Add iterative searcher to Foldseek

backend/server.go

@@ -264,6 +264,7 @@ func server(jobsystem JobSystem, config ConfigRoot) {
 		var dbs []string
 		var mode string
 		var email string
+		var iterativesearch bool
 		var taxfilter string
 
 		if strings.HasPrefix(req.Header.Get("Content-Type"), "multipart/form-data") {
@@ -285,6 +286,7 @@ func server(jobsystem JobSystem, config ConfigRoot) {
 			dbs = req.Form["database[]"]
 			mode = req.FormValue("mode")
 			email = req.FormValue("email")
+                        iterativesearch = req.FormValue("iterativesearch") == "true"
 			taxfilter = req.FormValue("taxfilter")
 		} else {
 			err := req.ParseForm()
@@ -296,6 +298,7 @@ func server(jobsystem JobSystem, config ConfigRoot) {
 			dbs = req.Form["database[]"]
 			mode = req.FormValue("mode")
 			email = req.FormValue("email")
+                        iterativesearch = req.FormValue("iterativesearch") == "true"
 			taxfilter = req.FormValue("taxfilter")
 		}
 
@@ -315,7 +318,7 @@ func server(jobsystem JobSystem, config ConfigRoot) {
 				modeWithoutComplex := strings.Join(append(modes[:modeIdx], modes[modeIdx+1:]...), "-")
 				request, err = NewComplexSearchJobRequest(query, dbs, databases, modeWithoutComplex, config.Paths.Results, email, taxfilter)
 			} else {
-				request, err = NewStructureSearchJobRequest(query, dbs, databases, mode, config.Paths.Results, email, taxfilter)
+				request, err = NewStructureSearchJobRequest(query, dbs, databases, mode, config.Paths.Results, email, iterativesearch, taxfilter)
 			}
 		} else {
 			http.Error(w, "Job type not supported by this server", http.StatusBadRequest)

backend/structuresearchjob.go

@@ -10,10 +10,11 @@ import (
 )
 
 type StructureSearchJob struct {
-	Size      int      `json:"size" validate:"required"`
-	Database  []string `json:"database" validate:"required"`
-	Mode      string   `json:"mode" validate:"oneof=3di tmalign 3diaa"`
-	TaxFilter string   `json:"taxfilter"`
+	Size      int        `json:"size" validate:"required"`
+	Database  []string   `json:"database" validate:"required"`
+	Mode      string     `json:"mode" validate:"oneof=3di tmalign 3diaa"`
+        IterativeSearch bool `json:"iterativesearch"`
+	TaxFilter string     `json:"taxfilter"
 	query     string
 }
 
@@ -22,6 +23,9 @@ func (r StructureSearchJob) Hash() Id {
 	h.Write(([]byte)(JobStructureSearch))
 	h.Write([]byte(r.query))
 	h.Write([]byte(r.Mode))
+        if r.IterativeSearch {
+           h.Write([]byte("Iterative"))
+        }
 	if r.TaxFilter != "" {
 		h.Write([]byte(r.TaxFilter))
 	}
@@ -48,11 +52,12 @@ func (r StructureSearchJob) WritePDB(path string) error {
 	return nil
 }
 
-func NewStructureSearchJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string, taxfilter string) (JobRequest, error) {
+func NewStructureSearchJobRequest(query string, dbs []string, validDbs []Params, mode string, resultPath string, email string, iterativeSearch bool, taxfilter string) (JobRequest, error) {
 	job := StructureSearchJob{
 		max(strings.Count(query, "HEADER"), 1),
 		dbs,
 		mode,
+                iterativeSearch,
 		taxfilter,
 		query,
 	}

backend/worker.go

@@ -405,6 +405,10 @@ mv -f -- "${BASE}/query.lookup_tmp" "${BASE}/query.lookup"
 					parameters = append(parameters, "0")
 				}
 
+				if job.IterativeSearch {
+    					parameters = append(parameters, "--num-iterations")
+    					parameters = append(parameters, "3") 
+				}
 				cmd, done, err := execCommand(config.Verbose, parameters...)
 				if err != nil {
 					errChan <- &JobExecutionError{err}

frontend/Search.vue

@@ -55,17 +55,27 @@
             <template v-else>
                 DBs
             </template>
-            &amp; search settings
         </template>
         <div slot="content">
             <databases
-                :selected="database"
-                :all-databases="databases"
-                @update:selected="database = $event"
-                @update:all-databases="databases = $event"
-                :hideEmail="hideEmail"
-                ></databases>
-
+                    :selected="database"
+                    :all-databases="databases"
+                    @update:selected="database = $event"
+                    @update:all-databases="databases = $event"
+                    :hideEmail="hideEmail"
+                    ></databases>
+        </div>
+        </panel>
+        <panel collapsible collapsed render-collapsed>
+        <template slot="header">
+            <template v-if="!$vuetify.breakpoint.smAndDown">
+                Search Parameters
+            </template>
+            <template v-else>
+                Params
+            </template>
+        </template>
+        <div slot="content">
             <v-radio-group v-model="mode">
                 <v-tooltip open-delay="300" top>
                     <template v-slot:activator="{ on }">
@@ -83,6 +93,21 @@
 
             <TaxonomyAutocomplete v-model="taxFilter"></TaxonomyAutocomplete>
 
+            <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">{{ $MDI.HelpCircleOutline }}</v-icon>
+                        </label>
+                    </template>
+                    <span>Improve sensitivity of search by performing an iterative search (--num-iterations 3).</span>
+                </v-tooltip>
+
+                <v-radio label="On" :value="true"></v-radio>
+                <v-radio label="Off" :value="false"></v-radio>
+            </v-radio-group>
+
             <v-tooltip v-if="!$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>
@@ -119,7 +144,7 @@
                     ({{
                         databases.filter(db => database.includes(db.path)).map(db => db.name).sort().join(", ")
                     }})
-                </template> with {{ $STRINGS.APP_NAME }} in <strong>{{ modes[mode] }}</strong> mode.
+                </template> with {{ $STRINGS.APP_NAME }} in <strong>{{ modes[mode] }}</strong> mode<span v-if="iterativeSearch"><strong> iterative</strong></span>.
                 <div v-if="errorMessage != ''" class="v-alert v-alert--outlined warning--text mt-2">
                     <span>{{ errorMessage }}</span>
                 </div>
@@ -176,6 +201,7 @@ export default {
             query: "",
             database: JSON.parse(storage.getItem('database') || '[]'),
             databases: JSON.parse(storage.getItem('databases') || '[]'),
+            iterativeSearch: JSON.parse(storage.getItem('iterativeSearch') || false),
             taxFilter: JSON.parse(storage.getItem('taxFilter') || 'null'),
             predictable: false,
             accessionLoading: false,
@@ -235,6 +261,9 @@ export default {
         databases(value) {
             storage.setItem('databases', JSON.stringify(value));
         },
+        iterativeSearch(value) {
+            storage.setItem('iterativeSearch', JSON.stringify(value));
+        },
         taxFilter(value) {
             storage.setItem('taxFilter', JSON.stringify(value));
         },
@@ -265,6 +294,9 @@ export default {
             if (this.taxFilter) {
                 request.taxfilter = this.taxFilter.value;
             }
+            if (this.iterativeSearch) {
+                request.iterativesearch = this.iterativeSearch.value;
+            }
             try {
                 this.inSearch = true;
                 const response = await this.$axios.post("api/ticket", convertToQueryUrl(request), {