Merge pull request #328 from SynBioDex/fix-reverse--complement

Reverse Complement Sequences
SynBioDex · Sep 25, 2024 · c3feff1 · c3feff1
2 parents f757578 + 8fa7058
commit c3feff1
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Showing 4 changed files with 25 additions and 10 deletions.
diff --git a/SBOLCanvasBackend/src/utils/SBOLToMx.java b/SBOLCanvasBackend/src/utils/SBOLToMx.java
@@ -14,7 +14,6 @@
 import java.util.List;
 import java.util.Set;
 import java.util.Stack;
-import java.util.concurrent.atomic.AtomicBoolean;
 
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.OutputKeys;

diff --git a/SBOLCanvasFrontend/src/app/graph-helpers.ts b/SBOLCanvasFrontend/src/app/graph-helpers.ts
@@ -1207,7 +1207,15 @@ export class GraphHelpers extends GraphBase {
                         if (child) childGlyphInfo = this.getFromInfoDict(child.value)
 
                         if (childGlyphInfo !== undefined && childGlyphInfo.sequence) {
-                            glyphInfo.sequence += childGlyphInfo.sequence
+                            let direction = this.graph.getCellStyle(child)[mx.mxConstants.STYLE_DIRECTION]
+
+                            // Cell is flipped
+                            if(direction === "west"){
+                                glyphInfo.sequence += this.reverseComplement(childGlyphInfo.sequence)
+                            }
+                            else{
+                                glyphInfo.sequence += childGlyphInfo.sequence
+                            }
                         }
                     }
                 }
@@ -2166,6 +2174,19 @@ export class GraphHelpers extends GraphBase {
         circuitContainer.refreshCircuitContainer(this.graph)
     }
 
+    private reverseComplement(glyphSequence: string){
+        glyphSequence = glyphSequence.split("").reverse().join("")
+        let reverseComplement = ""
+
+        const complementDict = {"a":"t", "t":"a", "c":"g", "g":"c"}
+
+        for(let base of glyphSequence.toLowerCase()){
+            reverseComplement += complementDict[base] || base
+        }
+
+        return glyphSequence === glyphSequence.toUpperCase() ? reverseComplement.toUpperCase() : reverseComplement
+    }
+
     protected createViewCell(uri: string, module: boolean = false): mxCell {
         // construct the view cell
         const cell1 = this.graph.getModel().getCell(1)

diff --git a/SBOLCanvasFrontend/src/app/graph.service.ts b/SBOLCanvasFrontend/src/app/graph.service.ts
@@ -297,13 +297,7 @@ export class GraphService extends GraphHelpers {
                         this.graph.setCellStyles(mx.mxConstants.STYLE_DIRECTION, "east", [cell])
                         console.debug("turning east")
                     }
-
-                    // if a glyph has been flipped its sequence needs to be reversed
-                    let glyphInfo
-                    if (cell) glyphInfo = this.getFromInfoDict(cell.value)
-                    glyphInfo.sequence = glyphInfo.sequence.split("").reverse().join("")
-
-                    this.metadataService.setSelectedGlyphInfo(glyphInfo)
+
                 } else if (cell.isInteraction()) {
                     this.flipInteractionEdge(cell)
                 } else if (cell.isInteractionNode()) {
@@ -654,6 +648,7 @@ export class GraphService extends GraphHelpers {
     */
     copy(){
         mx.mxClipboard.copy(this.graph, this.graph.getSelectionCells())
+        console.log(this.graph.getSelectionCell())
     }
 
     // Map old cells to newly created cells in the paste method 

diff --git a/SBOLCanvasFrontend/src/app/info-editor/info-editor.component.ts b/SBOLCanvasFrontend/src/app/info-editor/info-editor.component.ts
@@ -60,7 +60,7 @@ export class InfoEditorComponent implements OnInit {
   }
 
   getTypes() {
-    this.metadataService.loadTypes().subscribe(types => this.partTypes = types);
+    this.metadataService.loadTypes().subscribe(types => this.partTypes = types.filter(type => type != "Circular"));
   }
 
   getRoles() {