X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Ffactories%2FStockholmIO.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Ffactories%2FStockholmIO.java;h=a237251a04be1c4237b78847df30372542e76d92;hb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;hp=0000000000000000000000000000000000000000;hpb=9dabc02511e3a334a5749a504f57f69d6c9017bd;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/factories/StockholmIO.java b/srcjar/fr/orsay/lri/varna/factories/StockholmIO.java
new file mode 100644
index 0000000..a237251
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/factories/StockholmIO.java
@@ -0,0 +1,91 @@
+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;
+	}
+}