diff --git a/README.md b/README.md
index 4beb48917..7ef070b38 100644
--- a/README.md
+++ b/README.md
@@ -9,8 +9,8 @@ PHAT is under development in the Zehbe Lab ([http://zehbelab.weebly.com/](http:/
 **Project Supervisor/Principal Investigator:** Dr. Ingeborg Zehbe, LU/TBRHRI Research Chair & Senior Scientist    
 **Project Lead/Biologist:** Robert Jackson, PhD Biotech Candidate    
 **Project Lead/Software Developer:** Chris Gibb, HBSc Comp Sci Student  
-**Team Members:** Mitchell Pynn, Shane Liu, Jeremy Braun
+**Team Members:** Mitchell Pynn, Shane Liu, Jeremy Braun, Nick Catanzaro, Zachary Moorman
 
 **How to Cite PHAT (pre-print):**
 
-Gibb CM, Jackson R, Mohammed S, Fiaidhi J, Zehbe I. Pathogen-Host Analysis Tool (PHAT): an Integrative Platform to Analyze Pathogen-Host Relationships in Next-Generation Sequencing Data. bioRxiv. https://doi.org/10.1101/178327
+Gibb CM, Jackson R, Mohammed S, Fiaidhi J, Zehbe I. Pathogen-Host Analysis Tool (PHAT): an Integrative Platform to Analyze Pathogen-Host Relationships in Next-Generation Sequencing Data. bioRxiv. https://doi.org/10.1101/178327
\ No newline at end of file
diff --git a/src/CheckForUpdateProcess.ts b/src/CheckForUpdateProcess.ts
index 0e5338d2b..130cad04d 100644
--- a/src/CheckForUpdateProcess.ts
+++ b/src/CheckForUpdateProcess.ts
@@ -1,4 +1,5 @@
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
+import * as atomic from "./req/operations/atomicOperations";
 import * as getUpdate from "./req/getLatestUpdate";
 
 let flags : CompletionFlags = new CompletionFlags();
@@ -28,7 +29,7 @@ process.on
                         data : res
                     }
                 );
-                process.exit(0);
+                atomic.exitFork(0);
             }).catch((arg : any) => {
                 console.log(arg);
                 flags.done = true;
@@ -41,7 +42,7 @@ process.on
                         data : arg
                     }
                 );
-                process.exit(1);
+                atomic.exitFork(1);
             });
         }
     }
@@ -58,7 +59,7 @@ process.on
             data : err.message
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
 process.on("unhandledRejection",function(err : Error){
     console.log(err);
@@ -72,5 +73,5 @@ process.on("unhandledRejection",function(err : Error){
             data : err.message
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
\ No newline at end of file
diff --git a/src/DownloadAndInstallUpdateProcess.ts b/src/DownloadAndInstallUpdateProcess.ts
index 010dc1bf9..fb61199fc 100644
--- a/src/DownloadAndInstallUpdateProcess.ts
+++ b/src/DownloadAndInstallUpdateProcess.ts
@@ -3,6 +3,7 @@ import * as cp from "child_process";
 
 let GitHubReleases = require("github-releases");
 
+import * as atomic from "./req/operations/atomicOperations";
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
 import {getReadable} from "./req/getAppPath";
 
@@ -71,7 +72,7 @@ process.on
                         );
                         installer.unref();
                     }
-                    process.exit(0);
+                    atomic.exitFork(0);
 
                 });
             });
@@ -90,7 +91,7 @@ process.on
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
 process.on("unhandledRejection",function(err : string){
     console.log("ERROR "+err);
@@ -104,5 +105,5 @@ process.on("unhandledRejection",function(err : string){
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
\ No newline at end of file
diff --git a/src/InputBamFileProcess.ts b/src/InputBamFileProcess.ts
index 00defcd22..ad4d4a989 100644
--- a/src/InputBamFileProcess.ts
+++ b/src/InputBamFileProcess.ts
@@ -106,7 +106,7 @@ process.on(
                 flags.done = true
                 flags.success = true;
                 update();
-                process.exit(0);
+                atomic.exitFork(0);
             })();
         }
     }
diff --git a/src/LinkRefSeqToAlignmentProcess.ts b/src/LinkRefSeqToAlignmentProcess.ts
index c11606eef..3659b1983 100644
--- a/src/LinkRefSeqToAlignmentProcess.ts
+++ b/src/LinkRefSeqToAlignmentProcess.ts
@@ -98,7 +98,7 @@ process.on(
                 flags.success = true;
                 update();
 
-                process.exit(0);
+                atomic.exitFork(0);
             })();
         }
     }
diff --git a/src/OpenProjectProcess.ts b/src/OpenProjectProcess.ts
index e640c8e94..3e910d37d 100644
--- a/src/OpenProjectProcess.ts
+++ b/src/OpenProjectProcess.ts
@@ -1,3 +1,4 @@
+import * as atomic from "./req/operations/atomicOperations";
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
 import {ProjectManifest} from "./req/projectManifest";
 import {openProject} from "./req//openProject";
@@ -40,7 +41,7 @@ process.on
                         flags : flags,
                     }
                 );
-                process.exit(0);
+                atomic.exitFork(0);
             }).catch((err) => {
                 flags.done = true;
                 flags.failure = true;
@@ -52,7 +53,7 @@ process.on
                         data : err
                     }
                 );
-                process.exit(1);
+                atomic.exitFork(1);
             });
         }
     }  
@@ -69,7 +70,7 @@ process.on
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
 
 process.on("unhandledRejection",function(err : string){
@@ -84,5 +85,5 @@ process.on("unhandledRejection",function(err : string){
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
\ No newline at end of file
diff --git a/src/RenderCoverageTrackProcess.ts b/src/RenderCoverageTrackProcess.ts
index 134f061d2..ecf2b482e 100644
--- a/src/RenderCoverageTrackProcess.ts
+++ b/src/RenderCoverageTrackProcess.ts
@@ -1,3 +1,4 @@
+import * as atomic from "./req/operations/atomicOperations";
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
 import {AlignData} from "./req/alignData"
 import * as cf from "./req/renderer/circularFigure";
@@ -39,7 +40,7 @@ process.on
                         }
                     }
                 );
-                process.exit(0);
+                atomic.exitFork(0);
             });
         }
     }  
@@ -55,5 +56,5 @@ process.on
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
\ No newline at end of file
diff --git a/src/RenderSNPTrackProcess.ts b/src/RenderSNPTrackProcess.ts
index a08dd1ae8..f227b4ac0 100644
--- a/src/RenderSNPTrackProcess.ts
+++ b/src/RenderSNPTrackProcess.ts
@@ -1,3 +1,4 @@
+import * as atomic from "./req/operations/atomicOperations";
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
 import {AlignData} from "./req/alignData"
 import * as cf from "./req/renderer/circularFigure";
@@ -39,7 +40,7 @@ process.on
                         }
                     }
                 );
-                process.exit(0);
+                atomic.exitFork(0);
             });
         }
     }  
@@ -56,7 +57,7 @@ process.on
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
 
 process.on("unhandledRejection",function(err : string){
@@ -71,5 +72,5 @@ process.on("unhandledRejection",function(err : string){
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
diff --git a/src/RunAlignmentProcess.ts b/src/RunAlignmentProcess.ts
index eeaa17a90..6ff0fadd7 100644
--- a/src/RunAlignmentProcess.ts
+++ b/src/RunAlignmentProcess.ts
@@ -121,7 +121,7 @@ process.on(
                                                 flags.done = true;
                                                 flags.success = true;
                                                 update();
-                                                process.exit(0);
+                                                atomic.exitFork(0);
 
                                             });
                                         });
diff --git a/src/SaveCurrentProjectProcess.ts b/src/SaveCurrentProjectProcess.ts
index 9ecd83ca4..71127d7cf 100644
--- a/src/SaveCurrentProjectProcess.ts
+++ b/src/SaveCurrentProjectProcess.ts
@@ -1,11 +1,11 @@
-import {handleForkFailures} from "./req/operations/atomicOperations";
+import * as atomic from "./req/operations/atomicOperations";
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
 import {ProjectManifest} from "./req/projectManifest";
 import {saveCurrentProject} from "./req//saveCurrentProject";
 
 let proj : ProjectManifest;
 let flags : CompletionFlags = new CompletionFlags();
-handleForkFailures();
+atomic.handleForkFailures();
 process.on
 (
     "message",function(ev : AtomicOperationForkEvent)
@@ -29,7 +29,7 @@ process.on
                         flags : flags,
                     }
                 );
-                process.exit(0);
+                atomic.exitFork(0);
             }).catch((err) => {
                 flags.done = true;
                 flags.failure = true;
@@ -41,7 +41,7 @@ process.on
                         data : err
                     }
                 );
-                process.exit(1);
+                atomic.exitFork(1);
             });
         }
     }  
diff --git a/src/circularGenomeBuilder.html b/src/circularGenomeBuilder.html
index 97b3d23bb..cc8b849fe 100644
--- a/src/circularGenomeBuilder.html
+++ b/src/circularGenomeBuilder.html
@@ -69,6 +69,11 @@ <h5 class="modal-title" id="modalTitle">Modal title</h5>
             					<li><a href="#" id="deleteFigure">Delete Figure</a></li>
           					</ul>
 						</li>
+						<li class="dropdown">
+							<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Figure Options</a>
+							<ul class="dropdown-menu" id="figureOptions">
+							</ul>
+					  </li>
 						<li><a href="#" id="navBarLoadingText"></a></li>
       				</ul>
 					
diff --git a/src/circularGenomeBuilderRenderer.ts b/src/circularGenomeBuilderRenderer.ts
index 5b2ff79a1..bbf150e41 100644
--- a/src/circularGenomeBuilderRenderer.ts
+++ b/src/circularGenomeBuilderRenderer.ts
@@ -156,25 +156,33 @@ $
                                         totalTracks++;
                                         if(ops[i].flags.done && ops[i].flags.success)
                                         {
-                                            console.log("compiled "+ops[i].uuid);
                                             if(ops[i].uuid)
                                             {
+                                                console.log("compiled "+ops[i].uuid);
                                                 tc.removeTrack(ops[i].uuid);
                                                 genomeView.firstRender = true;
                                             }
+                                            else if(ops[i].compileBase)
+                                            {
+                                                console.log("compiled base figure");
+                                                tc.resetBaseFigureSVG();
+                                                genomeView.firstRender = true;
+                                            }
                                         }
                                     }
                                 }
                             }
                             if(totalTracks > 0)
                                 document.getElementById("navBarLoadingText").innerHTML = `Recalculating ${totalTracks} tracks`;
-                            if(totalTracks == 1)
+                            if(totalTracks == 0)
                             {
-                                setTimeout(function(){
-                                    document.getElementById("navBarLoadingText").innerHTML = ``;
-                                },1000);
+                                document.getElementById("navBarLoadingText").innerHTML = ``;
                             }
                         }
+                        else if(arg.val === undefined)
+                        {
+                            document.getElementById("navBarLoadingText").innerHTML = ``;
+                        }
                     }
                 }
                 viewMgr.render();
diff --git a/src/compileTemplatesProcess.ts b/src/compileTemplatesProcess.ts
index e0b58bd60..3abe4b857 100644
--- a/src/compileTemplatesProcess.ts
+++ b/src/compileTemplatesProcess.ts
@@ -81,8 +81,9 @@ function compileAndSend()
         data : {
             figure : figure
         }
+    },function(){
+        process.exit(0);
     });
-    process.exit(0);
 }
 
