X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Ffactories%2FStockholmIO.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Ffactories%2FStockholmIO.java;h=0000000000000000000000000000000000000000;hb=d27359893c99db0e749a59d8a7ab73ea751da09e;hp=a237251a04be1c4237b78847df30372542e76d92;hpb=9f55415c9f8005e9dcd8243453883ff853fd5b76;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/factories/StockholmIO.java b/src2/fr/orsay/lri/varna/factories/StockholmIO.java
deleted file mode 100644
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;
-	}
-}