updating some UI bugs

.gitignore

@@ -1,5 +1,7 @@
 # See https://help.github.com/articles/ignoring-files/ for more about ignoring files.
 
+app.js
+
 # dependencies
 /node_modules
 /.pnp

public/assets/app.js

@@ -99094,7 +99094,6 @@
             var header_count = (value.match(/>/g) || []).length;
             if (header_count === 1) {
               var fasta_regex = /^>(\S+).*\n(.+)/;
-              console.log("HEY THERE");
               var match = fasta_regex.exec(value);
               if (match) {
                 this.setState({

src/interface/mainform.js

@@ -225,6 +225,7 @@ class MainForm extends React.Component{
         <div className="box-header with-border">
           <p>The PSIPRED Workbench provides a range of protein structure prediction methods. The site can be used interactively via a web browser or programmatically via our REST API. For high-throughput analyses, downloads of all the algorithms are available.</p>
           <p><b>Amino acid</b> sequences enable: secondary structure prediction, including regions of disorder and transmembrane helix packing; contact analysis; fold recognition; structure modelling; and prediction of domains and function. In addition <b>PDB Structure files</b> allow prediction of protein-metal ion contacts, protein-protein hotspot residues, and membrane protein orientation.</p>
+          <p>For Help or Errors please email [email protected]</p>
           <hr id="hr_form"></hr>
         </div>
         <div className="box-header with-border"><h5 className="box-title">Data Input</h5></div>

src/interface/parsers.js

@@ -423,8 +423,8 @@ export function get_memsat_ranges(regex, data)
       let regions = match[1].split(',');
       regions.forEach(function(region, i){
         regions[i] = region.split('-');
-        regions[i][0] = parseInt(regions[i][0]);
-        regions[i][1] = parseInt(regions[i][1]);
+        regions[i][0] = parseInt(regions[i][0]-1);
+        regions[i][1] = parseInt(regions[i][1]-1);
       });
       return(regions);
     }
@@ -433,8 +433,8 @@ export function get_memsat_ranges(regex, data)
         // console.log(match[1]);
         let seg = match[1].split('-');
         let regions = [[], ];
-        regions[0][0] = parseInt(seg[0]);
-        regions[0][1] = parseInt(seg[1]);
+        regions[0][0] = parseInt(seg[0]-1);
+        regions[0][1] = parseInt(seg[1]-1);
         return(regions);
     }
     return(match[1]);
@@ -517,7 +517,7 @@ export function parse_memsatdata(annotations, file)
   {
     let prev_end = 0;
     topo_regions.forEach(function(region){
-      tmp_anno = tmp_anno.fill('TM', region[0], region[1]+1);
+      tmp_anno = tmp_anno.fill('TM', region[0], region[1]);
       if(prev_end > 0){prev_end -= 1;}
       tmp_anno = tmp_anno.fill(coil_type, prev_end, region[0]);
       if(coil_type === 'EC'){ coil_type = 'CY';}else{coil_type = 'EC';}
@@ -529,18 +529,19 @@ export function parse_memsatdata(annotations, file)
   //signal_regions = [[70,83], [102,117]];
   if(signal_regions !== 'Not detected.'){
     signal_regions.forEach(function(region){
-      tmp_anno = tmp_anno.fill('S', region[0], region[1]+1);
+      tmp_anno = tmp_anno.fill('S', region[0], region[1]);
     });
   }
   //reentrant_regions = [[40,50], [200,218]];
   if(reentrant_regions !== 'Not detected.'){
     reentrant_regions.forEach(function(region){
-      tmp_anno = tmp_anno.fill('RH', region[0], region[1]+1);
+      tmp_anno = tmp_anno.fill('RH', region[0], region[1]);
     });
   }
   tmp_anno.forEach(function(anno, i){
     annotations[i].memsat = anno;
   });
+  console.log(annotations);
   return(annotations);
 }
 //type is one of gen, pgen and dgen

src/interface/results_sequence.js

@@ -532,8 +532,8 @@ class ResultsSequence extends React.Component{
     console.log("DRAWING EMPTY ANNOTATION PANEL");
     draw_empty_annotation_panel(this.state, this.sequencePlot.current)
     //here is a good place to send the results and set up the polling.
-    this.timer = setInterval(() => this.getResults(), 20000);
-    //this.timer = setInterval(() => this.getResults(), 500);
+    //this.timer = setInterval(() => this.getResults(), 20000);
+    this.timer = setInterval(() => this.getResults(), 500);
 
   }