 process.on(
diff --git a/src/guiTests/req/closeToolBar.ts b/src/guiTests/req/closeToolBar.ts
index b1f8bc01a..ebd89d8af 100644
--- a/src/guiTests/req/closeToolBar.ts
+++ b/src/guiTests/req/closeToolBar.ts
@@ -11,7 +11,6 @@ export async function closeToolBar() : Promise<void>
                 {
                     console.log("Failed to open tool bar!");
                     console.log(toolBar);
-                    //process.exit(1);
                 }
                 toolBar[0].close();
                 resolve();
diff --git a/src/req/operations/CheckForUpdate.ts b/src/req/operations/CheckForUpdate.ts
index 805588187..a63d070b9 100644
--- a/src/req/operations/CheckForUpdate.ts
+++ b/src/req/operations/CheckForUpdate.ts
@@ -23,38 +23,26 @@ export class CheckForUpdate extends atomic.AtomicOperation
         this.closeLogOnSuccess = true;
         this.logRecord = atomic.openLog(this.name,"Check for Update");
         let self = this;
-        this.checkForUpdateProcess = cp.fork(getReadable("CheckForUpdate.js"));
-        this.addPID(this.checkForUpdateProcess.pid);
-        this.checkForUpdateProcess.on(
-            "message",function(ev : AtomicOperationForkEvent)
+        this.checkForUpdateProcess = atomic.makeFork("CheckForUpdate.js",<AtomicOperationForkEvent>{
+            setData : true,
+            data : <AtomicOperationIPC>{}
+        },function(ev : AtomicOperationForkEvent){
+            self.logObject(ev);
+            if(ev.finishedSettingData == true)
             {
-                self.logObject(ev);
-                if(ev.finishedSettingData == true)
-                {
-                    self.checkForUpdateProcess.send(
-                        <AtomicOperationForkEvent>{
-                            run : true
-                        }
-                    );
-                }
-                if(ev.update == true)
-                {
-                    self.extraData = ev.data;
-                    self.flags = ev.flags;
-                    self.update();
-                }
-            }
-        );
-        setTimeout(
-            function(){
                 self.checkForUpdateProcess.send(
                     <AtomicOperationForkEvent>{
-                        setData : true,
-                        data : <AtomicOperationIPC>{
-                        }
+                        run : true
                     }
                 );
-            },500
-        );
+            }
+            if(ev.update == true)
+            {
+                self.extraData = ev.data;
+                self.flags = ev.flags;
+                self.update();
+            }    
+        });
+        this.addPID(this.checkForUpdateProcess.pid);
     }
 }
\ No newline at end of file
diff --git a/src/req/operations/CompileTemplates.ts b/src/req/operations/CompileTemplates.ts
index f78986288..937b94815 100644
--- a/src/req/operations/CompileTemplates.ts
+++ b/src/req/operations/CompileTemplates.ts
@@ -30,42 +30,31 @@ export class CompileTemplates extends atomic.AtomicOperation
     public run() : void
     {
         let self = this;
-        this.compileTemplatesProcess = cp.fork(getReadable("compileTemplates.js"));
-        this.addPID(this.compileTemplatesProcess.pid);
-        self.compileTemplatesProcess.on(
-            "message",function(ev : AtomicOperationForkEvent){
-                if(ev.update == true)
+        this.compileTemplatesProcess = atomic.makeFork("compileTemplates.js",<AtomicOperationForkEvent>{
+            setData : true,
+            data : {
+                figure : self.figure,
+                uuid : self.uuid,
+                compileBase : self.compileBase
+            },
+            name : self.name,
+            description : "Compile Templates For Figure"
+        },function(ev : AtomicOperationForkEvent){
+            if(ev.update == true)
+            {
+                self.flags = ev.flags;
+                if(ev.flags.done)
+                {
+                    self.logRecord = ev.logRecord;
+                    atomic.recordLogRecord(ev.logRecord);
+                }
+                if(ev.flags.success)
                 {
-                    self.flags = ev.flags;
-                    if(ev.flags.done)
-                    {
-                        self.logRecord = ev.logRecord;
-                        atomic.recordLogRecord(ev.logRecord);
-                    }
-                    if(ev.flags.success)
-                    {
-                        self.figure = ev.data.figure;
-                    }
-                    self.update();
+                    self.figure = ev.data.figure;
                 }
+                self.update();
             }
-        );
-
-        setTimeout(
-            function(){
-                self.compileTemplatesProcess.send(
-                    <AtomicOperationForkEvent>{
-                        setData : true,
-                        data : {
-                            figure : self.figure,
-                            uuid : self.uuid,
-                            compileBase : self.compileBase
-                        },
-                        name : self.name,
-                        description : "Compile Templates For Figure"
-                    }
-                );
-            },10
-        );
+        });
+        this.addPID(this.compileTemplatesProcess.pid);
     }
 }
\ No newline at end of file
diff --git a/src/req/operations/DownloadAndInstallUpdate.ts b/src/req/operations/DownloadAndInstallUpdate.ts
index 55fd63b22..0e25bd30f 100644
--- a/src/req/operations/DownloadAndInstallUpdate.ts
+++ b/src/req/operations/DownloadAndInstallUpdate.ts
@@ -19,38 +19,27 @@ export class DownloadAndInstallUpdate extends atomic.AtomicOperation
     {
         this.logRecord = atomic.openLog(this.name,"Download and Install Update");
         let self = this;
-        this.downloadAndInstallUpdateProcess = cp.fork(getReadable("DownloadAndInstallUpdate.js"));
-        this.addPID(this.downloadAndInstallUpdateProcess.pid);
-        this.downloadAndInstallUpdateProcess.on(
-            "message",function(ev : AtomicOperationForkEvent)
-            {
-                if(ev.finishedSettingData == true)
-                {
-                    self.downloadAndInstallUpdateProcess.send(
-                        <AtomicOperationForkEvent>{
-                            run : true
-                        }
-                    );
-                }
-                if(ev.update == true)
-                {
-                    self.extraData = ev.data;
-                    self.flags = ev.flags;
-                    self.update();
-                }
+        this.downloadAndInstallUpdateProcess = atomic.makeFork("DownloadAndInstallUpdate.js",<AtomicOperationForkEvent>{
+            setData : true,
+            data : <AtomicOperationIPC>{
+                asset : self.asset
             }
-        );
-        setTimeout(
-            function(){
+        },function(ev : AtomicOperationForkEvent){
+            if(ev.finishedSettingData == true)
+            {
                 self.downloadAndInstallUpdateProcess.send(
                     <AtomicOperationForkEvent>{
-                        setData : true,
-                        data : <AtomicOperationIPC>{
-                            asset : self.asset
-                        }
+                        run : true
                     }
                 );
-            },500
-        );
+            }
+            if(ev.update == true)
+            {
+                self.extraData = ev.data;
+                self.flags = ev.flags;
+                self.update();
+            }    
+        });
+        this.addPID(this.downloadAndInstallUpdateProcess.pid);
     }
 }
\ No newline at end of file
diff --git a/src/req/operations/InputBamFile.ts b/src/req/operations/InputBamFile.ts
index f30197963..dcfd0aa41 100644
--- a/src/req/operations/InputBamFile.ts
+++ b/src/req/operations/InputBamFile.ts
@@ -22,50 +22,40 @@ export class InputBamFile extends atomic.AtomicOperation
         this.closeLogOnFailure = false;
         this.closeLogOnSuccess = false;
         let self = this;
-        this.inputBamFileProcess = cp.fork(getReadable("InputBamFile.js"));
-        this.addPID(this.inputBamFileProcess.pid);
-        self.inputBamFileProcess.on(
-            "message",function(ev : AtomicOperationForkEvent){
-                if(ev.finishedSettingData == true)
-                {
-                    self.inputBamFileProcess.send(
-                        <AtomicOperationForkEvent>{
-                            run : true
-                        }
-                    );
-                }
-                if(ev.update == true)
-                {
-                    self.flags = ev.flags;
-                    if(ev.flags.done)
-                    {
-                        self.alignData = ev.data.alignData;
-                        if(ev.flags.failure == true && self.alignData)
-                        {
-                            //make sure output dir is deleted on failure
-                            self.destinationArtifactsDirectories.push(getArtifactDir(self.alignData));
-                        }
-                        self.logRecord = ev.logRecord;
-                        atomic.recordLogRecord(ev.logRecord);
-                    }
-                    self.progressMessage = ev.progressMessage;
-                    self.update();
-                }
-            }
-        );
-        setTimeout(
-            function(){
+        this.inputBamFileProcess = atomic.makeFork("InputBamFile.js",<AtomicOperationForkEvent>{
+            setData : true,
+            data : {
+                bamPath : self.bamPath
+            },
+            name : self.name,
+            description : "Input Bam File"
+        },function(ev : AtomicOperationForkEvent){
+            if(ev.finishedSettingData == true)
+            {
                 self.inputBamFileProcess.send(
                     <AtomicOperationForkEvent>{
-                        setData : true,
-                        data : {
-                            bamPath : self.bamPath
-                        },
-                        name : self.name,
-                        description : "Input Bam File"
+                        run : true
                     }
                 );
             }
-        );
+            if(ev.update == true)
+            {
+                self.flags = ev.flags;
+                if(ev.flags.done)
+                {
+                    self.alignData = ev.data.alignData;
+                    if(ev.flags.failure == true && self.alignData)
+                    {
+                        //make sure output dir is deleted on failure
+                        self.destinationArtifactsDirectories.push(getArtifactDir(self.alignData));
+                    }
+                    self.logRecord = ev.logRecord;
+                    atomic.recordLogRecord(ev.logRecord);
+                }
+                self.progressMessage = ev.progressMessage;
+                self.update();
+            }    
+        });
+        this.addPID(this.inputBamFileProcess.pid);
     }
 }
\ No newline at end of file
diff --git a/src/req/operations/InstallUpdate.ts b/src/req/operations/InstallUpdate.ts
index 66dd250a5..08ca92630 100644
--- a/src/req/operations/InstallUpdate.ts
+++ b/src/req/operations/InstallUpdate.ts
@@ -20,20 +20,15 @@ export class InstallUpdate extends atomic.AtomicOperation
         let self = this;
         try
         {
-            this.installUpdateJob = cp.fork(getReadable("installUpdate.js"));
-            this.addPID(this.installUpdateJob.pid);
-            this.installUpdateJob.on
-            (
-                "message",function(data : any)
+            this.installUpdateJob = atomic.makeFork("installUpdate.js",{},function(data : any){
+                if(data.totalFiles)
                 {
-                    if(data.totalFiles)
-                    {
-                        self.filesInUpdate = data.totalFiles;
-                        self.update();
-                        self.setSuccess(self.flags);
-                    }
+                    self.filesInUpdate = data.totalFiles;
+                    self.update();
+                    self.setSuccess(self.flags);
                 }
-            );
+            });
+            this.addPID(this.installUpdateJob.pid);
 
