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

[jalview.git] / src2 / fr / orsay / lri / varna / factories / StockholmIO.java

diff --git a/src2/fr/orsay/lri/varna/factories/StockholmIO.java b/src2/fr/orsay/lri/varna/factories/StockholmIO.java
deleted file mode 100644 (file)
index a237251..0000000
--- a/src2/fr/orsay/lri/varna/factories/StockholmIO.java
+++ /dev/null
@@ -1,91 +0,0 @@
-package fr.orsay.lri.varna.factories;
-
-import java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.UnsupportedEncodingException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
-
-public class StockholmIO {
-       public static RNAAlignment readAlignementFromFile(String path) throws IOException
-       {
-               return StockholmIO.readAlignement(new BufferedReader(new FileReader(path)));
-       }
-       public static RNAAlignment readAlignementFromURL(String url) throws UnsupportedEncodingException, IOException
-       {
-               URL urlAb = new URL(url);
-               URLConnection urlConn = urlAb.openConnection(); 
-               urlConn.setUseCaches(false);
-               Reader r = new InputStreamReader(urlConn.getInputStream(),"UTF-8");
-               return readAlignement(new BufferedReader(r));
-       }
-
-       
-       /*public static Alignment readAlignement(Reader r) throws IOException
-       {
-               return readAlignement(new BufferedReader(r));
-       }*/
-       
-       public static RNAAlignment readAlignement(BufferedReader r) throws IOException
-       {
-               LinkedHashMap<String,StringBuffer> rawSeqs = new LinkedHashMap<String,StringBuffer>();
-               RNAAlignment result = new RNAAlignment();
-               String line = r.readLine(); 
-               String str = "";
-
-               while(line!=null)
-               {
-                       if (!line.startsWith("#"))
-                       {
-                               String[] data = line.split("\\s+");
-                               if (data.length>1)
-                               {
-                                       String seqName = data[0].trim();
-                                       String seq = data[1].trim();
-                                       if (!rawSeqs.containsKey(seqName))
-                                       {
-                                               rawSeqs.put(seqName,new StringBuffer());
-                                       }
-                                       StringBuffer val =  rawSeqs.get(seqName);
-                                       val.append(seq);
-                               }
-                               
-                       }
-                       else if (line.startsWith("#"))
-                       {
-                               String[] data = line.split("\\s+");
-                               if (line.startsWith("#=GC SS_cons"))
-                               {
-                                       str += data[2].trim();  
-                               }
-                               else if (line.startsWith("#=GS"))
-                               {
-                                       if (data[2].trim().equals("AC"))
-                                       {
-                                         result.setAccession(data[1].trim(),data[3].trim());
-                                         
-                                       }
-                               }
-                       }
-                               
-                       line = r.readLine(); 
-               }
-               result.setSecStr(str);
-               for(Map.Entry<String,StringBuffer> entry : rawSeqs.entrySet())
-               {
-                       String s = entry.getValue().toString();
-                       result.addSequence(entry.getKey(), s);
-               }
-               return result;
-       }
-}