JAL-3032 upgrade to Jmol 14.29.17; clearing of src2 directory

[jalview.git] / src2 / fr / orsay / lri / varna / models / templates / BatchBenchmarkPrepare.java

diff --git a/src2/fr/orsay/lri/varna/models/templates/BatchBenchmarkPrepare.java b/src2/fr/orsay/lri/varna/models/templates/BatchBenchmarkPrepare.java
deleted file mode 100644 (file)
index c3ab8ac..0000000
--- a/src2/fr/orsay/lri/varna/models/templates/BatchBenchmarkPrepare.java
+++ /dev/null
@@ -1,98 +0,0 @@
-/**
- * File written by Raphael Champeimont
- * UMR 7238 Genomique des Microorganismes
- */
-package fr.orsay.lri.varna.models.templates;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.util.ArrayList;
-import java.util.List;
-
-import fr.orsay.lri.varna.factories.RNAFactory;
-
-public class BatchBenchmarkPrepare {
-
-       /**
-        * We assume given directory contains a alignemnt.fasta file,
-        * of which the first sequence is the consensus structure,
-        * and the other sequences are aligned nucleotides. 
-        * The principle is to convert it to a set of secondary structure,
-        * using the following rule:
-        * - keep the same nucleotides as in original sequence
-        * - keep base pairs where both bases of the pair are non-gaps in our sequence
-        */
-       public void benchmarkAllDir(File rootdir) throws Exception {
-               File seqdir = new File(rootdir, "sequences");
-               if (!seqdir.exists()) {
-                       seqdir.mkdir();
-               }
-               
-               File templateFile = new File(rootdir, "template.xml");
-               
-               ArrayList<String> seqnames = new ArrayList<String>();
-               ArrayList<String> sequences = new ArrayList<String>();
-               BatchBenchmark.readFASTA(new File(rootdir, "alignment.fasta"), seqnames, sequences);
-               
-               BufferedWriter outbufASS = new BufferedWriter(new FileWriter(new File(rootdir, "all_secondary_structures.fasta")));
-               
-               String consensusSecStr = sequences.get(0);
-               int[] consensusSecStrInt = RNAFactory.parseSecStr(consensusSecStr);
-               
-               List<File> templates = new ArrayList<File>();
-               for (int i=1; i<seqnames.size(); i++) {
-                       String seqname = seqnames.get(i);
-                       String sequence = sequences.get(i);
-                       String sequenceUngapped = sequence.replaceAll("[\\.-]", "");
-                       System.out.println(seqname);
-                       String ss = "";
-                       String nt = "";
-                       for (int j=0; j<sequence.length(); j++) {
-                               if (sequence.charAt(j) != '.' && sequence.charAt(j) != '-') {
-                                       if (consensusSecStr.charAt(j) == '-' || consensusSecStr.charAt(j) == '.') {
-                                               nt += sequence.charAt(j);
-                                               ss += '.';
-                                       } else {
-                                               int k = consensusSecStrInt[j];
-                                               // k is the matching base, is it aligned to a base in our sequence?
-                                               if (sequence.charAt(k) != '.' && sequence.charAt(k) != '-') {
-                                                       nt += sequence.charAt(j);
-                                                       ss += consensusSecStr.charAt(j);
-                                               } else {
-                                                       nt += sequence.charAt(j);
-                                                       ss += '.';
-                                               }
-                                       }
-                               }
-                       }
-                       
-                       if (!sequenceUngapped.equals(nt)) {
-                               System.out.println(sequenceUngapped);
-                               System.out.println(nt);
-                               throw new Error("bug");
-                       }
-                       
-                       // We now have the sequence with its secondary structure.
-                       File outfile = new File(seqdir, seqname + ".dbn");
-                       BufferedWriter outbuf = new BufferedWriter(new FileWriter(outfile));
-                       outbuf.write(">" + seqname + "\n");
-                       outbuf.write(nt + "\n");
-                       outbuf.write(ss + "\n");
-                       outbuf.close();
-                       
-                       outbufASS.write(">" + seqname + "\n");
-                       outbufASS.write(ss + "\n");
-                       
-                       templates.add(templateFile);
-               }
-               
-               outbufASS.close();
-               
-       }
-       
-       public static void main(String[] args) throws Exception {
-               new BatchBenchmarkPrepare().benchmarkAllDir(new File(new File("templates"), "RNaseP_bact_a"));
-       }
-       
-}