Merge pull request #96 from snjlee58/master

Added sankey plot using taxonomy report

backend/alignment.go

@@ -190,6 +190,16 @@ type FastaEntry struct {
 type SearchResult struct {
 	Database   string      `json:"db"`
 	Alignments interface{} `json:"alignments"`
+	TaxonomyReport interface{} `json:"taxonomyreport"`
+}
+
+type TaxonomyReport struct {
+    Proportion    float64 `json:"proportion"`
+    CladeReads    int     `json:"clade_reads"`
+    TaxonReads    int     `json:"taxon_reads"`
+    Rank          string  `json:"rank"`
+    TaxonID       string  `json:"taxon_id"`
+    ScientificName string `json:"name"`
 }
 
 func dbpaths(path string) (string, string) {
@@ -320,13 +330,71 @@ func ReadAlignments[T any, U interface{ ~uint32 | ~int64 }](id Id, entries []U,
 			all = append(all, results)
 		}
 		reader.Delete()
+
+		// Read the taxonomy report
+        taxonomyReportPath := filepath.Join(base, "alis_" + db + "_report")
+        taxonomyReport, _ := ReadTaxonomyReport(taxonomyReportPath)
+
 		base := filepath.Base(name)
-		res = append(res, SearchResult{strings.TrimPrefix(base, "alis_"), all})
+		res = append(res, SearchResult{
+			strings.TrimPrefix(base, "alis_"), 
+			all,
+			taxonomyReport, // Include taxonomy report
+			})
 	}
 
 	return res, nil
 }
 
+func ReadTaxonomyReport(filePath string) ([]TaxonomyReport, error) {
+    file, err := os.Open(filePath)
+    if err != nil {
+        // Return an empty report for any error
+        return []TaxonomyReport{}, nil
+    }
+    defer file.Close()
+
+    var reports []TaxonomyReport
+    scanner := bufio.NewScanner(file)
+
+    for scanner.Scan() {
+        line := scanner.Text()
+        fields := strings.Split(line, "\t")
+        if len(fields) < 6 {
+			// Skip invalid lines
+            continue
+        }
+
+        // Parse the fields
+        proportion, err := strconv.ParseFloat(fields[0], 64)
+        if err != nil {
+            continue
+        }
+
+        cladeReads, err := strconv.Atoi(fields[1])
+        if err != nil {
+            continue
+        }
+
+        taxonReads, err := strconv.Atoi(fields[2])
+        if err != nil {
+            continue
+        }
+
+        report := TaxonomyReport{
+            Proportion:    proportion,
+            CladeReads:    cladeReads,
+            TaxonReads:    taxonReads,
+            Rank:          fields[3],
+            TaxonID:       fields[4],
+            ScientificName: strings.TrimSpace(fields[5]),
+        }
+        reports = append(reports, report)
+    }
+
+    return reports, nil
+}
+
 func Alignments(id Id, entry []int64, databases []string, jobsbase string) ([]SearchResult, error) {
 	return ReadAlignments[AlignmentEntry, int64](id, entry, databases, jobsbase)
 }

