From d929f199c39dcf919d4e4a619bdf7c46cfeac898 Mon Sep 17 00:00:00 2001
From: Colin Combe <colin.combe@ed.ac.uk>
Date: Fri, 3 Nov 2017 16:22:38 +0000
Subject: [PATCH] better error message for proteins missing from FASTA files

---
 build/crosslinkviewer.js | 4 ++--
 src/model/Match.js       | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/build/crosslinkviewer.js b/build/crosslinkviewer.js
index dfb5cb5d..2e600927 100644
--- a/build/crosslinkviewer.js
+++ b/build/crosslinkviewer.js
@@ -403,8 +403,8 @@ x.replace(m,"")):this.pepSeq2=null:this.pepSeq2=null;g=Z(g);k=Z(k);t=Z(t);u=Z(u)
 t&&(F+=t-1),null!==u&&(D+=u-1),this.associateWithLink(I,U,F,D,g[v]-0,this.pepSeq1.length,k[x],this.pepSeq2.length)}else for(v=0;v<t.length;v++)for(x=0;x<u.length;x++)I=v,U=x,I>=c.length&&(I=c.length-1),U>=f.length&&(U=f.length-1),I=c[I],U=f[U],F=t[v]-0,D=u[x]-0,this.associateWithLink(I,U,F,D,null,null,null,null);this.hd=!1;this.overlap=[];I===U&&(this.pepSeq1&&this.pepSeq2?(I=g[0],U=k[0],D=I+(this.pepSeq1.length-1),F=U+(this.pepSeq2.length-1),I>=U&&I<=F?(this.hd=!0,this.overlap[0]=I-1,this.overlap[1]=
 D<F?D:F):U>=I&&U<=D&&(this.hd=!0,this.overlap[0]=U-1,this.overlap[1]=F<D?F:D)):F===D&&(this.hd=!0,this.overlap[0]=F-1,this.overlap[1]=D));this.protein1=c;this.pepPos1=g;this.linkPos1=t;this.protein2=f;this.pepPos2=k;this.linkPos2=u}}
 Match.prototype.associateWithLink=function(c,g,f,k,m,p,s,t){var u,v,x;null===g?(v=this.controller.proteins.get(c),null===k?(u=""+c+"-null",x=null):(u=""+c+"-"+c,x=v)):c<=g?(u=""+c+"-"+g,v=this.controller.proteins.get(c),x=null!==g?this.controller.proteins.get(g):null):(u=""+g+"-"+c,v=this.controller.proteins.get(g),x=this.controller.proteins.get(c));var y=this.controller.proteinLinks.get(u);void 0===y&&(void 0!==v&&void 0!==x||alert("Something has gone wrong; a link has been added before a protein it links to. "+
-c+"-"+g),y=new ProteinLink(u,v,x,this.controller),this.controller.proteinLinks.set(u,y),v.addLink(y),null!==x&&x.addLink(y));u=!1;c===g||null===g?f-0<k-0||null===k?v=f+"-"+k:(v=k+"-"+f,u=!0):c<g?v=f+"-"+k:(v=k+"-"+f,u=!0);x=y.residueLinks.get(v);void 0===x&&(x=c===g?f-0<k-0||"n/a"===k?new ResidueLink(v,y,f,k,this.controller):new ResidueLink(v,y,k,f,this.controller):c==y.fromProtein.id?new ResidueLink(v,y,f,k,this.controller):new ResidueLink(v,y,k,f,this.controller),y.residueLinks.set(v,x),y.residueLinks.keys().length>
-ProteinLink.maxNoResidueLinks&&(ProteinLink.maxNoResidueLinks=y.residueLinks.keys().length));if("undefined"===typeof x.matches||null==x.matches)x.matches=[];!1===u?x.matches.push([this,m,p,s,t]):x.matches.push([this,s,t,m,p]);this.residueLinks.push(x)};
+c+"-"+g+" Are both of these IDs in your FASTA file?"),y=new ProteinLink(u,v,x,this.controller),this.controller.proteinLinks.set(u,y),v.addLink(y),null!==x&&x.addLink(y));u=!1;c===g||null===g?f-0<k-0||null===k?v=f+"-"+k:(v=k+"-"+f,u=!0):c<g?v=f+"-"+k:(v=k+"-"+f,u=!0);x=y.residueLinks.get(v);void 0===x&&(x=c===g?f-0<k-0||"n/a"===k?new ResidueLink(v,y,f,k,this.controller):new ResidueLink(v,y,k,f,this.controller):c==y.fromProtein.id?new ResidueLink(v,y,f,k,this.controller):new ResidueLink(v,y,k,f,this.controller),
+y.residueLinks.set(v,x),y.residueLinks.keys().length>ProteinLink.maxNoResidueLinks&&(ProteinLink.maxNoResidueLinks=y.residueLinks.keys().length));if("undefined"===typeof x.matches||null==x.matches)x.matches=[];!1===u?x.matches.push([this,m,p,s,t]):x.matches.push([this,s,t,m,p]);this.residueLinks.push(x)};
 Match.prototype.meetsFilterCriteria=function(){return this.isAmbig()&&!1===this.controller.ambigShown?!1:"function"==typeof this.controller.filter?this.controller.filter(this):"undefined"!==typeof this.controller.cutOff&&"undefined"!==typeof this.score?this.score>=this.controller.cutOff?!0:!1:!0};Match.prototype.isAmbig=function(){return 1<this.residueLinks.length||this.manuallyDashed?!0:!1};
 Match.prototype.toTableRow=function(){var c;c="<tr>"+("<td><p>"+this.id+"</p></td>");c+="<td><p>"+this.protein1+"</p></td>";c+="<td><p>"+this.pepPos1+"</p></td>";c+="<td><p>"+this.pepSeq1+"</p></td>";c+="<td><p>"+this.linkPos1+"</p></td>";c+="<td><p>"+this.protein2+"</p></td>";c+="<td><p>"+this.pepPos2+"</p></td>";c+="<td><p>"+this.pepSeq2+"</p></td>";c+="<td><p>"+this.linkPos2+"</p></td>";c+="<td><p>"+("undefined"!==typeof this.score?this.score.toFixed(4):"undefined")+"</p></td>";!0===this.controller.autoValidatedFound&&
 (c+="<td><p>"+this.autovalidated+"</p></td>");!0===this.controller.manualValidatedFound&&(c+="<td><p>"+this.validated+"</p></td>");return c+"</tr>"};xiNET.Link=function(){};xiNET.Link.prototype.mouseDown=function(c){this.controller.preventDefaultsAndStopPropagation(c);this.controller.force&&this.controller.force.stop();this.controller.dragElement=this;this.controller.clearSelection();this.setSelected(!0);c=this.controller.getEventPoint(c);this.controller.dragStart=this.controller.mouseToSVG(c.x,c.y);return!1};
diff --git a/src/model/Match.js b/src/model/Match.js
index c5ede5b8..8152f9f4 100644
--- a/src/model/Match.js
+++ b/src/model/Match.js
@@ -418,7 +418,7 @@ Match.prototype.associateWithLink = function (p1ID, p2ID, res1, res2, //followin
     if (link === undefined) {
         if (fromProt === undefined || toProt === undefined) {
             alert("Something has gone wrong; a link has been added before a protein it links to. " +
-                    p1ID + "-" + p2ID);
+                    p1ID + "-" + p2ID + " Are both of these IDs in your FASTA file?");
         }
         link = new ProteinLink(proteinLinkID, fromProt, toProt, this.controller);
         this.controller.proteinLinks.set(proteinLinkID, link);