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JAL-1824 updated caching procedure for pdb entries. Also refactored getPDBEntry metho...
[jalview.git]
/
src
/
MCview
/
PDBfile.java
diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
d81e734
..
58991f3
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-20,14
+20,6
@@
*/
package MCview;
*/
package MCview;
-import java.awt.Color;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
import jalview.analysis.AlignSeq;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.analysis.AlignSeq;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
@@
-37,6
+29,14
@@
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.util.MessageManager;
import jalview.io.FileParse;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
public class PDBfile extends jalview.io.AlignFile
{
private static String CALC_ID_PREFIX = "JalviewPDB";
public class PDBfile extends jalview.io.AlignFile
{
private static String CALC_ID_PREFIX = "JalviewPDB";
@@
-379,7
+379,7
@@
public class PDBfile extends jalview.io.AlignFile
final Object[] args = new Object[]
{ new FileParse(getDataName(), type) };
Object jmf = constructor.newInstance(args);
final Object[] args = new Object[]
{ new FileParse(getDataName(), type) };
Object jmf = constructor.newInstance(args);
- Alignment al = new Alignment((SequenceI[]) cl.getMethod(
+ AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
"getSeqsAsArray", new Class[]
{}).invoke(jmf));
cl.getMethod("addAnnotations", new Class[]
"getSeqsAsArray", new Class[]
{}).invoke(jmf));
cl.getMethod("addAnnotations", new Class[]
@@
-388,11
+388,11
@@
public class PDBfile extends jalview.io.AlignFile
{
if (sq.getDatasetSequence() != null)
{
{
if (sq.getDatasetSequence() != null)
{
- sq.getDatasetSequence().getPDBId().clear();
+ sq.getDatasetSequence().getAllPDBEntries().clear();
}
else
{
}
else
{
- sq.getPDBId().clear();
+ sq.getAllPDBEntries().clear();
}
}
replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
}
}
replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
@@
-456,16
+456,16
@@
public class PDBfile extends jalview.io.AlignFile
{
if (sq.getDatasetSequence() != null)
{
{
if (sq.getDatasetSequence() != null)
{
- if (sq.getDatasetSequence().getPDBId() != null)
+ if (sq.getDatasetSequence().getAllPDBEntries() != null)
{
{
- sq.getDatasetSequence().getPDBId().clear();
+ sq.getDatasetSequence().getAllPDBEntries().clear();
}
}
else
{
}
}
else
{
- if (sq.getPDBId() != null)
+ if (sq.getAllPDBEntries() != null)
{
{
- sq.getPDBId().clear();
+ sq.getAllPDBEntries().clear();
}
}
}
}
}
}