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documentation and proxy call to util.MapList.getToWord(mpos)
[jalview.git]
/
src
/
jalview
/
io
/
DBRefFetcher.java
diff --git
a/src/jalview/io/DBRefFetcher.java
b/src/jalview/io/DBRefFetcher.java
index
445c90a
..
6d589f9
100644
(file)
--- a/
src/jalview/io/DBRefFetcher.java
+++ b/
src/jalview/io/DBRefFetcher.java
@@
-36,7
+36,7
@@
import jalview.gui.*;
public class DBRefFetcher
\r
implements Runnable
\r
{
\r
public class DBRefFetcher
\r
implements Runnable
\r
{
\r
- AlignmentI dataset;
\r
+ SequenceI [] dataset;
\r
AlignFrame af;
\r
CutAndPasteTransfer output = new CutAndPasteTransfer();
\r
StringBuffer sbuffer = new StringBuffer();
\r
AlignFrame af;
\r
CutAndPasteTransfer output = new CutAndPasteTransfer();
\r
StringBuffer sbuffer = new StringBuffer();
\r
@@
-55,7
+55,7
@@
public class DBRefFetcher
try
\r
{
\r
// 1. Load the mapping information from the file
\r
try
\r
{
\r
// 1. Load the mapping information from the file
\r
- Mapping map = new Mapping(uni.getClass().getClassLoader());
\r
+ org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader());
\r
java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
\r
map.loadMapping(url);
\r
\r
java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
\r
map.loadMapping(url);
\r
\r
@@
-80,10
+80,18
@@
public class DBRefFetcher
* @param align DOCUMENT ME!
\r
* @param ap DOCUMENT ME!
\r
*/
\r
* @param align DOCUMENT ME!
\r
* @param ap DOCUMENT ME!
\r
*/
\r
- public DBRefFetcher(AlignmentI align, AlignFrame af)
\r
+ public DBRefFetcher(SequenceI [] seqs, AlignFrame af)
\r
{
\r
this.af = af;
\r
{
\r
this.af = af;
\r
- this.dataset = align.getDataset();
\r
+ SequenceI [] ds = new SequenceI[seqs.length];
\r
+ for (int i = 0; i < seqs.length; i++)
\r
+ {
\r
+ if(seqs[i].getDatasetSequence()!=null)
\r
+ ds[i] = seqs[i].getDatasetSequence();
\r
+ else
\r
+ ds[i] = seqs[i];
\r
+ }
\r
+ this.dataset = ds;
\r
}
\r
\r
public boolean fetchDBRefs(boolean waitTillFinished)
\r
}
\r
\r
public boolean fetchDBRefs(boolean waitTillFinished)
\r
@@
-157,16
+165,15
@@
public class DBRefFetcher
try
\r
{
\r
int seqIndex = 0;
\r
try
\r
{
\r
int seqIndex = 0;
\r
- Vector sequences = dataset.getSequences();
\r
\r
\r
- while (seqIndex < sequences.size())
\r
+ while (seqIndex < dataset.length)
\r
{
\r
StringBuffer queryString = new StringBuffer("uniprot:");
\r
\r
{
\r
StringBuffer queryString = new StringBuffer("uniprot:");
\r
\r
- for (int i = 0; (seqIndex < sequences.size()) && (i < 50);
\r
+ for (int i = 0; (seqIndex < dataset.length) && (i < 50);
\r
seqIndex++, i++)
\r
{
\r
seqIndex++, i++)
\r
{
\r
- Sequence sequence = (Sequence) sequences.get(seqIndex);
\r
+ SequenceI sequence = dataset[seqIndex];
\r
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.
\r
getDBRef(), new String[]
\r
{
\r
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.
\r
getDBRef(), new String[]
\r
{
\r