Remove gap costs changes for foldmason

Author: milot-mirdita

backend/foldmasonmsa.go

@@ -5,15 +5,12 @@ import (
 	"encoding/base64"
 	"os"
 	"path/filepath"
-	"strconv"
 	"strings"
 )
 
 type FoldMasonMSAJob struct {
 	Queries   []string `json:"queries"`
 	FileNames []string `json:"fileNames"`
-	GapOpen   int64    `json:"gapOpen"`
-	GapExtend int64    `json:"gapExtend"`
 }
 
 func (r FoldMasonMSAJob) Hash() Id {
@@ -22,8 +19,6 @@ func (r FoldMasonMSAJob) Hash() Id {
 	for _, query := range r.Queries {
 		h.Write([]byte(query))
 	}
-	h.Write([]byte(strconv.FormatInt(r.GapOpen, 10)))
-	h.Write([]byte(strconv.FormatInt(r.GapExtend, 10)))
 	bs := h.Sum(nil)
 	return Id(base64.URLEncoding.WithPadding(base64.NoPadding).EncodeToString(bs))
 }
@@ -61,8 +56,6 @@ func NewFoldMasonMSAJobRequest(
 	job := FoldMasonMSAJob{
 		queries,
 		fileNames,
-		gapOpen,
-		gapExtend,
 	}
 	request := JobRequest{
 		job.Hash(),

backend/worker.go

@@ -1435,10 +1435,6 @@ rm -rf -- "${BASE}/tmp"
 			filepath.Join(resultBase, "pdbs/"),
 			filepath.Join(resultBase, "foldmason"),
 			filepath.Join(resultBase, "tmp/"),
-			"--gap-open",
-			strconv.FormatInt(job.GapOpen, 10),
-			"--gap-extend",
-			strconv.FormatInt(job.GapExtend, 10),
 			"--report-mode",
 			"2",
 			"--report-paths",

frontend/FoldMasonSearch.vue

@@ -62,7 +62,7 @@
             </template>
             </panel>
         </v-flex>
-        <v-flex xs12>
+        <!-- <v-flex xs12>
             <panel collapsible collapsed render-collapsed>
             <template slot="header">Alignment settings</template>
             <template slot="toolbar-extra">
@@ -92,7 +92,7 @@
                 />
             </div>
             </panel>
-        </v-flex>
+        </v-flex> -->
         <v-flex>
             <panel>
             <template slot="content">
@@ -132,16 +132,6 @@ import Databases from './Databases.vue';
 import QueryTextarea from "./QueryTextarea.vue";
 import DragUploadBox from "./DragUploadBox.vue";
 
-const defaultParams = {
-    wg: true,
-    filterMsa: false,
-    compBias: false,
-    matchRatio: 0.52,
-    gapOpen: 20,
-    gapExtend: 2,
-    refineIters: 0
-};
-
 export default {
     name: "FoldMasonSearch",
     tool: "foldmason",
@@ -163,7 +153,6 @@ export default {
             inSearch: false,
             errorMessage: { type: null, message: "" },
             queries: [],   // [ { name: "file", text: "ATOM..." }, { name: "file", text: "ATOM..." } ...]
-            params: structuredClone(defaultParams),
             inFileDrag: false,
             accessionLoading: false,
         };
@@ -223,8 +212,6 @@ export default {
                 params.append('fileNames[]', v.name);
                 params.append('queries[]', new Blob([v.text], { type: 'text/plain' }), v.name);
             });
-            params.append('gapOpen', this.params.gapOpen);
-            params.append('gapExtend', this.params.gapExtend);
 
             try {
                 this.inSearch = true;
@@ -310,9 +297,6 @@ export default {
             );
             fr.readAsText(file)
         },
-        resetParams() {
-            this.params = structuredClone(defaultParams);
-        },
     }
 };
 </script>