         }
         catch(err)
diff --git a/src/req/operations/LinkRefSeqToAlignment.ts b/src/req/operations/LinkRefSeqToAlignment.ts
index 35221f58d..d2207f5c9 100644
--- a/src/req/operations/LinkRefSeqToAlignment.ts
+++ b/src/req/operations/LinkRefSeqToAlignment.ts
@@ -26,51 +26,41 @@ export class LinkRefSeqToAlignment extends atomic.AtomicOperation
         this.closeLogOnFailure = false;
         this.closeLogOnSuccess = false;
         let self = this;
-        this.linkRefSeqToAlignmentProcess = cp.fork(getReadable("LinkRefSeqToAlignment.js"));
-        this.addPID(this.linkRefSeqToAlignmentProcess.pid);
-        self.linkRefSeqToAlignmentProcess.on(
-            "message",function(ev : AtomicOperationForkEvent){
-                if(ev.finishedSettingData == true)
+        this.linkRefSeqToAlignmentProcess = atomic.makeFork("LinkRefSeqToAlignment.js",<AtomicOperationForkEvent>{
+            setData : true,
+            data : {
+                align : self.alignData,
+                fasta : self.fasta
+            },
+            name : self.name,
+            description : "Link Ref Seq To Alignment"
+        },function(ev : AtomicOperationForkEvent){
+            if(ev.finishedSettingData == true)
+            {
+                self.linkRefSeqToAlignmentProcess.send(
+                    <AtomicOperationForkEvent>{
+                        run : true
+                    }
+                );
+            }
+            if(ev.update == true)
+            {
+                self.flags = ev.flags;
+                if(ev.flags.success == true)
                 {
-                    self.linkRefSeqToAlignmentProcess.send(
-                        <AtomicOperationForkEvent>{
-                            run : true
-                        }
-                    );
+                    self.alignData = ev.data.alignData;
                 }
-                if(ev.update == true)
+                if(ev.flags.done)
                 {
-                    self.flags = ev.flags;
-                    if(ev.flags.success == true)
-                    {
-                        self.alignData = ev.data.alignData;
-                    }
-                    if(ev.flags.done)
-                    {
-                        self.logRecord = ev.logRecord;
-                        atomic.recordLogRecord(ev.logRecord);
-                    }
-                    self.step = ev.step;
-                    self.progressMessage = ev.progressMessage;
-                    console.log(self.step+" "+self.progressMessage);
-                    self.update();
+                    self.logRecord = ev.logRecord;
+                    atomic.recordLogRecord(ev.logRecord);
                 }
+                self.step = ev.step;
+                self.progressMessage = ev.progressMessage;
+                console.log(self.step+" "+self.progressMessage);
+                self.update();
             }
-        );
-        setTimeout(
-            function(){
-                self.linkRefSeqToAlignmentProcess.send(
-                    <AtomicOperationForkEvent>{
-                        setData : true,
-                        data : {
-                            align : self.alignData,
-                            fasta : self.fasta
-                        },
-                        name : self.name,
-                        description : "Link Ref Seq To Alignment"
-                    }
-                );
-            },500
-        );
+        });
+        this.addPID(this.linkRefSeqToAlignmentProcess.pid);
     }
 }
\ No newline at end of file
diff --git a/src/req/operations/OpenProject.ts b/src/req/operations/OpenProject.ts
index fbb3c783e..15f629071 100644
--- a/src/req/operations/OpenProject.ts
+++ b/src/req/operations/OpenProject.ts
@@ -27,49 +27,37 @@ export class OpenProject extends atomic.AtomicOperation
     {
         this.logRecord = atomic.openLog(this.name,"Open Project");
         let self = this;
-        this.openProjectProcess = cp.fork(getReadable("OpenProject.js"));
-        this.addPID(this.openProjectProcess.pid);
-        self.openProjectProcess.on(
-            "message",function(ev : AtomicOperationForkEvent)
+        this.openProjectProcess = atomic.makeFork("OpenProject.js",<AtomicOperationForkEvent>{
+            setData : true,
+            data : {
+                proj : self.proj,
+                externalProjectPath : self.externalProjectPath
+            },
+            readableBasePath : getReadable(""),
+            writableBasePath : getWritable(""),
+            readableAndWritableBasePath : getReadableAndWritable("")
+
+        },function(ev : AtomicOperationForkEvent){
+            self.logObject(ev);
+            if(ev.finishedSettingData == true)
             {
-                self.logObject(ev);
-                if(ev.finishedSettingData == true)
-                {
-                    self.openProjectProcess.send(
-                        <AtomicOperationForkEvent>{
-                            run : true
-                        }
-                    );
-                }
-                if(ev.update == true)
-                {
-                    self.extraData = ev.data;
-                    self.flags = ev.flags;
-                    if(ev.flags.success == true)
-                    {
-                        self.setSuccess(self.flags);
-                    }
-                    self.update();
-                }
-            }
-        );
-        setTimeout(
-            function(){
                 self.openProjectProcess.send(
                     <AtomicOperationForkEvent>{
-                        setData : true,
-                        data : {
-                            proj : self.proj,
-                            externalProjectPath : self.externalProjectPath
-                        },
-                        readableBasePath : getReadable(""),
-                        writableBasePath : getWritable(""),
-                        readableAndWritableBasePath : getReadableAndWritable("")
-
+                        run : true
                     }
                 );
-            },10
-        );
-
+            }
+            if(ev.update == true)
+            {
+                self.extraData = ev.data;
+                self.flags = ev.flags;
+                if(ev.flags.success == true)
+                {
+                    self.setSuccess(self.flags);
+                }
+                self.update();
+            }
+        });
+        this.addPID(this.openProjectProcess.pid);
     }
 }
\ No newline at end of file
diff --git a/src/req/operations/RenderCoverageTrack.ts b/src/req/operations/RenderCoverageTrack.ts
index cead8cdff..f2129b422 100644
--- a/src/req/operations/RenderCoverageTrack.ts
+++ b/src/req/operations/RenderCoverageTrack.ts
@@ -34,9 +34,40 @@ export class RenderCoverageTrackForContig extends atomic.AtomicOperation
     {
         this.logRecord = atomic.openLog(this.name,"Render Coverage Track");
         let self = this;
-        this.renderCoverageTrackProcess = cp.fork(getReadable("RenderCoverageTrack.js"));
+        this.renderCoverageTrackProcess = atomic.makeFork("RenderCoverageTrack.js",<AtomicOperationForkEvent>{
+            setData : true,
+            data : {
+                alignData : self.alignData,
+                contiguuid : self.contiguuid,
+                circularFigure : self.circularFigure,
+                colour : self.colour
+            }
+        },function(ev : AtomicOperationForkEvent){
+            if(ev.finishedSettingData == true)
+            {
+                self.renderCoverageTrackProcess.send(
+                    <AtomicOperationForkEvent>{
+                        run : true
+                    }
+                );
+            }
+
+            if(ev.update == true)
+            {
+                self.extraData = ev.data;
+                self.flags = ev.flags;
+                if(ev.flags.success == true)
+                {
+                    self.circularFigure = ev.data.circularFigure;
+                    self.contiguuid = ev.data.contiguuid;
+                    self.alignData = ev.data.alignData;
+                    self.colour = ev.data.colour;
+                }
+                self.update();
+            }
+        });
         this.addPID(this.renderCoverageTrackProcess.pid);
-        self.renderCoverageTrackProcess.on(
+        /*self.renderCoverageTrackProcess.on(
             "message",function(ev : AtomicOperationForkEvent)
             {
                 if(ev.finishedSettingData == true)
@@ -77,6 +108,6 @@ export class RenderCoverageTrackForContig extends atomic.AtomicOperation
                     }
                 );
             },500
-        );
+        );*/
     }
 }
\ No newline at end of file
diff --git a/src/req/operations/RenderSNPTrack.ts b/src/req/operations/RenderSNPTrack.ts
index 37770660b..7de0fb258 100644
--- a/src/req/operations/RenderSNPTrack.ts
+++ b/src/req/operations/RenderSNPTrack.ts
@@ -34,48 +34,37 @@ export class RenderSNPTrackForContig extends atomic.AtomicOperation
     {
         this.logRecord = atomic.openLog(this.name,"Render SNP Track");
         let self = this;
-        this.renderSNPTrackProcess = cp.fork(getReadable("RenderSNPTrack.js"));
-        this.addPID(this.renderSNPTrackProcess.pid);
-        self.renderSNPTrackProcess.on(
-            "message",function(ev : AtomicOperationForkEvent)
-            {
-                if(ev.finishedSettingData == true)
-                {
-                    self.renderSNPTrackProcess.send(
-                        <AtomicOperationForkEvent>{
-                            run : true
-                        }
-                    );
-                }
-                if(ev.update == true)
-                {
-                    self.extraData = ev.data;
-                    self.flags = ev.flags;
-                    if(ev.flags.success == true)
-                    {
-                        self.circularFigure = ev.data.circularFigure;
-                        self.contiguuid = ev.data.contiguuid;
-                        self.alignData = ev.data.alignData;
-                        self.colour = ev.data.colour;
-                    }
-                    self.update();
-                }
+        this.renderSNPTrackProcess = atomic.makeFork("RenderSNPTrack.js",<AtomicOperationForkEvent>{
+            setData : true,
+            data : {
+                alignData : self.alignData,
+                contiguuid : self.contiguuid,
+                circularFigure : self.circularFigure,
+                colour : self.colour
             }
-        );
-        setTimeout(
-            function(){
+        },function(ev : AtomicOperationForkEvent){
+            if(ev.finishedSettingData == true)
+            {
                 self.renderSNPTrackProcess.send(
                     <AtomicOperationForkEvent>{
-                        setData : true,
-                        data : {
-                            alignData : self.alignData,
-                            contiguuid : self.contiguuid,
-                            circularFigure : self.circularFigure,
-                            colour : self.colour
-                        }
+                        run : true
                     }
                 );
-            },500
-        );
+            }
+            if(ev.update == true)
+            {
+                self.extraData = ev.data;
+                self.flags = ev.flags;
+                if(ev.flags.success == true)
+                {
+                    self.circularFigure = ev.data.circularFigure;
+                    self.contiguuid = ev.data.contiguuid;
+                    self.alignData = ev.data.alignData;
+                    self.colour = ev.data.colour;
+                }
+                self.update();
+            }
+        });
+        this.addPID(this.renderSNPTrackProcess.pid);
     }
 }
\ No newline at end of file
diff --git a/src/req/operations/RunAlignment.ts b/src/req/operations/RunAlignment.ts
index 9f3061cd5..f421e3b3d 100644
--- a/src/req/operations/RunAlignment.ts
+++ b/src/req/operations/RunAlignment.ts
@@ -43,55 +43,45 @@ export class RunAlignment extends atomic.AtomicOperation
         this.closeLogOnFailure = false;
         this.closeLogOnSuccess = false;
         let self = this;
-        this.runAlignmentProcess = cp.fork(getReadable("RunAlignment.js"));
-        this.addPID(this.runAlignmentProcess.pid);
-        self.runAlignmentProcess.on(
-            "message",function(ev : AtomicOperationForkEvent){
-                if(ev.finishedSettingData == true)
-                {
-                    self.runAlignmentProcess.send(
-                        <AtomicOperationForkEvent>{
-                            run : true
-                        }
-                    );
-                }
-                if(ev.pid)
+        this.runAlignmentProcess = atomic.makeFork("RunAlignment.js",<AtomicOperationForkEvent>{
+            setData : true,
+            data : {
+                alignData : self.alignData
+            },
+            name : self.name,
+            description : "Run Alignment"
+        },function(ev : AtomicOperationForkEvent){
+            if(ev.finishedSettingData == true)
+            {
+                self.runAlignmentProcess.send(
+                    <AtomicOperationForkEvent>{
+                        run : true
+                    }
+                );
+            }
+            if(ev.pid)
+            {
+                self.addPID(ev.pid);
+                console.log(ev.pid);
+            }
+            if(ev.update == true)
+            {
+                self.flags = ev.flags;
+                if(ev.flags.success == true)
                 {
-                    self.addPID(ev.pid);
-                    console.log(ev.pid);
+                    self.alignData = ev.data.alignData;
                 }
-                if(ev.update == true)
+                if(ev.flags.done)
                 {
-                    self.flags = ev.flags;
-                    if(ev.flags.success == true)
-                    {
-                        self.alignData = ev.data.alignData;
-                    }
-                    if(ev.flags.done)
-                    {
-                        self.logRecord = ev.logRecord;
-                        atomic.recordLogRecord(ev.logRecord);
-                    }
-                    self.step = ev.step;
-                    self.progressMessage = ev.progressMessage;
-                    console.log(self.step+" "+self.progressMessage);
-                    self.update();
+                    self.logRecord = ev.logRecord;
+                    atomic.recordLogRecord(ev.logRecord);
                 }
+                self.step = ev.step;
+                self.progressMessage = ev.progressMessage;
+                console.log(self.step+" "+self.progressMessage);
+                self.update();
             }
-        );
-        setTimeout(
-            function(){
-                self.runAlignmentProcess.send(
-                    <AtomicOperationForkEvent>{
-                        setData : true,
-                        data : {
-                            alignData : self.alignData
-                        },
-                        name : self.name,
-                        description : "Run Alignment"
-                    }
-                );
-            },500
-        );
+        });
+        this.addPID(this.runAlignmentProcess.pid);
     }
 }
\ No newline at end of file
diff --git a/src/req/operations/SaveCurrentProject.ts b/src/req/operations/SaveCurrentProject.ts
index 261a671c1..f7f2ca32c 100644
--- a/src/req/operations/SaveCurrentProject.ts
+++ b/src/req/operations/SaveCurrentProject.ts
@@ -21,42 +21,30 @@ export class SaveCurrentProject extends atomic.AtomicOperation
     {
         this.logRecord = atomic.openLog(this.name,"Save Current Project");
         let self = this;
-        this.saveCurrentProjectProcess = cp.fork(getReadable("SaveCurrentProject.js"));
-        this.addPID(this.saveCurrentProjectProcess.pid);
-        self.saveCurrentProjectProcess.on(
-            "message",function(ev : AtomicOperationForkEvent)
+        this.saveCurrentProjectProcess = atomic.makeFork("SaveCurrentProject.js",<AtomicOperationForkEvent>{
+            setData : true,
+            data : self.proj
+        },function(ev : AtomicOperationForkEvent){
+            self.logObject(ev);
+            if(ev.finishedSettingData == true)
             {
-                self.logObject(ev);
-                if(ev.finishedSettingData == true)
-                {
-                    self.saveCurrentProjectProcess.send(
-                        <AtomicOperationForkEvent>{
-                            run : true
-                        }
-                    );
-                }
-                if(ev.update == true)
-                {
-                    self.extraData = ev.data;
-                    self.flags = ev.flags;
-                    if(ev.flags.success == true)
-                    {
-                        self.setSuccess(self.flags);
-                    }
-                    self.update();
-                }
-            }
-        );
-        setTimeout(
-            function(){
                 self.saveCurrentProjectProcess.send(
                     <AtomicOperationForkEvent>{
-                        setData : true,
-                        data : self.proj
+                        run : true
                     }
                 );
-            },500
-        );
-
+            }
+            if(ev.update == true)
+            {
+                self.extraData = ev.data;
+                self.flags = ev.flags;
+                if(ev.flags.success == true)
+                {
+                    self.setSuccess(self.flags);
+                }
+                self.update();
+            }
+        });
+        this.addPID(this.saveCurrentProjectProcess.pid);
     }
 }
\ No newline at end of file
diff --git a/src/req/operations/atomicOperations.ts b/src/req/operations/atomicOperations.ts
index 1d3641ad8..a9742b64d 100644
--- a/src/req/operations/atomicOperations.ts
+++ b/src/req/operations/atomicOperations.ts
@@ -1,6 +1,7 @@
 import {EventEmitter} from "events";
 import * as fs from "fs";
 import * as readline from "readline";
+import * as cp from "child_process";
 
