From: Natasha <cherstn@main-home.(none)>
Date: Wed, 12 Dec 2012 21:02:44 +0000 (+0000)
Subject: Output accession number for file in stockholm format
X-Git-Tag: Release_2_8_0b1~1^2~70^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=556a6d1cc13445f1ce1da5406daf516bf117c8cc;p=jalview.git

Output accession number for file in stockholm format
---

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 62fec79..c6a3ce4 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -44,7 +44,7 @@ import jalview.util.Format;
 public class StockholmFile extends AlignFile
 {
   // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
-  StringBuffer out;
+  StringBuffer out; // output buffer
   AlignmentI al;
   
   public StockholmFile()
@@ -143,8 +143,23 @@ public class StockholmFile extends AlignFile
       if (rend.search(line))
       {
         // End of the alignment, pass stuff back
-
         this.noSeqs = seqs.size();
+        
+        String propety = null;
+        Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam
+        Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam
+        if (getAlignmentProperty("AC") != null)
+        {
+          String dbType = getAlignmentProperty("AC").toString();
+          if (pf.search(dbType))
+          {
+            propety = "PFAM";
+          }
+          else if (rf.search(dbType))
+          {
+        	propety = "RFAM";
+          }
+        }
         // logger.debug("Number of sequences: " + this.noSeqs);
         Enumeration accs = seqs.keys();
         while (accs.hasMoreElements())
@@ -187,6 +202,9 @@ public class StockholmFile extends AlignFile
             String desc = (String) accAnnotations.get("DE");
             seqO.setDescription((desc == null) ? "" : desc);
           }
+          
+         
+            
           // Add DB References (if any)
           if (accAnnotations != null && accAnnotations.containsKey("DR"))
           {
@@ -196,10 +214,21 @@ public class StockholmFile extends AlignFile
               String src = dbr.substring(0, dbr.indexOf(";"));
               String acn = dbr.substring(dbr.indexOf(";") + 1);
               jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
-              // seqO.addDBRef(dbref);
-            }
-          }  
-
+            }            
+          }
+          
+          if (accAnnotations != null && accAnnotations.containsKey("AC") && propety != null)
+          {
+            String dbr = (String) accAnnotations.get("AC");
+            if (dbr != null)
+            {
+              String src = propety;
+              String acn = dbr.toString();
+              jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
+            }            
+          }
+          
+      
           Hashtable features = null;
           // We need to adjust the positions of all features to account for gaps
           try
@@ -548,9 +577,12 @@ public class StockholmFile extends AlignFile
     convert1 = openparen.replaceAll(annots);
     convert2 = closeparen.replaceAll(convert1);
     annots = convert2;
-
-    String type = (label.indexOf("_cons") == label.length() - 5) ? label
-            .substring(0, label.length() - 5) : label;
+    
+    String type = label;
+    if (label.contains("_cons")) {
+    	type = (label.indexOf("_cons") == label.length() - 5) ? label
+                .substring(0, label.length() - 5) : label;	
+    }	   
     boolean ss = false;
     type = id2type(type);
     if (type.equals("secondary structure"))
@@ -616,13 +648,14 @@ public class StockholmFile extends AlignFile
     }
     return annot;
   }
-
+  
   public String print(SequenceI[] s)
   {
 	  // find max length of id
 	    int max = 0;
 	    int maxid = 0;
 	    int in = 0;
+	    Hashtable dataRef = null;
 	    while ((in < s.length) && (s[in] != null))
 	    {
 	      String tmp = printId(s[in]);
@@ -635,17 +668,64 @@ public class StockholmFile extends AlignFile
 	      {
 	        maxid = tmp.length();
 	      }
-
+	      if (s[in].getDBRef() != null)
+	      {  
+	    	for (int idb = 0; idb < s[in].getDBRef().length; idb++)
+	    	{		
+	    	  if (dataRef == null) 
+	    		dataRef = new Hashtable();
+  
+	    	  String datAs1 = s[in].getDBRef()[idb].getSource().toString() + " ; " +s[in].getDBRef()[idb].getAccessionId().toString();
+	    	  dataRef.put(tmp, datAs1);
+            }
+          }
 	      in++;
 	    }
 	    maxid += 9;
 	    int i = 0;
 	    
+	    // output database type
+	    if (al.getProperties() != null)
+	    {
+	      if (!al.getProperties().isEmpty())
+	      {
+	        Enumeration key = al.getProperties().keys();
+	        Enumeration val = al.getProperties().elements();
+	        while (key.hasMoreElements())
+	        {  
+	    	   out.append("#=GF " + key.nextElement() + " " + val.nextElement());
+	           out.append(newline);
+	        }
+	      }  
+	    }
+	    
+	    // output  database accessions 
+	    if (dataRef != null)
+	    {
+	      Enumeration en = dataRef.keys();    
+	      while (en.hasMoreElements())
+	      {
+	         Object idd = en.nextElement();
+	         String type = (String) dataRef.remove(idd);
+	         out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS " +idd.toString() + " "));
+	         if (type.contains("PFAM") || type.contains("RFAM") )
+	         {
+	        
+	        	out.append(" AC " + type.substring(type.indexOf(";") + 1));
+	         } else
+	         {
+	    	    out.append(" DR " + type + " ");
+	         }
+	    	 out.append(newline);
+	      } 
+	    }
+	    
+	    // output annotations
 	    while (i < s.length && s[i] != null) 
 	    {
 	      if (s[i].getDatasetSequence() != null) 
 	      {
-	    	SequenceI ds = s[i].getDatasetSequence();
+	    	SequenceI ds = s[i].getDatasetSequence();	
 			AlignmentAnnotation[] alAnot;
 		    Annotation[] ann;
 		    Annotation annot;  
@@ -661,7 +741,7 @@ public class StockholmFile extends AlignFile
 			    }   
 			    String key = type2id(feature);
 			    
-		          // output annotations
+		       
 		        if (key == null)
 		            continue;
 		        
@@ -711,13 +791,16 @@ public class StockholmFile extends AlignFile
 	          continue;
 	        }
 	        String seq = "";
-	        String label = type2id(aa.label);
+	        String label;
+	        
+	        if (aa.label.equals("seq"))
+	          label = "seq_cons";
+	        else
+	          label = type2id(aa.label.toLowerCase())+"_cons";
 
 	        if (label == null) 
 	          label = aa.label; 	
-	        
-	        label += "_cons";
-	        
+	         
 	        out.append(new Format("%-" + maxid + "s").form("#=GC " + label+" "));
 	        for (int j = 0; j < aa.annotations.length; j++) 
 	        {
@@ -803,7 +886,7 @@ public class StockholmFile extends AlignFile
           break;
         }
       }  
-      if (key != null)
+      if (key != null) 
       {
          return (String) key;
       }