From 5e843947fc32d34012e8033b6c0eb8e25b44dd6a Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 19 Dec 2008 15:36:08 +0000
Subject: [PATCH] simple transformation of feature types like dbref and dbxref
 into database references

---
 src/jalview/ws/DasSequenceFeatureFetcher.java |  123 +++++++++++++++++--------
 1 file changed, 86 insertions(+), 37 deletions(-)

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 1038ed9..5f7f2ba 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -477,45 +477,48 @@ public class DasSequenceFeatureFetcher
         {
           for (int i = 0; i < features.length; i++)
           {
+            // standard DAS feature-> jalview sequence feature transformation
             SequenceFeature f = newSequenceFeature(features[i], source
                     .getNickname());
-            if (dbref.getMap() != null && f.getBegin() > 0
-                    && f.getEnd() > 0)
+            if (!parseSeqFeature(seq, f, features[i], source))
             {
-              debug("mapping from " + f.getBegin() + " - " + f.getEnd());
-              SequenceFeature vf[] = null;
-
-              try
-              {
-                vf = dbref.getMap().locateFeature(f);
-              } catch (Exception ex)
+              if (dbref.getMap() != null && f.getBegin() > 0
+                      && f.getEnd() > 0)
               {
-                Cache.log
-                        .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to help@jalview.org.");
-                Cache.log.info("Mapping feature from " + f.getBegin()
-                        + " to " + f.getEnd() + " in dbref "
-                        + dbref.getAccessionId() + " in "
-                        + dbref.getSource());
-                Cache.log.info("using das Source " + ds.getUrl());
-                Cache.log.info("Exception", ex);
-              }
+                debug("mapping from " + f.getBegin() + " - " + f.getEnd());
+                SequenceFeature vf[] = null;
 
-              if (vf != null)
-              {
-                for (int v = 0; v < vf.length; v++)
+                try
+                {
+                  vf = dbref.getMap().locateFeature(f);
+                } catch (Exception ex)
+                {
+                  Cache.log
+                          .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
+                  Cache.log.info("Mapping feature from " + f.getBegin()
+                          + " to " + f.getEnd() + " in dbref "
+                          + dbref.getAccessionId() + " in "
+                          + dbref.getSource());
+                  Cache.log.info("using das Source " + ds.getUrl());
+                  Cache.log.info("Exception", ex);
+                }
+
+                if (vf != null)
                 {
-                  debug("mapping to " + v + ": " + vf[v].getBegin() + " - "
-                          + vf[v].getEnd());
-                  seq.addSequenceFeature(vf[v]);
+                  for (int v = 0; v < vf.length; v++)
+                  {
+                    debug("mapping to " + v + ": " + vf[v].getBegin()
+                            + " - " + vf[v].getEnd());
+                    seq.addSequenceFeature(vf[v]);
+                  }
                 }
               }
-            }
-            else
-            {
-              seq.addSequenceFeature(f);
+              else
+              {
+                seq.addSequenceFeature(f);
+              }
             }
           }
-
           featuresAdded(seq);
         }
         else
@@ -578,10 +581,14 @@ public class DasSequenceFeatureFetcher
           {
             for (int i = 0; i < features.length; i++)
             {
+              // standard DAS feature-> jalview sequence feature transformation
               SequenceFeature f = newSequenceFeature(features[i], source
                       .getNickname());
-
-              seq.addSequenceFeature(f);
+              if (!parseSeqFeature(seq, f, features[i], source))
+              {
+                // just add as a simple sequence feature
+                seq.addSequenceFeature(f);
+              }
             }
 
             featuresAdded(seq);
@@ -609,6 +616,42 @@ public class DasSequenceFeatureFetcher
   }
 
   /**
+   * examine the given sequence feature to determine if it should actually
+   * be turned into sequence annotation or database cross references rather
+   * than a simple sequence feature. 
+   * @param seq the sequence to annotate
+   * @param f the jalview sequence feature generated from the DAS feature 
+   * @param map the sequence feature attributes
+   * @param source the source that emitted the feature
+   * @return true if feature was consumed as another kind of annotation.
+   */
+  protected boolean parseSeqFeature(SequenceI seq, SequenceFeature f, Map map,
+          Das1Source source)
+  {
+    // check if source has biosapiens or other sequence ontology label
+    if (f.getType()!=null && (f.getType().equalsIgnoreCase("DBXREF")
+            || f.getType().equalsIgnoreCase("DBREF")))
+    {
+      // try to parse the accession out
+      
+      DBRefEntry dbr = new DBRefEntry();
+      dbr.setVersion(source.getNickname());
+      StringTokenizer st = new StringTokenizer(f.getDescription(),":");
+      if (st.hasMoreTokens())
+      {
+        dbr.setSource(st.nextToken());
+      }
+      if (st.hasMoreTokens())
+      {
+        dbr.setAccessionId(st.nextToken());
+      }
+      seq.addDBRef(dbr);
+      return true;
+    }
+    return false;
+  }
+
+  /**
    * creates a jalview sequence feature from a das feature document
    * 
    * @param dasfeature
@@ -651,7 +694,11 @@ public class DasSequenceFeatureFetcher
       }
       try
       {
-        score = (float) Double.parseDouble(dasfeature.get("SCORE").toString());
+        Object scr = dasfeature.get("SCORE");
+        if (scr!=null)
+          {score = (float) Double.parseDouble(scr.toString());
+          
+          }
       } catch (Exception ex)
       {
       }
@@ -662,12 +709,14 @@ public class DasSequenceFeatureFetcher
       if (dasfeature.containsKey("LINK"))
       {
         // Do not put feature extent in link text for non-positional features
-        if (f.begin==0 && f.end==0)
-        {        f.addLink(f.getType()+"|"
-                + dasfeature.get("LINK"));
-        } else {
+        if (f.begin == 0 && f.end == 0)
+        {
+          f.addLink(f.getType() + "|" + dasfeature.get("LINK"));
+        }
+        else
+        {
           f.addLink(f.getType() + " " + f.begin + "_" + f.end + "|"
-                        + dasfeature.get("LINK"));
+                  + dasfeature.get("LINK"));
         }
       }
 
-- 
1.7.10.2