X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Futils%2FTranslateFormatRNaseP.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Futils%2FTranslateFormatRNaseP.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=7c999e5b6d5de4d2fccf836b8504cd80ed2f8f5d;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java b/srcjar/fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java
deleted file mode 100644
index 7c999e5..0000000
--- a/srcjar/fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java
+++ /dev/null
@@ -1,53 +0,0 @@
-/**
- * File written by Raphael Champeimont
- * UMR 7238 Genomique des Microorganismes
- */
-package fr.orsay.lri.varna.utils;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-public class TranslateFormatRNaseP {
-	public static void main(String[] args) throws Exception {
-		File templatesDir = new File(new File(System.getProperty("user.dir")), "templates");
-		File infile = new File(new File(templatesDir, "RNaseP_bact_a"), "a_bacterial_rnas.gb");
-		File outfile = new File(new File(templatesDir, "RNaseP_bact_a"), "alignment.fasta");
-		
-		BufferedReader inbuf = new BufferedReader(new FileReader(infile));
-		String line = inbuf.readLine();
-		String seqname;
-		List<String> seqnames = new ArrayList<String>();
-		List<String> sequences = new ArrayList<String>();
-		while (line != null) {
-			if (line.length() != 0) {
-				if (line.startsWith("LOCUS")) {
-					String parts[] = line.split("\\s+");
-					seqname = parts[1];
-					seqnames.add(seqname);
-					sequences.add("");
-				}
-				if (line.startsWith(" ")) {
-					String parts[] = line.split("\\s+");
-					for (int i=2; i<parts.length; i++) {
-						sequences.set(sequences.size()-1, sequences.get(sequences.size()-1) + parts[i]);
-					}
-				}
-			}
-			line = inbuf.readLine();
-		}
-		inbuf.close();
-		
-		BufferedWriter outbuf = new BufferedWriter(new FileWriter(outfile));
-		for (int i=2; i<seqnames.size(); i++) {
-			outbuf.write(">" + seqnames.get(i) + "\n");
-			outbuf.write(sequences.get(i) + "\n");
-		}
-		outbuf.close();
-	}
-}