 const uuidv4 : () => string = require("uuid/v4");
 import * as rimraf from "rimraf";
@@ -8,7 +9,7 @@ import * as mkdirp from "mkdirp";
 
 import {AtomicOperationForkEvent} from "./../atomicOperationsIPC";
 import {SpawnRequestParams} from "./../JobIPC";
-import {getReadableAndWritable} from "./../getAppPath";
+import {getReadableAndWritable,getReadable} from "./../getAppPath";
 
 /**
  * Class representing some operation which should be run atomically
@@ -294,7 +295,7 @@ export abstract class AtomicOperation
      */
     public logObject(obj : any) : void
     {
-        logString(this.logRecord,JSON.stringify(obj));
+        logString(this.logRecord,JSON.stringify(obj,undefined,4));
     }
 }
 
@@ -315,6 +316,62 @@ export class ForkLogger extends AtomicOperation
     public run(){}
 }
 
+
+/**
+ * Forks target, passing data and piping stdout/stderr to console.
+ * Calls cb on messages from the forked ChildProcess
+ * 
+ * @export
+ * @param {string} target 
+ * @param {*} data 
+ * @param {(ev : any) => void} cb 
+ * @returns {cp.ChildProcess} 
+ */
+export function makeFork(target : string,data : any,cb : (ev : any) => void) : cp.ChildProcess
+{
+    let res = cp.fork(
+        getReadable(target),[],<cp.ForkOptions>{
+            silent : true
+        }
+    );
+
+    res.stdout.on("data",function(data : Buffer){
+        console.log(data.toString());
+    });
+
+    res.stderr.on("data",function(data : Buffer){
+        console.error(data.toString());
+    });
+
+    res.on("message",function(ev : any){
+        cb(ev);
+    });
+
+    res.on("exit",function(code : number){
+        console.log(`${target} exited with ${code}`);
+    });
+
+    setTimeout(
+        function(){
+            res.send(data);
+        },10
+    );
+
+    return res;
+}
+
+/**
+ * Disconnects IPC channel and triggers a process exit of retCode
+ * 
+ * @export
+ * @param {number} retCode 
+ */
+export function exitFork(retCode : number) : void
+{
+    process.disconnect();
+    process.exitCode = retCode;
+}
+
 /**
  * Registers traps for unhandled errors in the current process. Logs exception details and stack traces
  * using the provided logger
@@ -345,7 +402,7 @@ export function handleForkFailures(logger? : ForkLogger,progressMessage? : strin
         }
 
         process.send(failureObj);
-        process.exit(1);
+        exitFork(1);
 
     };
     (process as NodeJS.EventEmitter).on("uncaughtException",function(err : Error){
diff --git a/src/req/renderer/circularFigure.ts b/src/req/renderer/circularFigure.ts
index 7ab4ba320..332595e40 100644
--- a/src/req/renderer/circularFigure.ts
+++ b/src/req/renderer/circularFigure.ts
@@ -174,6 +174,8 @@ export class CircularFigure
     public radius : number;
     public height : number;
     public width : number;
+    public isInteractive : boolean;
+    public showContigNames : boolean;
     public circularFigureBPTrackOptions : CircularFigureBPTrackOptions;
     public renderedCoverageTracks : Array<RenderedCoverageTrackRecord>;
     public renderedSNPTracks : Array<RenderedSNPTrackRecord>;
@@ -203,6 +205,18 @@ export class CircularFigure
             this.contigs[1].loaded = true;
         }
         this.customContigs = new Array<Contig>();
+        this.isInteractive = true;
+        this.showContigNames = true;
+        let totalBP = 0;
+        for(let i = 0; i != this.contigs.length; ++i)
+        {
+            totalBP += this.contigs[i].bp;
+        }
+        if(this.contigs.length >= 50 || totalBP >= 1000000)
+        {
+            this.isInteractive = false;
+            this.showContigNames = false;
+        }
         cacheBaseFigure(this);
     }
 }
@@ -232,7 +246,7 @@ export abstract class FigureCanvas
  * @param {number} [end=-1] 
  * @returns {string} 
  */
-export function renderContig(contig : Contig,start : number = -1,end : number = -1) : string
+export function renderContig(figure : CircularFigure,contig : Contig,start : number = -1,end : number = -1) : string
 {
     if(start == -1)
         start = contig.start;
@@ -247,12 +261,13 @@ export function renderContig(contig : Contig,start : number = -1,end : number =
             vAdjust : contig.vAdjust,
             markerStyle : `fill:${contig.color};opacity:${contig.opacity};`,
             uuid : contig.uuid,
-            onClick : "markerOnClick"
+            onClick : "markerOnClick",
+            isInteractive : figure.isInteractive
         })}
             ${markerLabel.add(
             {
                 type : "path",
-                text : contig.alias,
+                text : figure.showContigNames ?  contig.alias : "",
                 labelStyle : `fill:${contig.fontFill};opacity:${contig.opacity};`
             })}
             ${markerLabel.end()}
@@ -280,7 +295,8 @@ export function renderBaseFigure(figure : CircularFigure) : string
             {
                 text : figure.name,
                 labelStyle : "font-size:20px;font-weight:400",
-                onClick : "figureNameOnClick"
+                onClick : "figureNameOnClick",
+                isInteractive : figure.isInteractive
             })}
             ${trackLabel.end()}
             ${(()=>
@@ -289,12 +305,12 @@ export function renderBaseFigure(figure : CircularFigure) : string
                 let lastLocation = 0;
                 for(let i = 0; i != figure.contigs.length; ++i)
                 {
-                    res += renderContig(figure.contigs[i],lastLocation,lastLocation+figure.contigs[i].bp);
+                    res += renderContig(figure,figure.contigs[i],lastLocation,lastLocation+figure.contigs[i].bp);
                     lastLocation = lastLocation + figure.contigs[i].bp;
                 }
                 for(let i = 0; i != figure.customContigs.length; ++i)
                 {
-                    res += renderContig(figure.customContigs[i],figure.customContigs[i].start,figure.customContigs[i].end);
+                    res += renderContig(figure,figure.customContigs[i],figure.customContigs[i].start,figure.customContigs[i].end);
                 }
                 return res; 
             })()}
@@ -363,6 +379,20 @@ export function getBaseFigureSVGFromCache(figure : CircularFigure) : string
     return (<any>fs.readFileSync(getReadableAndWritable(`rt/circularFigures/${figure.uuid}/baseFigure.svg`)));
 }
 
