From 0d6e36143a2d7471edb7ef386d0b79095e0cd63e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 21 Jul 2006 08:45:54 +0000
Subject: [PATCH] DBRefs now array
---
src/jalview/io/DBRefFetcher.java | 6 +++---
src/jalview/io/DasSequenceFeatureFetcher.java | 19 ++++++++-----------
src/jalview/io/ModellerDescription.java | 12 +++++-------
src/jalview/io/WSWUBlastClient.java | 5 ++---
src/jalview/util/DBRefUtils.java | 21 ++++++++++++++-------
5 files changed, 32 insertions(+), 31 deletions(-)
diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index 4488d02..01e67cf 100644
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -135,13 +135,13 @@ public class DBRefFetcher implements Runnable
seqIndex++, i++)
{
Sequence sequence = (Sequence) sequences.get(seqIndex);
- Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {
+ DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {
jalview.datamodel.DBRefSource.UNIPROT});
if (uprefs!=null)
{
// we know the id for this entry, so don't note its ID in the unknownSequences list
- for (int j=0,k=uprefs.size(); j<k; j++)
- ids.add(((DBRefEntry) uprefs.get(j)).getAccessionId());
+ for (int j=0,k=uprefs.length; j<k; j++)
+ ids.add(uprefs[j].getAccessionId());
unknownSequences.add(sequence);
} else {
if (!ids.contains(sequence.getName()))
diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index b4dd1f6..1d63e5b 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -95,15 +95,14 @@ public class DasSequenceFeatureFetcher implements Runnable
int refCount = 0;
for(int i=0; i<sequences.length; i++)
{
- Vector dbref = sequences[i].getDBRef();
+ DBRefEntry [] dbref = sequences[i].getDBRef();
if(dbref!=null)
{
- for(int j=0; j<dbref.size(); j++)
+ for(int j=0; j<dbref.length; j++)
{
- DBRefEntry entry = (DBRefEntry)dbref.elementAt(j);
- System.out.println(entry.getSource()
+ System.out.println(dbref[j].getSource()
+" "+jalview.datamodel.DBRefSource.UNIPROT);
- if(entry.getSource()
+ if(dbref[j].getSource()
.equals(jalview.datamodel.DBRefSource.UNIPROT))
{
System.out.println("got a match");
@@ -344,7 +343,7 @@ public class DasSequenceFeatureFetcher implements Runnable
int seqIndex = 0;
while (seqIndex < sequences.length)
{
- Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
+ DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
new String[] {
jalview.datamodel.DBRefSource.PDB,
jalview.datamodel.DBRefSource.UNIPROT});
@@ -356,15 +355,14 @@ public class DasSequenceFeatureFetcher implements Runnable
if (uprefs != null)
{
// we know the id for this entry, so don't note its ID in the unknownSequences list
- for (int j = 0; j < uprefs.size(); j++)
+ for (int j = 0; j < uprefs.length; j++)
{
// 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
org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
for (int l=0; l<cs.length; l++)
{
- if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)
- uprefs.get(j)))
+ if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))
{
Cache.log.debug("Launched fetcher for coordinate system " +
cs[l].getName());
@@ -372,8 +370,7 @@ public class DasSequenceFeatureFetcher implements Runnable
createFeatureFetcher(sequences[seqIndex],
dasSource.getUrl(),
- ( (DBRefEntry) uprefs.get(j)).
- getAccessionId(),
+ uprefs[j].getAccessionId(),
dasSource.getNickname());
}
}
diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 1e4f905..300a9ba 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -224,19 +224,17 @@ public class ModellerDescription
if (seq.getDatasetSequence() != null &&
seq.getDatasetSequence().getDBRef() != null)
{
- Vector dbr = seq.getDatasetSequence().getDBRef();
+ jalview.datamodel.DBRefEntry [] dbr = seq.getDatasetSequence().getDBRef();
int i, j;
- for (i = 0, j = dbr.size(); i < j; i++)
+ for (i = 0, j = dbr.length; i < j; i++)
{
- jalview.datamodel.DBRefEntry dref = (jalview.datamodel.DBRefEntry)
- dbr.elementAt(i);
- if (dref != null)
+ if (dbr[i] != null)
{
// JBPNote PDB dbRefEntry needs properties to propagate onto ModellerField
// JBPNote Need to get info from the user about whether the sequence is the one being modelled, or if it is a template.
- if (dref.getSource().equals(jalview.datamodel.DBRefSource.PDB))
+ if (dbr[i].getSource().equals(jalview.datamodel.DBRefSource.PDB))
{
- fields.put(Fields[LOCALID], dref.getAccessionId());
+ fields.put(Fields[LOCALID], dbr[i].getAccessionId());
t = 2;
break;
}
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 391c9a8..782e0ed 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -163,14 +163,13 @@ public class WSWUBlastClient
}
}
- Vector entries = oldseq.getDBRef();
+ DBRefEntry [] entries = oldseq.getDBRef();
if (entries != null)
{
- DBRefEntry entry = (DBRefEntry) entries.elementAt(0);
oldseq.addDBRef(new jalview.datamodel.
DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,
"0",
- entry.getAccessionId()));
+ entries[0].getAccessionId()));
}
}
}
diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 2f844da..d3788ea 100755
--- 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;
--
1.7.10.2