DBRefs now array

diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index 4488d02..01e67cf 100644 (file)
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -135,13 +135,13 @@ public class DBRefFetcher implements Runnable
              seqIndex++, i++)\r
         {\r
           Sequence sequence = (Sequence) sequences.get(seqIndex);\r
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {\r
+          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {\r
               jalview.datamodel.DBRefSource.UNIPROT});\r
           if (uprefs!=null)\r
           {\r
             // we know the id for this entry, so don't note its ID in the unknownSequences list\r
-            for (int j=0,k=uprefs.size(); j<k; j++)\r
-              ids.add(((DBRefEntry) uprefs.get(j)).getAccessionId());\r
+            for (int j=0,k=uprefs.length; j<k; j++)\r
+              ids.add(uprefs[j].getAccessionId());\r
             unknownSequences.add(sequence);\r
           } else {\r
             if (!ids.contains(sequence.getName()))\r

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index b4dd1f6..1d63e5b 100755 (executable)
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -95,15 +95,14 @@ public class DasSequenceFeatureFetcher implements Runnable
     int refCount = 0;\r
     for(int i=0; i<sequences.length; i++)\r
     {\r
-      Vector dbref = sequences[i].getDBRef();\r
+      DBRefEntry [] dbref = sequences[i].getDBRef();\r
       if(dbref!=null)\r
       {\r
-        for(int j=0; j<dbref.size(); j++)\r
+        for(int j=0; j<dbref.length; j++)\r
         {\r
-          DBRefEntry entry = (DBRefEntry)dbref.elementAt(j);\r
-          System.out.println(entry.getSource()\r
+          System.out.println(dbref[j].getSource()\r
                              +" "+jalview.datamodel.DBRefSource.UNIPROT);\r
-          if(entry.getSource()\r
+          if(dbref[j].getSource()\r
              .equals(jalview.datamodel.DBRefSource.UNIPROT))\r
           {\r
             System.out.println("got a match");\r
@@ -344,7 +343,7 @@ public class DasSequenceFeatureFetcher implements Runnable
       int seqIndex = 0;\r
       while (seqIndex < sequences.length)\r
       {\r
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),\r
+          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),\r
               new String[]  {\r
               jalview.datamodel.DBRefSource.PDB,\r
               jalview.datamodel.DBRefSource.UNIPROT});\r
@@ -356,15 +355,14 @@ public class DasSequenceFeatureFetcher implements Runnable
             if (uprefs != null)\r
             {\r
               // we know the id for this entry, so don't note its ID in the unknownSequences list\r
-              for (int j = 0;  j < uprefs.size(); j++)\r
+              for (int j = 0;  j < uprefs.length; j++)\r
               {\r
 \r
                 // Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end\r
                 org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
                 for (int l=0; l<cs.length; l++)\r
                 {\r
-                  if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)\r
-                      uprefs.get(j)))\r
+                  if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))\r
                   {\r
                     Cache.log.debug("Launched fetcher for coordinate system " +\r
                                     cs[l].getName());\r
@@ -372,8 +370,7 @@ public class DasSequenceFeatureFetcher implements Runnable
 \r
                     createFeatureFetcher(sequences[seqIndex],\r
                                          dasSource.getUrl(),\r
-                                         ( (DBRefEntry) uprefs.get(j)).\r
-                                         getAccessionId(),\r
+                                          uprefs[j].getAccessionId(),\r
                                          dasSource.getNickname());\r
                   }\r
                 }\r

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 1e4f905..300a9ba 100755 (executable)
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -224,19 +224,17 @@ public class ModellerDescription
       if (seq.getDatasetSequence() != null &&\r
           seq.getDatasetSequence().getDBRef() != null)\r
       {\r
-        Vector dbr = seq.getDatasetSequence().getDBRef();\r
+        jalview.datamodel.DBRefEntry [] dbr = seq.getDatasetSequence().getDBRef();\r
         int i, j;\r
-        for (i = 0, j = dbr.size(); i < j; i++)\r
+        for (i = 0, j = dbr.length; i < j; i++)\r
         {\r
-          jalview.datamodel.DBRefEntry dref = (jalview.datamodel.DBRefEntry)\r
-              dbr.elementAt(i);\r
-          if (dref != null)\r
+          if (dbr[i] != null)\r
           {\r
             // JBPNote PDB dbRefEntry needs properties to propagate onto ModellerField\r
             // JBPNote Need to get info from the user about whether the sequence is the one being modelled, or if it is a template.\r
-            if (dref.getSource().equals(jalview.datamodel.DBRefSource.PDB))\r
+            if (dbr[i].getSource().equals(jalview.datamodel.DBRefSource.PDB))\r
             {\r
-              fields.put(Fields[LOCALID], dref.getAccessionId());\r
+              fields.put(Fields[LOCALID], dbr[i].getAccessionId());\r
               t = 2;\r
               break;\r
             }\r

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 391c9a8..782e0ed 100755 (executable)
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -163,14 +163,13 @@ public class WSWUBlastClient
             }\r
           }\r
 \r
-          Vector entries = oldseq.getDBRef();\r
+          DBRefEntry [] entries = oldseq.getDBRef();\r
           if (entries != null)\r
           {\r
-            DBRefEntry entry = (DBRefEntry) entries.elementAt(0);\r
             oldseq.addDBRef(new jalview.datamodel.\r
                                                  DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,\r
                 "0",\r
-                entry.getAccessionId()));\r
+                entries[0].getAccessionId()));\r
           }\r
         }\r
       }\r

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 2f844da..d3788ea 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -4,6 +4,7 @@ import java.util.*;
 
 import jalview.datamodel.*;
 
+
 public class DBRefUtils
 {
     /**
@@ -15,23 +16,29 @@ public class DBRefUtils
      * @param sources String[] array of source DBRef IDs to retrieve
      * @return Vector
      */
-    public static Vector selectRefs(java.util.Vector dbrefs, String[] sources) {
+    public static DBRefEntry [] selectRefs(DBRefEntry [] dbrefs, String[] sources) {
       if (dbrefs==null)
         return null;
       if (sources==null)
         return dbrefs;
       Hashtable srcs = new Hashtable();
       Vector res=new Vector();
+
       for (int i=0; i<sources.length; i++)
         srcs.put(new String(sources[i]), new Integer(i));
-      for (int i=0, j=dbrefs.size(); i<j; i++)
-        if (dbrefs.get(i) instanceof jalview.datamodel.DBRefEntry) {
-          jalview.datamodel.DBRefEntry entry = (jalview.datamodel.DBRefEntry) dbrefs.get(i);
-          if (srcs.containsKey(entry.getSource()))
-            res.add(entry);
+      for (int i = 0, j = dbrefs.length; i < j; i++)
+        {
+          if (srcs.containsKey(dbrefs[i].getSource()))
+            res.add(dbrefs[i]);
         }
+
       if (res.size()>0)
-        return res;
+      {
+        DBRefEntry [] reply = new DBRefEntry[res.size()];
+        for(int i=0; i<res.size(); i++)
+          reply[i] = (DBRefEntry)res.elementAt(i);
+        return reply;
+      }
       res = null;
       // there are probable  memory leaks in the hashtable!
       return null;