Deactivate file I/O announcement for CLI

src/main/java/CommandLineInterface.java

@@ -1,6 +1,7 @@
 import org.apache.commons.cli.*;
 
 import java.io.IOException;
+import java.util.Arrays;
 import java.util.stream.Stream;
 
 /*
@@ -48,21 +49,15 @@ import java.util.stream.Stream;
 public class CommandLineInterface {
 
     public static void startCLI(String[] args) {
-        //These command line options are a big mess
-        //Really, I don't think command line tools are expected to work in this many different modes
-        //making cells, making plates, and matching are the sort of thing that UNIX philosophy would say
-        //should be three separate programs.
-        //There might be a way to do it with option parameters?
-
         //main options set - for the four different program modes
         Options mainOptions = buildMainOptions();
         CommandLineParser parser = new DefaultParser();
         try{
-            CommandLine line = parser.parse(mainOptions, args);
+            CommandLine line = parser.parse(mainOptions, Arrays.copyOfRange(args, 0, 1));
 
             if (line.hasOption("cells")) {
                 Options cellOptions = buildCellOptions();
-                line = parser.parse(cellOptions, args);
+                line = parser.parse(cellOptions, Arrays.copyOfRange(args, 1, args.length));
                 Integer number = Integer.valueOf(line.getOptionValue("n"));
                 Integer diversity = Integer.valueOf(line.getOptionValue("d"));
                 String filename = line.getOptionValue("o");
@@ -71,7 +66,7 @@ public class CommandLineInterface {
 
             else if (line.hasOption("plate")) {
                 Options plateOptions = buildPlateOptions();
-                line = parser.parse(plateOptions, args);
+                line = parser.parse(plateOptions, Arrays.copyOfRange(args, 1, args.length));
                 //get the cells
                 String cellFilename = line.getOptionValue("c");
                 CellSample cells = getCells(cellFilename);
@@ -122,7 +117,7 @@ public class CommandLineInterface {
 
             else if (line.hasOption("graph")) { //Making a graph
                 Options graphOptions = buildGraphOptions();
-                line = parser.parse(graphOptions, args);
+                line = parser.parse(graphOptions, Arrays.copyOfRange(args, 1, args.length));
                 String cellFilename = line.getOptionValue("c");
                 String plateFilename = line.getOptionValue("p");
                 String outputFilename = line.getOptionValue("o");
@@ -132,7 +127,7 @@ public class CommandLineInterface {
                 Plate plate = getPlate(plateFilename);
                 GraphWithMapData graph = Simulator.makeGraph(cells, plate, false);
                 if (!line.hasOption("no-binary")) { //output binary file unless told not to
-                    GraphDataObjectWriter writer = new GraphDataObjectWriter(outputFilename, graph);
+                    GraphDataObjectWriter writer = new GraphDataObjectWriter(outputFilename, graph, false);
                     writer.writeDataToFile();
                 }
                 if (line.hasOption("graphml")) { //if told to, output graphml file
@@ -143,7 +138,7 @@ public class CommandLineInterface {
 
             else if (line.hasOption("match")) { //can add a flag for which match type in future, spit this in two
                 Options matchOptions = buildMatchCDR3options();
-                line = parser.parse(matchOptions, args);
+                line = parser.parse(matchOptions, Arrays.copyOfRange(args, 1, args.length));
                 String graphFilename = line.getOptionValue("g");
                 String outputFilename = line.getOptionValue("o");
                 Integer minThreshold = Integer.parseInt(line.getOptionValue("min"));
@@ -193,8 +188,8 @@ public class CommandLineInterface {
                 .longOpt("make-cells")
                 .desc("Makes a cell sample file of distinct T cells")
                 .build();
-        Option makePlate = Option.builder("plates")
+        Option makePlate = Option.builder("plate")
-                .longOpt("make-plates")
+                .longOpt("make-plate")
                 .desc("Makes a sample plate file. Requires a cell sample file.")
                 .build();
         Option makeGraph = Option.builder("graph")
@@ -324,12 +319,15 @@ public class CommandLineInterface {
         Option outputGraphML = Option.builder("graphml")
                 .desc("Output GraphML file")
                 .build();
-        Option outputSerializedBinary = Option.builder("no-binary")
+        Option outputSerializedBinary = Option.builder("nb")
+                .longOpt("no-binary")
                 .desc("Don't output serialized binary file")
                 .build();
         graphOptions.addOption(cellFilename);
         graphOptions.addOption(plateFilename);
         graphOptions.addOption(outputFileOption());
+        graphOptions.addOption(outputGraphML);
+        graphOptions.addOption(outputSerializedBinary);
         return graphOptions;
     }
 
@@ -389,7 +387,7 @@ public class CommandLineInterface {
     private static GraphWithMapData getGraph(String graphFilename) {
         assert graphFilename != null;
         try{
-            GraphDataObjectReader reader = new GraphDataObjectReader(graphFilename);
+            GraphDataObjectReader reader = new GraphDataObjectReader(graphFilename, false);
             return reader.getData();
 
         }

src/main/java/InteractiveInterface.java

@@ -375,7 +375,7 @@ public class InteractiveInterface {
             data = BiGpairSEQ.getGraphInMemory();
         }
         else {
-            GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename);
+            GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename, true);
             data = dataReader.getData();
             if(BiGpairSEQ.cacheGraph()) {
                 BiGpairSEQ.setGraphInMemory(data, graphFilename);