efischer/BiGpairSEQ
1
0
Fork 0
Code Issues Pull Requests Projects Releases 13 Wiki Activity

implement option menu for file caching

Browse Source
This commit is contained in:
efischer
2022-02-23 20:35:31 -06:00
parent 4bcda9b66c
commit c068c3db3c
2 changed files with 61 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

26
src/main/java/BiGpairSEQ.java
View File

@@ -10,6 +10,9 @@ public class BiGpairSEQ {
private static String plateFilename = null; private static String plateFilename = null;
private static GraphWithMapData graphInMemory = null; private static GraphWithMapData graphInMemory = null;
private static String graphFilename = null; private static String graphFilename = null;
private static boolean cacheCells = false;
private static boolean cachePlate = false;
private static boolean cacheGraph = true;
public static void main(String[] args) { public static void main(String[] args) {
if (args.length == 0) { if (args.length == 0) {
@@ -92,4 +95,27 @@ public class BiGpairSEQ {
graphFilename = filename; graphFilename = filename;
} }
public static boolean cacheCells() {
return cacheCells;
}
public static void setCacheCells(boolean cacheCells) {
BiGpairSEQ.cacheCells = cacheCells;
}
public static boolean cachePlate() {
return cachePlate;
}
public static void setCachePlate(boolean cachePlate) {
BiGpairSEQ.cachePlate = cachePlate;
}
public static boolean cacheGraph() {
return cacheGraph;
}
public static void setCacheGraph(boolean cacheGraph) {
BiGpairSEQ.cacheGraph = cacheGraph;
}
} }

35
src/main/java/InteractiveInterface.java
View File

@@ -27,6 +27,7 @@ public class InteractiveInterface {
//Need to re-do the CDR3/CDR1 matching to correspond to new pattern //Need to re-do the CDR3/CDR1 matching to correspond to new pattern
//System.out.println("5) Generate CDR3/CDR1 occupancy graph"); //System.out.println("5) Generate CDR3/CDR1 occupancy graph");
//System.out.println("6) Simulate CDR3/CDR1 T cell matching"); //System.out.println("6) Simulate CDR3/CDR1 T cell matching");
System.out.println("8) Options");
System.out.println("9) About/Acknowledgments"); System.out.println("9) About/Acknowledgments");
System.out.println("0) Exit"); System.out.println("0) Exit");
try { try {
@@ -37,6 +38,7 @@ public class InteractiveInterface {
case 3 -> makeCDR3Graph(); case 3 -> makeCDR3Graph();
case 4 -> matchCDR3s(); case 4 -> matchCDR3s();
//case 6 -> matchCellsCDR1(); //case 6 -> matchCellsCDR1();
case 8 -> options();
case 9 -> acknowledge(); case 9 -> acknowledge();
case 0 -> quit = true; case 0 -> quit = true;
default -> throw new InputMismatchException("Invalid input."); default -> throw new InputMismatchException("Invalid input.");
@@ -493,6 +495,39 @@ public class InteractiveInterface {
// } // }
// } // }
private static void options(){
boolean backToMain = false;
while(!backToMain) {
System.out.println("-------------OPTIONS----------------");
System.out.println("1) Turn cell sample file caching " + getOnOff(!BiGpairSEQ.cacheCells()));
System.out.println("2) Turn sample plate file caching " + getOnOff(!BiGpairSEQ.cachePlate()));
System.out.println("3) Turn graph/data file caching " + getOnOff(!BiGpairSEQ.cacheGraph()));
System.out.println("0) Return to main menu");
try {
input = sc.nextInt();
switch (input) {
case 1 -> BiGpairSEQ.setCacheCells(!BiGpairSEQ.cacheCells());
case 2 -> BiGpairSEQ.setCachePlate(!BiGpairSEQ.cachePlate());
case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
case 0 -> backToMain = true;
default -> throw new InputMismatchException("Invalid input.");
}
} catch (InputMismatchException ex) {
System.out.println(ex);
sc.next();
}
}
}
private static String getOnOff(boolean b) {
if (b) {
return "on";
}
else {
return "off";
}
}
private static void acknowledge(){ private static void acknowledge(){
System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation"); System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation");
System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences."); System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences.");