of search by performing an iterative search (--num-iterations 3).</span> | ||
| </v-tooltip> | ||
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| <v-radio label="On" :value="true"></v-radio> | ||
| <v-radio label="Off" :value="false"></v-radio> | ||
| </v-radio-group> | ||
| </div> | ||
| </panel> | ||
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| </v-flex> | ||
| <v-flex> | ||
| <panel> | ||
| <template slot="content"> | ||
| <div class="actions" :style="!$vuetify.breakpoint.xsOnly ?'display:flex; align-items: center;' : null"> | ||
| <v-btn color="primary" :block="$vuetify.breakpoint.xsOnly" x-large v-on:click="search" :disabled="searchDisabled"><v-icon>{{ $MDI.Magnify }}</v-icon> Search</v-btn> |
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| <v-tooltip v-if="!$ELECTRON && !hideEmail" open-delay="300" top> | ||
| <template v-slot:activator="{ on }"> | ||
| <v-text-field v-on="on" label="Notification Email (Optional)" placeholder="[email protected]" v-model="email"></v-text-field> | ||
| </template> | ||
| <span>Send an email when the job is done.</span> | ||
| </v-tooltip> | ||
| </div> | ||
| </panel> | ||
| </v-flex> | ||
| <v-flex> | ||
| <panel> | ||
| <template slot="content"> | ||
| <div class="actions" :style="!$vuetify.breakpoint.xsOnly ?'display:flex; align-items: center;' : null"> | ||
| <v-item-group class="v-btn-toggle"> | ||
| <v-btn color="primary" :block="false" x-large v-on:click="search" :disabled="searchDisabled"><v-icon>{{ $MDI.Magnify }}</v-icon> Search</v-btn> | ||
| <v-btn v-if="isMultimer" color="secondary" :block="false" x-large v-on:click="goToMultimer"><v-icon>{{ $MDI.Multimer }}</v-icon> Go to Multimer</v-btn> | ||
| </v-item-group> | ||
| <div :style="!$vuetify.breakpoint.xsOnly ? 'margin-left: 1em;' : 'margin-top: 1em;'"> | ||
| <span><strong>Summary</strong></span><br> | ||
| Search <template v-if="taxFilter"> | ||
| <strong>{{ taxFilter.text }}</strong> in | ||
| </template> | ||
| <template v-if="database.length == databases.length"> | ||
| <strong>all available</strong> databases | ||
| <v-divider class="my-2"></v-divider> | ||
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| <v-radio-group v-model="iterativeSearch"> | ||
| <v-tooltip open-delay="300" top> | ||
| <template v-slot:activator="{ on }"> | ||
| <label v-on="on"> | ||
| Iterative search | ||
| <v-icon color="#FFFFFFB3" style="margin-top:-3px" small v-on="on">{{ $MDI.HelpCircleOutline }}</v-icon> | ||
| </label> | ||
| </template> | ||
| <span>Improve sensitivity of search by performing an iterative search (--num-iterations 3).</span> | ||
| </v-tooltip> | ||
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| <v-radio label="On" :value="true"></v-radio> | ||
| <v-radio label="Off" :value="false"></v-radio> | ||
| </v-radio-group> |
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Please keep email in addition to the new iterative search
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| :label="$STRINGS['MODE_TITLE_' + i]" | ||
| ></v-radio> | ||
| </v-radio-group> | ||
| <div slot="content"> | ||
| <!-- Mode Section --> | ||
| <v-radio-group v-model="mode"> | ||
| <v-tooltip open-delay="300" top> | ||
| <template v-slot:activator="{ on }"> | ||
| <label v-on="on">Mode <v-icon color="#FFFFFFB3" style="margin-top:-3px" small v-on="on">{{ $MDI.HelpCircleOutline }}</v-icon></label> | ||
| </template> | ||
| <span v-html="$STRINGS.MODE_HELP"></span> | ||
| </v-tooltip> | ||
| <v-radio hide-details | ||
| v-for="i in ($STRINGS.MODE_COUNT - 0)" | ||
| :key="i" | ||
| :value="$STRINGS['MODE_KEY_' + i]" | ||
| :label="$STRINGS['MODE_TITLE_' + i]"> | ||
| </v-radio> |
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Please revert the whitespace changes
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| <panel collapsible collapsed render-collapsed> | ||
| <template slot="header"> | ||
| <template v-if="!$vuetify.breakpoint.smAndDown"> | ||
| Databases | ||
| </template> | ||
| <template v-else> | ||
| DBs | ||
| </template> | ||
| & search settings | ||
| </template> | ||
| <div slot="content"> | ||
| <databases | ||
| :selected="database" | ||
| :all-databases="databases" | ||
| @update:selected="database = $event" | ||
| @update:all-databases="databases = $event" | ||
| :hideEmail="hideEmail" | ||
| ></databases> | ||
| <div class="actions input-buttons-panel"> | ||
| <div class="input-buttons-left"> | ||
| <load-acession-button v-if="$APP == 'foldseek'" @select="query = $event" @loading="accessionLoading = $event" :preload-source="preloadSource" :preload-accession="preloadAccession"></load-acession-button> | ||
| <file-button id="file" :label="$STRINGS.UPLOAD_LABEL" v-on:upload="upload"></file-button> | ||
| <PredictStructureButton v-if="$APP == 'foldseek'" :query="query" v-model="predictable" v-on:predict="query = $event"></PredictStructureButton> | ||
| </div> | ||
| <file-button id="localFile" label="Upload previous results" @upload="uploadJSON"></file-button> | ||
