JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / srcjar / fr / orsay / lri / varna / utils / TranslateFormatRNaseP.java

diff --git a/srcjar/fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java b/srcjar/fr/orsay/lri/varna/utils/TranslateFormatRNaseP.java
deleted file mode 100644 (file)
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();
-       }
-}