+/**
+ * Deletes the contents of the current disk SVG cache for the base figure of figure
+ * 
+ * @export
+ * @param {CircularFigure} figure 
+ */
+export function deleteBaseFigureSVGFromCache(figure : CircularFigure) : void
+{
+    try
+    {
+        fs.unlinkSync(getReadableAndWritable(`rt/circularFigures/${figure.uuid}/baseFigure.svg`));
+    }
+    catch(err){}
+}
 
 /**
  * Returns the distance from the begginning of the figure to the begginning of the contig specified by contiguuid
diff --git a/src/req/renderer/circularGenome/trackLabel.ts b/src/req/renderer/circularGenome/trackLabel.ts
index 7fc835a0e..26ca38c17 100644
--- a/src/req/renderer/circularGenome/trackLabel.ts
+++ b/src/req/renderer/circularGenome/trackLabel.ts
@@ -1,15 +1,16 @@
 export function add(
-    options? : {
+    options : {
         text? : string,
         labelStyle? : string,
         vAdjust? : string,
         wAdjust? : string,
-        onClick? : string
+        onClick? : string,
+        isInteractive : boolean
     }
 ) : string
 {
     let res = `
-        <tracklabel class="trackLabelHover" ${(()=>{return options.onClick ? `ng-click="${options.onClick}()"` : "";})()} ${
+        <tracklabel ${options.isInteractive ?  `class="trackLabelHover" ${(()=>{return options.onClick ? `ng-click="${options.onClick}()"` : "";})()}` : ""} ${
             (
                 ()=>
                 {
diff --git a/src/req/renderer/circularGenome/trackMarker.ts b/src/req/renderer/circularGenome/trackMarker.ts
index c17d0fa68..5e80f0a45 100644
--- a/src/req/renderer/circularGenome/trackMarker.ts
+++ b/src/req/renderer/circularGenome/trackMarker.ts
@@ -1,5 +1,5 @@
 export function add(
-    options? : {
+    options : {
         start? : string,
         end? : string,
         markerStyle? : string,
@@ -9,13 +9,14 @@ export function add(
         vAdjust? : number,
         wAdjust? : string,
         uuid? : string,
-        onClick? : string
+        onClick? : string,
+        isInteractive : boolean
     }
 ) : string
 {
     let res = `
         <trackmarker 
-        markerclass="trackMarkerHover" markerclick="${options.onClick}($event,$marker,'${options.uuid}')" ${
+        ${options.isInteractive ? `markerclass="trackMarkerHover"` : ""} markerclick="${options.onClick}($event,$marker,'${options.uuid}')" ${
             (
                 ()=>
                 {
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/centreFigure.ts b/src/req/renderer/circularGenomeBuilderRenderer/centreFigure.ts
index 970389c81..6dcfd994d 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/centreFigure.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/centreFigure.ts
@@ -1,4 +1,11 @@
 import * as cf from "./../circularFigure";
+/**
+ * Center div based on the dimensions of figure and the window
+ * 
+ * @export
+ * @param {HTMLElement} div 
+ * @param {cf.CircularFigure} figure 
+ */
 export function centreFigure(div : HTMLElement,figure : cf.CircularFigure) : void
 {
     if(div)
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/displayFigure.ts b/src/req/renderer/circularGenomeBuilderRenderer/displayFigure.ts
index 445903e3e..a78452163 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/displayFigure.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/displayFigure.ts
@@ -7,7 +7,54 @@ import * as viewMgr from "./../viewMgr";
 import * as masterView from "./masterView";
 import {GenomeView} from "./genomeView";
 import {centreFigure} from "./centreFigure";
+/**
+ * Displays the currently set figure
+ * 
+ * @export
+ * @param {GenomeView} self 
+ * @returns {Promise<void>} 
+ */
 export async function displayFigure(self : GenomeView) : Promise<void>
+{
+    if(!self.genome.isInteractive)
+        return await displayNonInteractiveFigure(self);
+    else
+        return await displayInteractiveFigure(self);
+
+}
+/**
+ * Renders a figure as a non-interactive SVG using the specified canvas
+ * 
+ * @export
+ * @param {GenomeView} self 
+ * @returns {Promise<void>} 
+ */
+export async function displayNonInteractiveFigure(self : GenomeView) : Promise<void>
+{
+    return new Promise<void>((resolve,reject) => {
+        tc.refreshCache(self.genome);
+        removeDiv(self);
+
+        let $div : any = $(`
+            <div id="${self.div}">
+                ${getSelectedDataTrackSVGsFromCache(self)}
+                ${tc.baseFigureSVG ? tc.baseFigureSVG : ""}
+            </div>
+        `);
+
+        $(document.body).append($div);
+        centreFigure(document.getElementById(self.div),self.genome);
+        resolve();
+    });
+}
+/**
+ * Renders a figure as interactive using Angular bindings using the specified canvas
+ * 
+ * @export
+ * @param {GenomeView} self 
+ * @returns {Promise<void>} 
+ */
+export async function displayInteractiveFigure(self : GenomeView) : Promise<void>
 {
     //This is an unholy mess adapted from the example given inline in the
     //angular source code https://github.com/angular/angular.js/blob/master/src/auto/injector.js
@@ -25,19 +72,8 @@ export async function displayFigure(self : GenomeView) : Promise<void>
             return new Promise<void>((resolve,reject) => {
                 setImmediate(function(){
                     setImmediate(function(){
-                        try
-                        {
-                            document.body.removeChild(document.getElementById("controls"));
-                        }
-                        catch(err){}
-                        try
-                        {
-                            //Remove the div this view is bound to
-                            document.body.removeChild(document.getElementById(self.div));
-                        }
-                        catch(err){}
-                        $("#"+self.div).remove();
-
+                        
+                        removeDiv(self);
         
                         for(let i = 0; i != self.genome.contigs.length; ++i)
                         {
@@ -68,39 +104,11 @@ export async function displayFigure(self : GenomeView) : Promise<void>
                             $div = $(`
                                 <div id="${self.div}">
                                     
-                                        ${(()=>{
-                                            let res = "";
-                                            for(let i = 0; i != self.genome.renderedCoverageTracks.length; ++i)
-                                            {
-                                                if(self.genome.renderedCoverageTracks[i].checked)
-                                                {
-                                                    try
-                                                    {
-                                                        res += `<div style="position:absolute;z-index:-99;">`;
-                                                        res += tc.getCachedCoverageTrack(self.genome.renderedCoverageTracks[i]);
-                                                        res += `</div>`;
-                                                    }
-                                                    catch(err){}
-                                                }
-                                            }
-                                            for(let i = 0; i != self.genome.renderedSNPTracks.length; ++i)
-                                            {
-                                                if(self.genome.renderedSNPTracks[i].checked)
-                                                {
-                                                    try
-                                                    {
-                                                        res += `<div style="position:absolute;z-index:-99;">`;
-                                                        res += tc.getCachedSNPTrack(self.genome.renderedSNPTracks[i]);
-                                                        res += `</div>`;
-                                                    }
-                                                    catch(err){}
-                                                }
-                                            }
-                                            return res;
-                                        })()}
-                                        <div id="toCompile">
-                                            ${templates}
-                                        </div>
+                                    ${getSelectedDataTrackSVGsFromCache(self)}
+
+                                    <div id="toCompile">
+                                        ${templates}
+                                    </div>
                                 </div>
                             `);
                             $(document.body).append($div);
@@ -151,4 +159,65 @@ export async function displayFigure(self : GenomeView) : Promise<void>
             });
         });
     });
+}
+
+/**
+ * Delete the div used by self for rendering
+ * 
+ * @export
+ * @param {GenomeView} self 
+ */
+export function removeDiv(self : GenomeView) : void
+{
+    try
+    {
+        document.body.removeChild(document.getElementById("controls"));
+    }
+    catch(err){}
+    try
+    {
+        //Remove the div this view is bound to
+        document.body.removeChild(document.getElementById(self.div));
+    }
+    catch(err){}
+    $("#"+self.div).remove();
+}
+
+/**
+ * Returns SVGs for all selected tracks, wrapped in divs ready for rendering
+ * 
+ * @export
+ * @param {GenomeView} self 
+ * @returns {string} 
+ */
+export function getSelectedDataTrackSVGsFromCache(self : GenomeView) : string
+{
+    let res = "";
+    for(let i = 0; i != self.genome.renderedCoverageTracks.length; ++i)
+    {
+        if(self.genome.renderedCoverageTracks[i].checked)
+        {
+            try
+            {
+                res += `<div style="position:absolute;z-index:-99;">`;
+                res += tc.getCachedCoverageTrack(self.genome.renderedCoverageTracks[i]);
+                res += `</div>`;
+            }
+            catch(err){}
+        }
+    }
+    for(let i = 0; i != self.genome.renderedSNPTracks.length; ++i)
+    {
+        if(self.genome.renderedSNPTracks[i].checked)
+        {
+            try
+            {
+                res += `<div style="position:absolute;z-index:-99;">`;
+                res += tc.getCachedSNPTrack(self.genome.renderedSNPTracks[i]);
+                res += `</div>`;
+            }
+            catch(err){}
+        }
+    }
+    return res;
 }
\ No newline at end of file
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/exportToSVG.ts b/src/req/renderer/circularGenomeBuilderRenderer/exportToSVG.ts
index 9ff6ac433..452de661f 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/exportToSVG.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/exportToSVG.ts
@@ -2,6 +2,15 @@ import * as fs from "fs";
 
 import {GenomeView} from "./genomeView";
 import * as cf from "./../circularFigure";
+/**
+ * Writes the SVG to fileName. Allows DOM updates to interleave execution
+ * 
+ * @export
+ * @param {GenomeView} self 
+ * @param {string} fileName 
+ * @param {string} svg 
+ * @returns {Promise<void>} 
+ */
 export async function writeSVG(self : GenomeView,fileName : string,svg : string) : Promise<void>
 {
     return new Promise<void>((resolve,reject) => {
@@ -20,6 +29,13 @@ export async function writeSVG(self : GenomeView,fileName : string,svg : string)
     });
 }
 
