Changeset 944 for js/human_3d_alignment

Timestamp:

06/05/20 17:27:32 (5 years ago)

Author:

Maciej Komosinski

Message:

Loads genotypes properly using Framsticks SDK methods instead of ad-hoc js parsing

File:

• js/human_3d_alignment/src/utils/genotypes.js (modified) (2 diffs)

js/human_3d_alignment/src/utils/genotypes.js

@@ -30 +30 @@
         rawFile.onload = (e) => {
             if (rawFile.readyState === 4) {
-                if (rawFile.status === 200) {
-                    this.readGenotypesFromText(rawFile.responseText);
+                if (rawFile.status === 200 || rawFile.status === 0) {
+                      this.readGenotypesFromGenotypeLoader(rawFile.responseText);
                 } else {
                     console.error(rawFile.statusText);
@@ -44 +44 @@
 
     /**
-     * Read genotypes from text read from genotypes.gen. TODO mk> This function should be removed; use SDK functionality instead for reliable parsing.
+     * Read genotypes from text read from genotypes.gen.
      * @param {string} text 
      */
-    readGenotypesFromText(text) {
-        let textTable = text.split('org:\n');
-        let i = 1;
-        while (i < textTable.length) {
-            let lines = textTable[i].split('\n');
-            if (lines[0].includes('name:')) {
-                let j = 0;
-                let gen = '';
-                let name = '';
-                let id = '';
-                while (j < lines.length) {
-                    if (lines[j].includes('name:')) {
-                        name += lines[j].split(':')[1];
-                    } else if (lines[j].includes('genotype:')) {
-                        gen += lines[j].replace('genotype:', '');
-                        let k = j + 1;
-                        while (!lines[k].includes('info_timestamp:')) {
-                            if (lines[k] != '\n') {
-                                gen += ' ' + lines[k];
-                            } else {
-                                gen += ' '
-                            }
-                            k++;
-                        }
-                        gen = gen.split('~').join('');
-                    } else if (lines[j].includes('num:')) {
-                        id += lines[j].split(':')[1];
-                    }
-                    j++;
-                }
-                if (!gen.includes('//0')) {
-                    this.name.push(name);
-                    this.genotype.push(gen);
-                    this.id.push(id);
-                }
-            }
+    readGenotypesFromGenotypeLoader(text) {
+        let textStringFile = new Module.StringFILE2(text, 0);
+        let genotypeLoader = new Module.GenotypeMiniLoader(textStringFile);
+        let loaded = genotypeLoader.loadNextGenotype();
+        let i = 0;
+        while (loaded.genotype.c_str()!="")
+        {
+            this.name.push(loaded.name.c_str());
+            this.genotype.push(loaded.genotype.c_str());
+            this.id.push(i);
+            i++;
 
-            i++;
+            loaded = genotypeLoader.loadNextGenotype();
         }
         this.loaded = true;
         this.parent.start();
     }
-
 }