renamed operation

src/InputRenderer.ts

@@ -11,7 +11,7 @@ import * as fastqView from "./req/renderer/inputRenderer/FastqView";
 import * as fastaView from "./req/renderer/inputRenderer/FastaView";
 
 import {AtomicOperation} from "./req/operations/atomicOperations";
-import {IndexFastaForAlignment} from "./req/operations/indexFastaForAlignment";
+import {IndexFastaForBowTie2Alignment} from "./req/operations/indexFastaForBowTie2Alignment";
 import {IndexFastaForVisualization} from "./req/operations/indexFastaForVisualization";
 import {InputBamFile} from "./req/operations/InputBamFile";
 import {LinkRefSeqToAlignment} from "./req/operations/LinkRefSeqToAlignment";
@@ -166,7 +166,7 @@ $
                                 for(let i = 0; i != ops.length; ++i)
                                 {
                                     if(ops[i].name == "inputBamFile" || ops[i].name == "linkRefSeqToAlignment" ||
-                                    ops[i].name == "indexFastaForVisualization" || ops[i].name == "indexFastaForAlignment" ||
+                                    ops[i].name == "indexFastaForVisualization" || ops[i].name == "indexFastaForBowTie2Alignment" ||
                                     ops[i].name == "linkRefSeqToAlignment" || ops[i].name == "importFileIntoProject")
                                     {
                                         masterView.shouldAllowTriggeringOps = false;

src/guiTests/req/input/indexSuccess.ts

@@ -1,5 +1,5 @@
 import * as atomicOp from "./../../../req/operations/atomicOperations";
-import {IndexFastaForAlignment} from "./../../../req/operations/indexFastaForAlignment";
+import {IndexFastaForBowTie2Alignment} from "../../../req/operations/indexFastaForBowTie2Alignment";
 
 /**
  * Resolves when indexFastaAlignment completes successfully, crashes the process
@@ -11,7 +11,7 @@ import {IndexFastaForAlignment} from "./../../../req/operations/indexFastaForAli
 export async function indexSuccess() : Promise<void>
 {
     return new Promise<void>((resolve,reject) => {
-        atomicOp.updates.on("indexFastaForAlignment",function(op : IndexFastaForAlignment){
+        atomicOp.updates.on("indexFastaForBowTie2Alignment",function(op : IndexFastaForBowTie2Alignment){
             if(op.flags.done && op.flags.failure)
             {
                 console.log("Failed to index");

src/req/main/main.ts

@@ -20,7 +20,7 @@ import * as dataMgr from "./dataMgr";
 import * as atomicOp from "./../operations/atomicOperations";
 import {AtomicOperationIPC} from "./../atomicOperationsIPC";
 import {GenerateQCReport} from "./../operations/GenerateQCReport";
-import {IndexFastaForAlignment} from "./../operations/indexFastaForAlignment";
+import {IndexFastaForBowTie2Alignment} from "../operations/indexFastaForBowTie2Alignment";
 import {IndexFastaForVisualization} from "./../operations/indexFastaForVisualization";
 import {RunAlignment} from "./../operations/RunAlignment";
 import {RenderCoverageTrackForContig} from "./../operations/RenderCoverageTrack";
@@ -93,7 +93,7 @@ app.on
 		winMgr.windowCreators["projectSelection"].Create();
 
 		atomicOp.register("generateFastQCReport",GenerateQCReport);
-		atomicOp.register("indexFastaForAlignment",IndexFastaForAlignment);
+		atomicOp.register("indexFastaForBowTie2Alignment",IndexFastaForBowTie2Alignment);
 		atomicOp.register("indexFastaForVisualization",IndexFastaForVisualization);
 		atomicOp.register("runAlignment",RunAlignment);
 		atomicOp.register("renderCoverageTrackForContig",RenderCoverageTrackForContig);
@@ -299,7 +299,7 @@ ipc.on(
 		console.log(arg);
 		dataMgr.setKey("application","operations",atomicOp.operationsQueue);
 		winMgr.publishChangeForKey("application","operations");
-		if(arg.opName =="indexFastaForAlignment" || arg.opName == "indexFastaForVisualization" || arg.opName == "generateFastQCReport")
+		if(arg.opName =="indexFastaForBowTie2Alignment" || arg.opName == "indexFastaForVisualization" || arg.opName == "generateFastQCReport")
 		{
 			let list : Array<File> = dataMgr.getKey(arg.channel,arg.key);
 			for(let i : number = 0; i != list.length; ++i)
@@ -606,7 +606,7 @@ ipc.on(
 	}
 );
 atomicOp.updates.on(
-	"indexFastaForAlignment",function(op : IndexFastaForAlignment)
+	"indexFastaForBowTie2Alignment",function(op : IndexFastaForBowTie2Alignment)
 	{
 		dataMgr.setKey("application","operations",atomicOp.operationsQueue);
 		winMgr.publishChangeForKey("application","operations");

src/req/operations/indexFasta/bowTie2Build.ts

@@ -1,7 +1,7 @@
 import * as fs from "fs";
 
 import {getReadable} from "./../../getAppPath";
-import {IndexFastaForAlignment} from "./../indexFastaForAlignment";
+import {IndexFastaForBowTie2Alignment} from "../indexFastaForBowTie2Alignment";
 import {getPath} from "./../../file";
 
 import {SpawnRequestParams} from "./../../JobIPC";
@@ -11,10 +11,10 @@ import {Job,JobCallBackObject} from "./../../main/Job";
  * Builds a bowtie2 index
  * 
  * @export
- * @param {IndexFastaForAlignment} op 
+ * @param {IndexFastaForBowTie2Alignment} op 
  * @returns {(Promise<string | undefined>)} 
  */
-export function bowTie2Build(op : IndexFastaForAlignment) : Promise<string | undefined>
+export function bowTie2Build(op : IndexFastaForBowTie2Alignment) : Promise<string | undefined>
 {
     return new Promise((resolve,reject) => {
         let jobCallBack : JobCallBackObject = {

src/req/operations/indexFastaForAlignment.ts → src/req/operations/indexFastaForBowTie2Alignment.ts

