Adjusting help strings

josemduarte · josemduarte · commit a35adcf6f0ff · 2020-07-04T14:29:07.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
@@ -297,8 +297,6 @@ private void runPairwise() throws ConfigurationException{
 			}
 		}
 
-
-
 		String name2 = params.getPdb2();
 		String file2 = params.getFile2();
 		if ( name2 == null && file2 == null ){
@@ -449,9 +447,9 @@ private void runPairwise() throws ConfigurationException{
 		}
 	}
 
-	/** check if the result should be written to the local file system
+	/**
+	 * check if the result should be written to the local file system
 	 *
-	 * @param params2
 	 * @param afpChain
 	 * @param ca1
 	 * @param ca2
@@ -525,21 +523,17 @@ private void checkWriteFile( AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean
 		FileOutputStream out; // declare a file output object
 		PrintStream p; // declare a print stream object
 
-			// Create a new file output stream
-			out = new FileOutputStream(fileName);
-
-			// Connect print stream to the output stream
-			p = new PrintStream( out );
-
-			p.println (output);
-
-			p.close();
+		// Create a new file output stream
+		out = new FileOutputStream(fileName);
 
+		// Connect print stream to the output stream
+		p = new PrintStream( out );
 
+		p.println (output);
 
+		p.close();
 	}
 
-
 	private String getAutoFileName(AFPChain afpChain){
 		String fileName =afpChain.getName1()+"_" + afpChain.getName2()+"_"+afpChain.getAlgorithmName();
 
@@ -550,7 +544,6 @@ private String getAutoFileName(AFPChain afpChain){
 		return fileName;
 	}
 
-
 	private Structure getStructure(AtomCache cache, String name1, String file)
 	{
 
@@ -654,18 +647,6 @@ public String printHelp() {
 		buf.append("   -outFile (mandatory) a file that will contain the summary of all the pairwise alignments").append(newline);
 		buf.append(newline);
 
-		buf.append("--- database searches ---").append(newline);
-		buf.append("   -searchFile (mandatory) path to a PDB file that should be used in the search").append(newline);
-		buf.append("   -outFile (mandatory) a directory that will contain the results of the DB search").append(newline);
-		buf.append("   -nrCPU (optional) Number of CPUs to use for the database search. By default will use the all, but one CPU in the system.").append(newline);
-		buf.append("   -pdbFilePath (mandatory) Path to the directory in your file system that contains the PDB files.").append(newline);
-		buf.append("   -saveOutputDir (optional) a directory that will contain the detailed outputs of the alignments. By default will write XML files, if used together with -outputPDB, will write PDB files of the alignment.").append(newline);
-		buf.append(newline);
-
-		buf.append(" Once DB seaches are complete it is possible to view the results with:").append(newline);
-		buf.append("   -showDBresult (optional) path to a DB outFile to show. Also provide the -pdbFilePath parameter to enable visualisation of results.").append(newline);
-		buf.append(newline);
-
 		ConfigStrucAligParams params = alg.getParameters();
 		List<String> paramNames = params.getUserConfigParameters();
 		List<String> paramHelp = params.getUserConfigHelp();