+/**
+ * Serializes the canvas div. Allows DOM updates to interleave execution
+ * 
+ * @export
+ * @param {GenomeView} self 
+ * @returns {Promise<string>} 
+ */
 export async function serializeFigure(self : GenomeView) : Promise<string>
 {
     return new Promise<string>((resolve,reject) => {
@@ -47,6 +63,13 @@ export async function serializeFigure(self : GenomeView) : Promise<string>
     valid SVG. Here, we pass all of the raw templates needed for the current figure to angular to compile into
     one single SVG that is ready for serialization.
 */
+/**
+ * JIT compiles the entire figure into one SVG, ignoring all precompiled SVGS. Allows DOM updates to interleave execution
+ * 
+ * @export
+ * @param {GenomeView} self 
+ * @returns {Promise<void>} 
+ */
 export async function renderSVG(self : GenomeView) : Promise<void>
 {
     return new Promise<void>((resolve,reject) => {
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/genomeView.ts b/src/req/renderer/circularGenomeBuilderRenderer/genomeView.ts
index 25e125502..70b736063 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/genomeView.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/genomeView.ts
@@ -16,17 +16,51 @@ import {displayFigure} from "./displayFigure";
 import {centreFigure} from "./centreFigure";
 import {writeLoadingModal} from "./writeLoadingModal";
 import {setSelectedContigByUUID} from "./writeContigEditorModal";
+import {reCacheBaseFigure} from "./reCacheBaseFigure";
+import * as tc from "./templateCache";
 
 import {writeSVG,serializeFigure,renderSVG} from "./exportToSVG";
 
 require("angular");
 require("@chgibb/angularplasmid");
 let app : any = angular.module('myApp',['angularplasmid']);
+/**
+ * Manages the display and behaviour of the figure being edited
+ * 
+ * @export
+ * @class GenomeView
+ * @extends {viewMgr.View}
+ * @implements {cf.FigureCanvas}
+ */
 export class GenomeView extends viewMgr.View implements cf.FigureCanvas
 {
+    /**
+     * The current figure being displayed
+     * 
+     * @type {cf.CircularFigure}
+     * @memberof GenomeView
+     */
     public genome : cf.CircularFigure;
+    /**
+     * Reconstruct the figure using cached data
+     * 
+     * @type {boolean}
+     * @memberof GenomeView
+     */
     public firstRender : boolean;
+    /**
+     * Aligns for this figure
+     * 
+     * @type {Array<AlignData>}
+     * @memberof GenomeView
+     */
     public alignData : Array<AlignData>;
+    /**
+     * Bound Angular scope for genome
+     * 
+     * @type {*}
+     * @memberof GenomeView
+     */
     public scope : any;
     public constructor(name : string,div : string)
     {
@@ -35,8 +69,17 @@ export class GenomeView extends viewMgr.View implements cf.FigureCanvas
     }
     public onMount() : void{}
     public onUnMount() : void{}
+    /**
+     * Update the Angular scope for genome
+     * 
+     * @param {cf.FigureCanvas} [scope] 
+     * @returns {void} 
+     * @memberof GenomeView
+     */
     public updateScope(scope? : cf.FigureCanvas) : void
     {
+        if(!this.genome.isInteractive)
+            return;
         if(scope)
             this.scope = scope;
         this.scope.genome = this.genome;
@@ -51,6 +94,11 @@ export class GenomeView extends viewMgr.View implements cf.FigureCanvas
         this.scope.div = this.div;
     }
     
+    /**
+     * Export genome to SVG
+     * 
+     * @memberof GenomeView
+     */
     public exportSVG()
     {   
         let self = this;
@@ -96,6 +144,14 @@ export class GenomeView extends viewMgr.View implements cf.FigureCanvas
             }
         );
     }
+    /**
+     * Called when a trackMarker is clicked by the user
+     * 
+     * @param {*} $event 
+     * @param {*} $marker 
+     * @param {string} uuid 
+     * @memberof GenomeView
+     */
     public markerOnClick($event : any,$marker : any,uuid : string) : void
     {
         let masterView = <masterView.View>viewMgr.getViewByName("masterView");
@@ -104,6 +160,11 @@ export class GenomeView extends viewMgr.View implements cf.FigureCanvas
         masterView.showModal();
         viewMgr.render();
     }
+    /**
+     * Called when the name of the figure is clicked by the user
+     * 
+     * @memberof GenomeView
+     */
     public figureNameOnClick() : void
     {
         let self = this;
@@ -116,14 +177,20 @@ export class GenomeView extends viewMgr.View implements cf.FigureCanvas
                 let masterView = <masterView.View>viewMgr.getViewByName("masterView");
                 let genomeView = <GenomeView>viewMgr.getViewByName("genomeView",masterView.views);
 
-                genomeView.firstRender = true;
+                
                 //Save changes
-                masterView.dataChanged();
+                masterView.saveFigureChanges();
                 //Re render
+                genomeView.firstRender = true;
                 viewMgr.render();
             }
         });
     }
+    /**
+     * Should be called when genome.radius changes
+     * 
+     * @memberof GenomeView
+     */
     public inputRadiusOnChange()
     {
         this.genome.height = this.genome.radius*10;
@@ -131,6 +198,11 @@ export class GenomeView extends viewMgr.View implements cf.FigureCanvas
         //Re center figure
         this.postRender();
     }
+    /**
+     * Should be called when the track interval changes
+     * 
+     * @memberof GenomeView
+     */
     public showBPTrackOnChange()
     {
         let masterView = <masterView.View>viewMgr.getViewByName("masterView");
@@ -172,6 +244,11 @@ export class GenomeView extends viewMgr.View implements cf.FigureCanvas
             return " ";
         return undefined;
     }
+    /**
+     * Recenter figure and clean artifacts
+     * 
+     * @memberof GenomeView
+     */
     public postRender() : void
     {
         if(this.genome !== undefined)
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/masterView.ts b/src/req/renderer/circularGenomeBuilderRenderer/masterView.ts
index 9813db1fd..5b40d6ca9 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/masterView.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/masterView.ts
@@ -9,7 +9,8 @@ const dialogs = Dialogs();
 import {SaveKeyEvent} from "./../../ipcEvents";
 import {AtomicOperationIPC} from "./../../atomicOperationsIPC";
 import * as viewMgr from "./../viewMgr";
-import {CircularFigure,} from "./../circularFigure";
+import {CircularFigure} from "./../circularFigure";
+import {reCacheBaseFigure} from "./reCacheBaseFigure";
 import {Fasta} from "./../../fasta";
 import {AlignData} from "./../../alignData";
 
@@ -20,6 +21,7 @@ import {writeAlignsModal} from "./writeAlignsModal";
 import {writeAvailableTracksModal} from "./writeAvailableTracksModal";
 import {writeContigEditorModal} from "./writeContigEditorModal";
 import {writeContigCreatorModal} from "./writeContigCreatorModal";
+import {writeEditContigsModal} from "./writeEditContigsModal";
 import {writeLoadingModal} from "./writeLoadingModal";
 
 
@@ -32,6 +34,13 @@ export function addView(arr : Array<viewMgr.View>,div : string)
 {
     arr.push(new View(div));
 }
+/**
+ * Manages the display and the behaviour of the figure editor
+ * 
+ * @export
+ * @class View
+ * @extends {viewMgr.View}
+ */
 export class View extends viewMgr.View
 {
     public views : Array<viewMgr.View>;
@@ -42,6 +51,7 @@ export class View extends viewMgr.View
     public availableTracksModalOpen : boolean;
     public contigEditorModalOpen : boolean;
     public contigCreatorModalOpen : boolean;
+    public editContigsModalOpen : boolean;
     public loadingModal : boolean;
     public constructor(div : string)
     {
@@ -53,8 +63,15 @@ export class View extends viewMgr.View
         this.availableTracksModalOpen = false;
         this.contigEditorModalOpen = false;
         this.contigCreatorModalOpen = false;
+        this.editContigsModalOpen = false;
         this.loadingModal = false;
     }
+    /**
+     * Retrieve all the alignments run for the currently open figure
+     * 
+     * @returns {(Array<AlignData> | undefined)} 
+     * @memberof View
+     */
     public getAlignsForOpenGenome() : Array<AlignData> | undefined
     {
         let res : Array<AlignData> = new Array<AlignData>();
@@ -72,6 +89,11 @@ export class View extends viewMgr.View
             return undefined;
         return res;
     }
+    /**
+     * Show the modal, with whatever happens to be on it. Bootstrap only allows a single modal
+     * 
+     * @memberof View
+     */
     public showModal() : void
     {
         try
@@ -81,6 +103,11 @@ export class View extends viewMgr.View
         }
         catch(err){}
     }
+    /**
+     * Dismiss the modal
+     * 
+     * @memberof View
+     */
     public dismissModal() : void
     {
         (<any>$(".modal")).modal("hide");
@@ -91,7 +118,14 @@ export class View extends viewMgr.View
         this.availableTracksModalOpen = false;
         this.contigCreatorModalOpen = false;
         this.contigEditorModalOpen = false;
+        this.editContigsModalOpen = false;
     }
+    /**
+     * Highlight the currently open figure in the "Figures" dropdown
+     * 
+     * @returns {void} 
+     * @memberof View
+     */
     public setSelectedFigureInDropDown() : void
     {
         let genomeView = <GenomeView.GenomeView>viewMgr.getViewByName("genomeView",this.views);
@@ -109,6 +143,11 @@ export class View extends viewMgr.View
             }
         }
     }
+    /**
+     * Update the textbox in the navbar with the radius of the open figure
+     * 
+     * @memberof View
+     */
     public setFigureRadiusInInput() : void
     {
         let genomeView = <GenomeView.GenomeView>viewMgr.getViewByName("genomeView",this.views);
@@ -118,6 +157,11 @@ export class View extends viewMgr.View
         else
             el.value = genomeView.genome.radius.toString();
     }
+    /**
+     * Update the textbox in the navbar with the track interval of the open figure
+     * 
+     * @memberof View
+     */
     public setFigureBPIntervalInput() : void
     {
         let genomeView = <GenomeView.GenomeView>viewMgr.getViewByName("genomeView",this.views);
@@ -127,6 +171,12 @@ export class View extends viewMgr.View
         else
             el.value = genomeView.genome.circularFigureBPTrackOptions.interval.toString();
     }
+    /**
+     * Update the checkbox in the navbar with the interval status of the open figure
+     * 
+     * @returns {void} 
+     * @memberof View
+     */
     public setShowBPIntervalCheckBox() : void
     {
         let genomeView = <GenomeView.GenomeView>viewMgr.getViewByName("genomeView",this.views);
@@ -138,6 +188,11 @@ export class View extends viewMgr.View
         else if(genomeView.genome.circularFigureBPTrackOptions.showLabels == 1)
             checkbox.checked = true;
     }
+    /**
+     * On startup. Apply behaviour to static dropdowns and controls
+     * 
+     * @memberof View
+     */
     public onMount() : void
     {
         GenomeView.addView(this.views,"genomeView");
@@ -148,7 +203,7 @@ export class View extends viewMgr.View
         let genomeView = <GenomeView.GenomeView>viewMgr.getViewByName("genomeView",this.views);
         let self = this;
         window.onbeforeunload = function(e){
-            self.dataChanged();
+            self.saveFigureChanges();
         }
         document.getElementById("figures").onclick = function(this : HTMLElement,ev : MouseEvent){
             for(let i = 0; i != self.fastaInputs.length; ++i)
@@ -160,7 +215,7 @@ export class View extends viewMgr.View
                         self.fastaInputs[i].uuid,
                         self.fastaInputs[i].contigs
                     ));
-                    self.dataChanged();
+                    self.saveFigureChanges();
                     genomeView.genome = self.circularFigures[self.circularFigures.length - 1];
                     genomeView.firstRender = true;
                     viewMgr.render();
@@ -180,6 +235,34 @@ export class View extends viewMgr.View
                 }
             }
         }
+        document.getElementById("figureOptions").onclick = function(this : HTMLElement,ev : MouseEvent){
+            if((<any>event.target).id == `${genomeView.genome.uuid}ToggleInteractivity`)
+            {
+                genomeView.genome.isInteractive = !genomeView.genome.isInteractive;
+                self.saveFigureChanges();
+                genomeView.firstRender = true;
+                viewMgr.render();
+            }
+            if((<any>event.target).id == `${genomeView.genome.uuid}ToggleContigNames`)
+            {
+                genomeView.genome.showContigNames = !genomeView.genome.showContigNames;
+                self.saveFigureChanges();
+                genomeView.firstRender = true;
+                viewMgr.render();
+            }
+            if((<any>event.target).id == `EditFigureName`)
+            {
+                genomeView.figureNameOnClick();
+            }
+            if((<any>event.target).id ==`EditContigs`)
+            {
+                self.editContigsModalOpen = true;
+                writeEditContigsModal();
+                self.showModal();
+
+            }
+        }
+
         document.getElementById("showBPIntervalCheckBox").onclick = function(this : HTMLElement,ev : MouseEvent){
             document.getElementById("updateNavBarButton").click();
         }
@@ -237,6 +320,8 @@ export class View extends viewMgr.View
 