| </div> | ||
| </template> | ||
| </panel> | ||
| </v-flex> | ||
| <v-flex xs12> | ||
| <!-- Databases Section --> | ||
| <panel collapsible collapsed> | ||
| <template slot="header"> | ||
| <template v-if="!$vuetify.breakpoint.smAndDown"> | ||
| Databases | ||
| </template> | ||
| <template v-else> | ||
| DBs | ||
| </template> | ||
| </template> | ||
| <div slot="content"> | ||
| <!-- Existing Database Selection --> | ||
| <div class="input-group"> | ||
| <v-tooltip open-delay="300" top> | ||
| <template v-slot:activator="{ on }"> | ||
| <label v-on="on">Databases <v-icon color="#FFFFFFB3" style="margin-top:-3px" small v-on="on">{{ $MDI.HelpCircleOutline }}</v-icon></label> | ||
| </template> | ||
| <span v-if="$ELECTRON || hideEmail">Choose the databases to search against and the result mode.</span> | ||
| <span v-else>Choose the databases to search against, the result mode, and optionally an email to notify you when the job is done.</span> | ||
| </v-tooltip> | ||
| </div> | ||
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| <template v-if="databases.length > 0"> | ||
| <v-checkbox v-for="(db, index) in databases" v-model="database" :key="index" :value="db.path" :label="db.name + ' ' + db.version" :append-icon="(db.status == 'ERROR' || db.status == 'UNKNOWN') ? $MDI.AlertCircleOutline : ((db.status == 'PENDING' || db.status == 'RUNNING') ? $MDI.ProgressWrench : undefined)" :disabled="db.status != 'COMPLETE'" hide-details></v-checkbox> | ||
| </template> | ||
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| <div v-if="databasesNotReady" class="alert alert-info mt-1"> | ||
| <span>Databases are loading...</span> | ||
| </div> | ||
| </div> | ||
| </panel> | ||
|
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| <v-radio-group v-model="mode"> | ||
| <v-tooltip open-delay="300" top> | ||
| <template v-slot:activator="{ on }"> | ||
| <label v-on="on">Mode <v-icon color="#FFFFFFB3" style="margin-top:-3px" small v-on="on">{{ $MDI.HelpCircleOutline }}</v-icon></label> | ||
| <!-- Search Parameters Section --> | ||
| <panel collapsible collapsed> | ||
| <template slot="header"> | ||
| <template v-if="!$vuetify.breakpoint.smAndDown"> | ||
| Search Parameters | ||
| </template> | ||
| <template v-else> | ||
| Params | ||
| </template> | ||
| </template> | ||
| <span v-html="$STRINGS.MODE_HELP"></span> | ||
| </v-tooltip> | ||
| <v-radio hide-details | ||
| v-for="i in ($STRINGS.MODE_COUNT - 0)" | ||
| :key="i" | ||
| :value="$STRINGS['MODE_KEY_' + i]" | ||
| :label="$STRINGS['MODE_TITLE_' + i]" | ||
| ></v-radio> | ||
| </v-radio-group> | ||
| <div slot="content"> | ||
| <!-- Mode Section --> |
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Please revert unrelated changes
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| <file-button id="localFile" label="Upload previous results" @upload="uploadJSON"></file-button> | ||
| </div> | ||
| </div> | ||
| </template> | ||
| </panel> | ||
| </v-flex> | ||
| <v-flex xs12> | ||
| <panel collapsible collapsed render-collapsed> | ||
| <template slot="header"> | ||
| <template v-if="!$vuetify.breakpoint.smAndDown"> | ||
| Databases | ||
| </template> | ||
| <template v-else> | ||
| DBs | ||
| </template> | ||
| & search settings | ||
| </template> | ||
| <div slot="content"> | ||
| <databases | ||
| :selected="database" | ||
| :all-databases="databases" | ||
| @update:selected="database = $event" | ||
| @update:all-databases="databases = $event" | ||
| :hideEmail="hideEmail" | ||
| ></databases> | ||
| <div class="actions input-buttons-panel"> | ||
| <div class="input-buttons-left"> | ||
| <load-acession-button v-if="$APP == 'foldseek'" @select="query = $event" @loading="accessionLoading = $event" :preload-source="preloadSource" :preload-accession="preloadAccession"></load-acession-button> | ||
| <file-button id="file" :label="$STRINGS.UPLOAD_LABEL" v-on:upload="upload"></file-button> | ||
| <PredictStructureButton v-if="$APP == 'foldseek'" :query="query" v-model="predictable" v-on:predict="query = $event"></PredictStructureButton> | ||
| </div> | ||
| <file-button id="localFile" label="Upload previous results" @upload="uploadJSON"></file-button> |
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| if (localStorageEnabled && localStorage.database) { | ||
| this.database = JSON.parse(localStorage.database); | ||
| } | ||
| if (localStorageEnabled && localStorage.databases) { | ||
| this.databases = JSON.parse(localStorage.databases); | ||
| } | ||
| if (localStorageEnabled && localStorage.iterativeSearch) { | ||
| this.iterativeSearch = JSON.parse(localStorage.iterativeSearch); | ||
| } | ||
| if (localStorageEnabled && localStorage.taxFilter) { | ||
| this.taxFilter = JSON.parse(localStorage.taxFilter); | ||
| } |
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These should be set somewhere else, they were removed in the last refactoring
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