@@ -1,15 +1,15 @@
 import * as atomic from "./atomicOperations";
-import {Fasta,getFaiPath} from "./../fasta";
-import {getContigsFromFastaFile} from "./../fastaContigLoader";
-import {getPath} from "./../file";
+import {Fasta,getFaiPath} from "../fasta";
+import {getContigsFromFastaFile} from "../fastaContigLoader";
+import {getPath} from "../file";
 
-import {getReadable,getReadableAndWritable} from "./../getAppPath";
+import {getReadable,getReadableAndWritable} from "../getAppPath";
 
-import {Job} from "./../main/Job";
+import {Job} from "../main/Job";
 
 import {bowTie2Build} from "./indexFasta/bowTie2Build";
 import {samToolsFaidx} from "./indexFasta/samToolsFaidx";
-export class IndexFastaForAlignment extends atomic.AtomicOperation
+export class IndexFastaForBowTie2Alignment extends atomic.AtomicOperation
 {
     public fasta : Fasta;
 

src/req/renderer/inputRenderer/masterView.ts

@@ -177,7 +177,7 @@ export class View extends viewMgr.View
                      ipc.send(
                         "runOperation",
                         <AtomicOperationIPC>{
-                            opName : "indexFastaForAlignment",
+                            opName : "indexFastaForBowTie2Alignment",
                             channel : "input",
                             key : "fastaInputs",
                             uuid : this.fastaInputs[i].uuid

src/req/tests/registerOperations.ts

@@ -1,7 +1,7 @@
 import * as atomic from "./../operations/atomicOperations";
 
 import {GenerateQCReport} from "./../operations/GenerateQCReport";
-import {IndexFastaForAlignment} from "./../operations/indexFastaForAlignment";
+import {IndexFastaForBowTie2Alignment} from "../operations/indexFastaForBowTie2Alignment";
 import {IndexFastaForVisualization} from "./../operations/indexFastaForVisualization";
 import {RunAlignment} from "./../operations/RunAlignment";
 import {RenderCoverageTrackForContig} from "./../operations/RenderCoverageTrack";
@@ -18,7 +18,7 @@ import {BLASTSegment} from "./../operations//BLASTSegment";
 export function registerOperations() : void
 {
     atomic.register("generateFastQCReport",GenerateQCReport);
-    atomic.register("indexFastaForAlignment",IndexFastaForAlignment);
+    atomic.register("indexFastaForBowTie2Alignment",IndexFastaForBowTie2Alignment);
     atomic.register("indexFastaForVisualization",IndexFastaForVisualization);
     atomic.register("runAlignment",RunAlignment);
     atomic.register("renderCoverageTrackForContig",RenderCoverageTrackForContig);

src/req/tests/testHPV16Index.ts

@@ -1,10 +1,10 @@
 import * as atomic from "./../operations/atomicOperations";
-import {IndexFastaForAlignment} from "./../operations/indexFastaForAlignment";
+import {IndexFastaForBowTie2Alignment} from "../operations/indexFastaForBowTie2Alignment";
 import * as hpv16Ref from "./hpv16Ref";
 export async function testHPV16Index() : Promise<void>
 {
     return new Promise<void>((resolve,reject) => {
-        atomic.updates.removeAllListeners().on("indexFastaForAlignment",function(op : IndexFastaForAlignment){
+        atomic.updates.removeAllListeners().on("indexFastaForBowTie2Alignment",function(op : IndexFastaForBowTie2Alignment){
             if(op.flags.failure)
             {
                 console.log(`Failed to index ${op.fasta.alias}`);

src/req/tests/testHPV18Index.ts

@@ -1,10 +1,10 @@
 import * as atomic from "./../operations/atomicOperations";
-import {IndexFastaForAlignment} from "./../operations/indexFastaForAlignment";
+import {IndexFastaForBowTie2Alignment} from "../operations/indexFastaForBowTie2Alignment";
 import * as hpv18Ref from "./hpv18Ref";
 export async function testHPV18Index() : Promise<void>
 {
     return new Promise<void>((resolve,reject) => {
-        atomic.updates.removeAllListeners().on("indexFastaForAlignment",function(op : IndexFastaForAlignment){
+        atomic.updates.removeAllListeners().on("indexFastaForBowTie2Alignment",function(op : IndexFastaForBowTie2Alignment){
             if(op.flags.failure)
             {
                 console.log(`Failed to index ${op.fasta.alias}`);

src/tests.ts

@@ -105,7 +105,7 @@ async function runTests() : Promise<void>
 		}
 
 		console.log("Starting to index hpv16");
-		atomic.addOperation("indexFastaForAlignment",hpv16Ref.get());
+		atomic.addOperation("indexFastaForBowTie2Alignment",hpv16Ref.get());
 		try
 		{
 			await testHPV16Index();
@@ -117,7 +117,7 @@ async function runTests() : Promise<void>
 		}
 
 		console.log("Starting to index hpv18");
-		atomic.addOperation("indexFastaForAlignment",hpv18Ref.get());
+		atomic.addOperation("indexFastaForBowTie2Alignment",hpv18Ref.get());
 		try
 		{
 			await testHPV18Index();