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OnlyAddPDBEntries
author
amwaterhouse
<Andrew Waterhouse>
Thu, 10 Nov 2005 11:08:31 +0000
(11:08 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Thu, 10 Nov 2005 11:08:31 +0000
(11:08 +0000)
src/jalview/io/SequenceFeatureFetcher.java
patch
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diff --git
a/src/jalview/io/SequenceFeatureFetcher.java
b/src/jalview/io/SequenceFeatureFetcher.java
index
8bd9bab
..
5ecb417
100755
(executable)
--- a/
src/jalview/io/SequenceFeatureFetcher.java
+++ b/
src/jalview/io/SequenceFeatureFetcher.java
@@
-196,7
+196,6
@@
public class SequenceFeatureFetcher implements Runnable
return;
\r
\r
SequenceI sequence = null;
\r
return;
\r
\r
SequenceI sequence = null;
\r
- // String pdb = null;
\r
\r
Vector entries = getUniprotEntries(file);
\r
\r
\r
Vector entries = getUniprotEntries(file);
\r
\r
@@
-217,7
+216,7
@@
public class SequenceFeatureFetcher implements Runnable
\r
if (sequence == null)
\r
{
\r
\r
if (sequence == null)
\r
{
\r
- System.out.println("not found");
\r
+ System.out.println(idmatch+" not found");
\r
continue;
\r
}
\r
\r
continue;
\r
}
\r
\r
@@
-229,7
+228,6
@@
public class SequenceFeatureFetcher implements Runnable
int absStart = entry.getUniprotSequence().getContent().indexOf(
\r
nonGapped.toString());
\r
\r
int absStart = entry.getUniprotSequence().getContent().indexOf(
\r
nonGapped.toString());
\r
\r
- int residueOffset = 0;
\r
if (absStart == -1)
\r
{
\r
// Is UniprotSequence contained in dataset sequence?
\r
if (absStart == -1)
\r
{
\r
// Is UniprotSequence contained in dataset sequence?
\r
@@
-244,9
+242,9
@@
public class SequenceFeatureFetcher implements Runnable
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- if(entry.getFeatures()!=null)
\r
+ if(entry.getFeature()!=null)
\r
{
\r
{
\r
- Enumeration e = entry.getFeatures().elements();
\r
+ Enumeration e = entry.getFeature().elements();
\r
while (e.hasMoreElements())
\r
{
\r
SequenceFeature sf = (SequenceFeature) e.nextElement();
\r
while (e.hasMoreElements())
\r
{
\r
SequenceFeature sf = (SequenceFeature) e.nextElement();
\r
@@
-266,7
+264,19
@@
public class SequenceFeatureFetcher implements Runnable
int absEnd = absStart + nonGapped.toString().length();
\r
absStart += 1;
\r
\r
int absEnd = absStart + nonGapped.toString().length();
\r
absStart += 1;
\r
\r
- sequence.setSequenceFeatures(entry.getFeatures());
\r
+ Enumeration e = entry.getDbReference().elements();
\r
+ Vector onlyPdbEntries = new Vector();
\r
+ while(e.hasMoreElements())
\r
+ {
\r
+ PDBEntry pdb = (PDBEntry)e.nextElement();
\r
+ if(!pdb.getType().equals("PDB"))
\r
+ continue;
\r
+
\r
+ onlyPdbEntries.addElement(pdb);
\r
+ }
\r
+
\r
+ sequence.setPDBId(onlyPdbEntries);
\r
+ sequence.setSequenceFeatures(entry.getFeature());
\r
sequence.setStart(absStart);
\r
sequence.setEnd(absEnd);
\r
\r
sequence.setStart(absStart);
\r
sequence.setEnd(absEnd);
\r
\r