mmseqs detection for interactive mode

steineggerlab · Mar 2, 2023 · 35e52bb · 35e52bb
1 parent 6fefa1b
commit 35e52bb
Show file tree

Hide file tree

Showing 5 changed files with 18 additions and 15 deletions.
diff --git a/src/envs/config/PathConfig.java b/src/envs/config/PathConfig.java
@@ -92,21 +92,24 @@ public static int setHmmsearchPath(String path) {
 	}
 
 	public static String MMseqsPath = "mmseqs";
-	public static void setMMseqsPath(String path) {
+	public static int setMMseqsPath(String path) {
 		try {
 			Prompt.talk("MMseqs binary check : " + ANSIHandler.wrapper(path, 'B'));
 			String[] exec = Shell.exec("file -b " + path);
 			if(!exec[0].contains("exec") && !exec[0].contains("link")) {
 				ExceptionHandler.pass(path);
 				ExceptionHandler.handle(ExceptionHandler.INVALID_BINARY);
+				return 1;
 			}
 		}
 		catch(Exception e) {
 			e.printStackTrace();
 			ExceptionHandler.handle(ExceptionHandler.EXCEPTION);
+			return 2;
 		}
 
 		MMseqsPath = path;
+		return 0;
 	}
 
 	public static String TrinityPath = "Trinity";

diff --git a/src/module/ProfileModule.java b/src/module/ProfileModule.java
@@ -223,7 +223,7 @@ private static void solveDependency() {
 		if(AugustusWrapper.checkConfigFile()) {
 			ExceptionHandler.handle(ExceptionHandler.INVALID_PPX_CONFIG);
 		}
-		if(MMseqsWrapper.solve()) {
+		if(!MMseqsWrapper.solve()) {
 			ExceptionHandler.pass(PathConfig.MMseqsPath);
 			ExceptionHandler.handle(ExceptionHandler.DEPENDENCY_UNSOLVED);
 		}
@@ -467,18 +467,18 @@ else if(buf.startsWith("n") || buf.startsWith("N")) {
 		}
 		proceed = false;
 		if(solvedPath != null) command.append(" --augustus ").append(solvedPath);
-/*		
-		// --hmmsearch
+
+		// --mmseqs
 		solvedPath = null;
 		while(!proceed) {
-			if(HmmsearchWrapper.solve()) proceed = true;
+			if(MMseqsWrapper.solve()) proceed = true;
 			else {
-				Prompt.print("Failed to solve : " + PathConfig.HmmsearchPath);
+				Prompt.print("Failed to solve : " + PathConfig.MMseqsPath);
 				while(!proceed) {
-					Prompt.print_nnc("Enter the location of hmmsearch binary (--hmmsearch) : ");
+					Prompt.print_nnc("Enter the location of MMseqs2 binary (--mmseqs) : ");
 					buf = stream.readLine();
 					if(buf.length() == 0) continue;
-					if(PathConfig.setHmmsearchPath(buf) == 0) {
+					if(PathConfig.setMMseqsPath(buf) == 0) {
 						solvedPath = buf;
 						proceed = true;
 					}
@@ -487,8 +487,8 @@ else if(buf.startsWith("n") || buf.startsWith("N")) {
 			}
 		}
 		proceed = false;
-		if(solvedPath != null) command += " --hmmsearch " + solvedPath;
-*/		
+		if(solvedPath != null) command.append(" --mmseqs ").append(solvedPath);
+
 		/* set runtime configurations */
 		// --cpu
 		while(!proceed) {

diff --git a/src/module/ProfileProModule.java b/src/module/ProfileProModule.java
@@ -140,7 +140,7 @@ private static int parseArgument(String[] args) throws ParseException {
 	private static void solveDependency() {
 		Prompt.talk("Solving dependencies...");
 
-		if(MMseqsWrapper.solve()) {
+		if(!MMseqsWrapper.solve()) {
 			ExceptionHandler.pass(PathConfig.MMseqsPath);
 			ExceptionHandler.handle(ExceptionHandler.DEPENDENCY_UNSOLVED);
 		}

diff --git a/src/module/ProfileRnaModule.java b/src/module/ProfileRnaModule.java
@@ -211,7 +211,7 @@ private static void solveDependency() {
 		if(AugustusWrapper.checkConfigFile()) {
 			ExceptionHandler.handle(ExceptionHandler.INVALID_PPX_CONFIG);
 		}
-		if(MMseqsWrapper.solve()) {
+		if(!MMseqsWrapper.solve()) {
 			ExceptionHandler.pass(PathConfig.MMseqsPath);
 			ExceptionHandler.handle(ExceptionHandler.DEPENDENCY_UNSOLVED);
 		}

diff --git a/src/wrapper/MMseqsWrapper.java b/src/wrapper/MMseqsWrapper.java
@@ -99,10 +99,10 @@ public String[] exec() {
 	public static boolean solve() {
 		String cmd = PathConfig.MMseqsPath + " 2>&1";
 		String[] raw = Shell.exec(cmd);
-		if(raw[0].contains("not found")) return true;
+		if(raw[0].contains("not found")) return false;
 		for(int error_loc = 0; !raw[error_loc].contains("MMseqs2"); error_loc++) {
-			if(error_loc + 1 == raw.length) return true;
+			if(error_loc + 1 == raw.length) return false;
 		}
-		return false;
+		return true;
 	}
 }