frontend/ResultView.vue

@@ -92,11 +92,17 @@
                         <v-tab v-for="entry in hits.results" :key="entry.db">{{ entry.db }} ({{ entry.alignments ? Object.values(entry.alignments).length : 0 }})</v-tab>
                     </v-tabs>
                     <div v-for="(entry, index) in hits.results" :key="entry.db" v-if="selectedDatabases == 0 || (index + 1) == selectedDatabases">
-                    <v-flex class="d-flex" :style="{ 'flex-direction' : $vuetify.breakpoint.xsOnly ? 'column' : null }">
+                    <v-flex class="d-flex" :style="{ 'flex-direction' : $vuetify.breakpoint.xsOnly ? 'column' : null, 'align-items': 'center' }">
                         <h2 style="margin-top: 0.5em; margin-bottom: 1em; display: inline-block;">
                             <span style="text-transform: uppercase;">{{ entry.db }}</span> <small>{{ entry.alignments ? Object.values(entry.alignments).length : 0 }} hits</small>
                         </h2>
-                        <v-btn-toggle mandatory v-model="tableMode" class="ml-auto">
+
+                        <!-- Button to toggle Sankey Diagram visibility -->
+                        <v-btn @click="isSankeyVisible = !isSankeyVisible" class="ml-auto mr-2" large>
+                            {{ isSankeyVisible ? 'Hide Sankey' : 'Show Sankey' }}
+                        </v-btn>
+
+                        <v-btn-toggle mandatory v-model="tableMode" >
                             <v-btn>
                                 Graphical
                             </v-btn>
@@ -106,7 +112,9 @@
                             </v-btn>
                         </v-btn-toggle>
                     </v-flex>
-
+                    <v-flex v-if="isSankeyVisible && entry.taxonomyreport">
+                        <SankeyDiagram :rawData="entry.taxonomyreport" :currentSelectedNodeId="selectedTaxId" @selectTaxon="handleSankeySelect"></SankeyDiagram>
+                    </v-flex>
                     <table class="v-table result-table" style="position:relativ; margin-bottom: 3em;">
                         <colgroup>
                             <template v-if="isComplex">
@@ -177,7 +185,7 @@
                             </tr>
                         </thead>
                         <tbody>
-                            <template v-for="(group, groupidx) in entry.alignments">
+                            <template v-for="(group, groupidx) in filteredAlignments(entry.alignments)" >
                                 <tr v-for="(item, index) in group" :class="['hit', { 'active' : item.active }]">
                                 <template v-if="index == 0 && isComplex">
                                 <td class="thin" data-label="Query TM-score" :rowspan="group.length">{{ group[0].complexqtm.toFixed(2) }}</td>
@@ -251,6 +259,7 @@
 import Panel from './Panel.vue';
 import AlignmentPanel from './AlignmentPanel.vue';
 import Ruler from './Ruler.vue';
+import SankeyDiagram from './SankeyDiagram.vue';
 
 import { debounce } from './lib/debounce';
 
@@ -265,13 +274,16 @@ function getAbsOffsetTop($el) {
 
 export default {
     name: 'ResultView',
-    components: { Panel, AlignmentPanel, Ruler },
+    components: { Panel, AlignmentPanel, Ruler, SankeyDiagram },
     data() {
         return {
             alignment: null,
             activeTarget: null,
             alnBoxOffset: 0,
             selectedDatabases: 0,
+            isSankeyVisible: false,
+            selectedTaxId: null,
+            filteredHitsTaxIds: [],
             tableMode: 0,
             menuActivator: null,
             menuItems: [],
@@ -363,7 +375,30 @@ export default {
                 this.menuItems = items;
                 this.menuActivator.click(event);
             }
-        }
+        },
+        handleSankeySelect({ nodeId, descendantIds }) {
+            this.selectedTaxId = nodeId;
+            this.filteredHitsTaxIds = descendantIds ? descendantIds.map(Number) : null; 
+        },
+        filteredAlignments(alignments) {
+            // Convert alignments to an array if it is an object
+            if (alignments && !Array.isArray(alignments)) {
+                alignments = Object.values(alignments);
+            }
+
+            if (!Array.isArray(alignments)) {
+                return []; // Return an empty array if conversion fails
+            }
+
+            if (!this.filteredHitsTaxIds || this.filteredHitsTaxIds.length === 0) {
+                return alignments; // Return all groups if no filteredAlignments
+            }
+
+            // Filter each group to only include items with taxId in filteredAlignments
+            return alignments
+                .map(group => group.filter(item => this.filteredHitsTaxIds.includes(Number(item.taxId))))
+                .filter(group => group.length > 0);
+        },
     }
 };
 </script>
@@ -424,7 +459,6 @@ src: url(assets/InconsolataClustal2.woff2),
     }
 }
 
-
 .theme--dark {
     .result-table {
         a:not([href])  {