         document.getElementById("updateNavBarButton").onclick = function(this : HTMLElement,ev : MouseEvent){
             let radiusHasChanged = false;
+            let trackIntervalChanged = false;
+            let showIntervalChanged = false;
             if(!genomeView.genome)
                     return;
             let radius = parseInt((<HTMLInputElement>document.getElementById("figureRadiusInput")).value);
@@ -249,22 +334,29 @@ export class View extends viewMgr.View
 
             let trackInterval = parseInt((<HTMLInputElement>document.getElementById("figureBPIntervalInput")).value);
             if(trackInterval)
+            {
+                if(trackInterval != genomeView.genome.circularFigureBPTrackOptions.interval)
+                    trackIntervalChanged = true;
                 genomeView.genome.circularFigureBPTrackOptions.interval = trackInterval;
+            }
 
             let showInterval = ((<HTMLInputElement>document.getElementById("showBPIntervalCheckBox")).checked);
             if(showInterval !== undefined)
             {
+                if((showInterval === true && genomeView.genome.circularFigureBPTrackOptions.showLabels == 0) || (showInterval === false && genomeView.genome.circularFigureBPTrackOptions.showLabels == 1))
+                    showIntervalChanged = true;
                 if(showInterval === true)
                     genomeView.genome.circularFigureBPTrackOptions.showLabels = 1;
                 else
                     genomeView.genome.circularFigureBPTrackOptions.showLabels = 0;
             }
-            if(radiusHasChanged)
+            if(radiusHasChanged || trackIntervalChanged || showIntervalChanged)
             {
-                tc.triggerReCompileForAllTracks(genomeView.genome);
+                genomeView.firstRender = true;
+                tc.triggerReCompileForWholeFigure(genomeView.genome);
+                self.saveFigureChanges();
             }
             genomeView.updateScope();
-            self.dataChanged();
             viewMgr.render();
         }
 
@@ -280,8 +372,15 @@ export class View extends viewMgr.View
             this.views[i].onUnMount();
         }
     }
+    /**
+     * Update dynamic dropdowns and controls. Call render on GenomeView
+     * 
+     * @returns {string} 
+     * @memberof View
+     */
     public renderView() : string
     {
+        let genomeView = <GenomeView.GenomeView>viewMgr.getViewByName("genomeView",this.views);
         let res = "";
         for(let i = 0; i != this.fastaInputs.length; ++i)
         {
@@ -306,6 +405,17 @@ export class View extends viewMgr.View
             }
         }
         document.getElementById("figures").innerHTML = res;
+
+        res = ""
+        if(genomeView.genome)
+        {
+            res += `<li><a href="#" id="${genomeView.genome.uuid}ToggleInteractivity">${genomeView.genome.isInteractive ? "Disable Interactivity" : "Enable Interactivity"}</a></li>`;
+            res += `<li><a href="#" id="${genomeView.genome.uuid}ToggleContigNames">${genomeView.genome.showContigNames ? "Don't Show Contig Names" : "Show Contig Names"}</a></li>`;
+            res += `<li><a href="#" id="EditFigureName">Edit Figure Name</a></li>`;
+            res += `<li><a href="#" id="EditContigs">Edit Contigs</a></li>`;
+        }
+        document.getElementById("figureOptions").innerHTML = res;
+
         for(let i = 0; i != this.views.length; ++i)
         {
             this.views[i].render();
@@ -336,6 +446,11 @@ export class View extends viewMgr.View
         this.setFigureBPIntervalInput();
         this.setShowBPIntervalCheckBox();
     }
+    /**
+     * Save circular figures for the open project
+     * 
+     * @memberof View
+     */
     public dataChanged() : void
     {
         ipc.send(
@@ -348,6 +463,21 @@ export class View extends viewMgr.View
             }
         );
     }
+    /**
+     * Save changes to the open figure. Resets SVG caches to force figure updating
+     * 
+     * @memberof View
+     */
+    public saveFigureChanges() : void
+    {
+        let genomeView = <GenomeView.GenomeView>viewMgr.getViewByName("genomeView",this.views);       
+        this.dataChanged();
+        if(genomeView.genome)
+        {
+            tc.resetCaches();
+            reCacheBaseFigure(genomeView.genome);
+        }
+    }
     public divClickEvents(event : JQueryEventObject) : void
     {
         let genomeView = <GenomeView.GenomeView>viewMgr.getViewByName("genomeView",this.views);        
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/reCacheBaseFigure.ts b/src/req/renderer/circularGenomeBuilderRenderer/reCacheBaseFigure.ts
index bec62b53d..a0936fd00 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/reCacheBaseFigure.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/reCacheBaseFigure.ts
@@ -1,18 +1,12 @@
 import * as cf from "./../circularFigure";
-export async function reCacheBaseFigure(figure : cf.CircularFigure) : Promise<void>
+/**
+ * Rerenders figure's template cache, resets SVG cache
+ * 
+ * @export
+ * @param {cf.CircularFigure} figure 
+ */
+export function reCacheBaseFigure(figure : cf.CircularFigure) : void
 {
-    return new Promise<void>((resolve,reject) => {
-        (async function() : Promise<void> {
-            return new Promise<void>((resolve,reject) => {
-                setImmediate(function(){
-                    setImmediate(function(){
-                        cf.cacheBaseFigure(figure);
-                        resolve();
-                    });
-                });
-            });
-        })().then(() => {
-            resolve();
-        });
-    });
+    cf.cacheBaseFigure(figure);
+    cf.deleteBaseFigureSVGFromCache(figure);
 }
\ No newline at end of file
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/templateCache.ts b/src/req/renderer/circularGenomeBuilderRenderer/templateCache.ts
index 516d45162..c1a86fa1e 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/templateCache.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/templateCache.ts
@@ -37,17 +37,41 @@ class CachedSNPTrackSVG
     }
 }
 
-let baseFigureTemplateString = "";
+export let baseFigureSVG : string = undefined;
 
 let coverageTrackCache = new Array<CachedCoverageTrackSVG>();;
 let SNPTrackCache = new Array<CachedSNPTrackSVG>();
 
+/**
+ * Clear the in-memory cache of the SVG for the base figure
+ * 
+ * @export
+ */
+export function resetBaseFigureSVG() : void
+{
+    baseFigureSVG = undefined;
+}
+
+/**
+ * Clear all in-memory caches
+ * 
+ * @export
+ */
 export function resetCaches() : void
 {
     coverageTrackCache = new Array<CachedCoverageTrackSVG>();
     SNPTrackCache = new Array<CachedSNPTrackSVG>();
+    baseFigureSVG = undefined
 }
 
+/**
+ * Update caches for newFigure with new data (if changes are detected).
+ * Will reset and rebuild caches if this function is called with a figure
+ * different from the one used the last time it was called
+ * 
+ * @export
+ * @param {cf.CircularFigure} newFigure 
+ */
 export function refreshCache(newFigure : cf.CircularFigure) : void
 {
     if(!figure || newFigure.uuid != figure.uuid)
@@ -55,6 +79,28 @@ export function refreshCache(newFigure : cf.CircularFigure) : void
         resetCaches();
         figure = newFigure;
     }
+    console.log(newFigure);
+    if(!newFigure.isInteractive)
+    {
+        if(!baseFigureSVG)
+        {
+            try
+            {
+                baseFigureSVG = cf.getBaseFigureSVGFromCache(figure);
+            }
+            catch(err)
+            {
+                ipc.send(
+                    "runOperation",
+                    <AtomicOperationIPC>{
+                        opName : "compileTemplates",
+                        figure : newFigure,
+                        compileBase : true
+                    }
+                );
+            }
+        }
+    }
 
     //load tracks which had not been loaded previously
     let found = false;
@@ -123,24 +169,16 @@ export function refreshCache(newFigure : cf.CircularFigure) : void
             }
         }
     }
-
-    /*for(let i = 0; i != newFigure.renderedSNPTracks.length; ++i)
-    {
-        found = false;
-        for(let k = 0; k != SNPTrackCache.length; ++k)
-        {
-            if(newFigure.renderedSNPTracks[i].uuid == SNPTrackCache[k].trackRecord.uuid)
-            {
-                found = true;
-                break;
-            }
-        }
-        if(!found)
-            SNPTrackCache.push(new CachedSNPTrackSVG(newFigure.renderedSNPTracks[i]));
-    }*/
 }
 
-//retrieve loaded tracks
+
+/**
+ * Retrieve an (already loaded) SVG for the specified coverage track
+ * 
+ * @export
+ * @param {cf.RenderedCoverageTrackRecord} trackRecord 
+ * @returns {string} 
+ */
 export function getCachedCoverageTrack(trackRecord : cf.RenderedCoverageTrackRecord) : string
 {
     for(let i = 0; i != coverageTrackCache.length; ++i)
@@ -151,6 +189,13 @@ export function getCachedCoverageTrack(trackRecord : cf.RenderedCoverageTrackRec
     throw new Error(`Could not fetch ${trackRecord.uuid} from cache`);
 }
 
+/**
+ * Retrieve an (already loaded) SVG for the specified SNP track
+ * 
+ * @export
+ * @param {cf.RenderedSNPTrackRecord} trackRecord 
+ * @returns {string} 
+ */
 export function getCachedSNPTrack(trackRecord : cf.RenderedSNPTrackRecord) : string
 {
     for(let i = 0; i != SNPTrackCache.length; ++i)
@@ -161,6 +206,13 @@ export function getCachedSNPTrack(trackRecord : cf.RenderedSNPTrackRecord) : str
     throw new Error(`Could not fetch ${trackRecord.uuid} from cache`);
 }
 
+/**
+ * Deletes the track specified by uuid from the in-memory cache
+ * 
+ * @export
+ * @param {string} uuid 
+ * @returns {void} 
+ */
 export function removeTrack(uuid : string) : void
 {
     for(let i = 0; i != coverageTrackCache.length; ++i)
@@ -183,10 +235,28 @@ export function removeTrack(uuid : string) : void
     }
 }
 
-export function triggerReCompileForAllTracks(newFigure : cf.CircularFigure) : void
+/**
+ * Triggers a compile for each compononent of newFigure (including non-visible data tracks) regardless of cache status.
+ * Will only trigger a compile for the base figure if the figure is non-interactive
+ * @export
+ * @param {cf.CircularFigure} newFigure 
+ * @returns {void} 
+ */
+export function triggerReCompileForWholeFigure(newFigure : cf.CircularFigure) : void
 {
     if(!figure)
         return;
+    if(!figure.isInteractive)
+    {
+        ipc.send(
+            "runOperation",
+            <AtomicOperationIPC>{
+                opName : "compileTemplates",
+                figure : newFigure,
+                compileBase : true
+            }
+        );
+    }
     for(let i = 0; i != coverageTrackCache.length; ++i)
     {
         ipc.send(
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/writeAlignsModal.ts b/src/req/renderer/circularGenomeBuilderRenderer/writeAlignsModal.ts
index de493ad78..c750cac2e 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/writeAlignsModal.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/writeAlignsModal.ts
@@ -3,6 +3,11 @@ import * as masterView from "./masterView";
 import * as genomeView from "./genomeView";
 import {writeAvailableTracksModal,setSelectedAlign} from "./writeAvailableTracksModal";
 import {getReadable} from "./../../getAppPath";
+/**
+ * Writes the alignment selection menu into the modal
+ * 
+ * @export
+ */
 export function writeAlignsModal() : void
 {
     let masterView = <masterView.View>viewMgr.getViewByName("masterView");
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/writeAvailableTracksModal.ts b/src/req/renderer/circularGenomeBuilderRenderer/writeAvailableTracksModal.ts
index 557bb8884..fc4e15b3a 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/writeAvailableTracksModal.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/writeAvailableTracksModal.ts
@@ -10,10 +10,21 @@ import {getReadable} from "./../../getAppPath";
 
 require("@claviska/jquery-minicolors");
 let selectedAlign : AlignData;
+/**
+ * Set the selected alignment to view track options for
+ * 
+ * @export
+ * @param {AlignData} align 
+ */
 export function setSelectedAlign(align : AlignData) : void
 {
     selectedAlign = align;
 }
+/**
+ * Writes the data track selection menu into the modal
+ * 
+ * @export
+ */
 export function writeAvailableTracksModal() : void
 {
     let masterView = <masterView.View>viewMgr.getViewByName("masterView");
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/writeContigCreatorModal.ts b/src/req/renderer/circularGenomeBuilderRenderer/writeContigCreatorModal.ts
index cd7435bf6..c6990d243 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/writeContigCreatorModal.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/writeContigCreatorModal.ts
@@ -4,6 +4,11 @@ import * as genomeView from "./genomeView";
 import * as cf from "./../circularFigure";
 import {reCacheBaseFigure} from "./reCacheBaseFigure";
 import {writeLoadingModal} from "./writeLoadingModal";
+/**
+ * Writes the contig creation menu into the modal
+ * 
+ * @export
+ */
 export function writeContigCreatorModal() : void
 {
     let masterView = <masterView.View>viewMgr.getViewByName("masterView");
@@ -61,12 +66,11 @@ export function writeContigCreatorModal() : void
             masterView.loadingModal = true;
             writeLoadingModal();
             setTimeout(function(){
-                reCacheBaseFigure(genomeView.genome).then(() => {
-                    masterView.loadingModal = false;
-                    masterView.dismissModal();
-                    genomeView.firstRender = true;
-                    viewMgr.render();
-                });
+                reCacheBaseFigure(genomeView.genome);
+                masterView.loadingModal = false;
+                masterView.dismissModal();
+                genomeView.firstRender = true;
+                viewMgr.render();
             },10);
 
             viewMgr.render();
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/writeContigEditorModal.ts b/src/req/renderer/circularGenomeBuilderRenderer/writeContigEditorModal.ts
index 9d81a9f0a..3f9f6a6b0 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/writeContigEditorModal.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/writeContigEditorModal.ts
@@ -9,6 +9,13 @@ import {reCacheBaseFigure} from "./reCacheBaseFigure";
 import {writeLoadingModal} from "./writeLoadingModal";
 let contig : cf.Contig;
 let editedAlias = "";
+/**
+ * Set the contig to edit by uuid
+ * 
+ * @export
+ * @param {string} uuid 
+ * @returns {void} 
+ */
 export function setSelectedContigByUUID(uuid : string) : void
 {
     let masterView = <masterView.View>viewMgr.getViewByName("masterView");
@@ -35,6 +42,11 @@ export function setSelectedContigByUUID(uuid : string) : void
     }
 }
 
+/**
+ * Writes the contig editor menu into the modal
+ * 
+ * @export
+ */
 export function writeContigEditorModal() : void
 {
     if(!contig)
@@ -105,21 +117,8 @@ export function writeContigEditorModal() : void
         }
         masterView.contigEditorModalOpen = false;
         masterView.dismissModal();
-
-        masterView.dataChanged();
-
-        masterView.loadingModal = true;
-        writeLoadingModal();
-
-        setTimeout(function(){
-            reCacheBaseFigure(genomeView.genome).then(() => {
-                masterView.loadingModal = false;
-                masterView.dismissModal();
-                genomeView.firstRender = true;
-                viewMgr.render();
-            });
-        },10);
-
+        genomeView.firstRender = true;
+        masterView.saveFigureChanges();
         viewMgr.render();
     
     }
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/writeEditContigsModal.ts b/src/req/renderer/circularGenomeBuilderRenderer/writeEditContigsModal.ts
new file mode 100644
index 000000000..b29fb6dc6
--- /dev/null
+++ b/src/req/renderer/circularGenomeBuilderRenderer/writeEditContigsModal.ts
@@ -0,0 +1,69 @@
+import * as viewMgr from "./../viewMgr";
+import * as masterView from "./masterView";
+import * as genomeView from "./genomeView";
+
+/**
+ * Writes the list of contigs to edit into the modal
+ * 
+ * @export
+ */
+export function writeEditContigsModal() : void
+{
+    let masterView = <masterView.View>viewMgr.getViewByName("masterView");
+    let genomeView = <genomeView.GenomeView>viewMgr.getViewByName("genomeView",masterView.views);
+
+    let title = `Select Contig to Edit`;
+
+    let body = ``;
+    if(!genomeView.genome)
+    {
+        body = `
+            <p>You must select a figure to edit before you can view it's contigs to edit.</p>
+        `;
+    }
+    else if(genomeView.genome)
+    {
+        body += `<h5>Custom Contigs</h5>`;
+        if(genomeView.genome.customContigs.length > 0)
+        {
+            for(let i = 0; i != genomeView.genome.customContigs.length; ++i)
+            {
+                body += `<p class="activeHover" id="${genomeView.genome.customContigs[i].uuid}Edit">${genomeView.genome.customContigs[i].name}</p>`;
+            }
+        }
+        else
+        {
+            body += `<p>No custom contigs</p>`;
+        }
+
+        body += `<h5>Reference Contigs</h5>`;
+
+        for(let i = 0; i != genomeView.genome.contigs.length; ++i)
+        {
+            body += `<p class="activeHover" id="${genomeView.genome.contigs[i].uuid}Edit">${genomeView.genome.contigs[i].name}</p>`;
+        }
+    }
+
+    let footer = ``;
+
+    document.getElementById("modalTitle").innerHTML = title;
+    document.getElementById("modalBody").innerHTML = body;
+    document.getElementById("modalFooter").innerHTML = footer;
+
+    if(genomeView.genome.customContigs.length > 0)
+    {
+        for(let i = 0; i != genomeView.genome.customContigs.length; ++i)
+        {
+            document.getElementById(`${genomeView.genome.customContigs[i].uuid}Edit`).onclick = function(this : HTMLElement,ev : MouseEvent){
+                genomeView.markerOnClick(undefined,undefined,genomeView.genome.customContigs[i].uuid);
+            }
+        }
+    }
+    
+    for(let i = 0; i != genomeView.genome.contigs.length; ++i)
+    {
+        document.getElementById(`${genomeView.genome.contigs[i].uuid}Edit`).onclick = function(this : HTMLElement,ev : MouseEvent){
+            genomeView.markerOnClick(undefined,undefined,genomeView.genome.contigs[i].uuid);
+        }
+    }
+}
\ No newline at end of file
diff --git a/src/req/renderer/circularGenomeBuilderRenderer/writeLoadingModal.ts b/src/req/renderer/circularGenomeBuilderRenderer/writeLoadingModal.ts
index dae01ae8a..d92772632 100644
--- a/src/req/renderer/circularGenomeBuilderRenderer/writeLoadingModal.ts
+++ b/src/req/renderer/circularGenomeBuilderRenderer/writeLoadingModal.ts
@@ -1,3 +1,8 @@
+/**
+ * Writes a generic loading message into the modal. May be modified by #loadingText after being written
+ * 
+ * @export
+ */
 export function writeLoadingModal() : void
 {
     let title = `Loading...`;