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Undo changes to JabaWsServerQuery.java
[jalview.git]
/
src
/
jalview
/
structure
/
StructureSelectionManager.java
diff --git
a/src/jalview/structure/StructureSelectionManager.java
b/src/jalview/structure/StructureSelectionManager.java
index
9396be1
..
ac2897d
100644
(file)
--- a/
src/jalview/structure/StructureSelectionManager.java
+++ b/
src/jalview/structure/StructureSelectionManager.java
@@
-28,7
+28,7
@@
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
+import jalview.io.AppletFormatAdapter;
import jalview.util.MessageManager;
import java.io.PrintStream;
import jalview.util.MessageManager;
import java.io.PrintStream;
@@
-260,11
+260,10
@@
public class StructureSelectionManager
{
for (AlignmentAnnotation ala : ds.getAnnotation())
{
{
for (AlignmentAnnotation ala : ds.getAnnotation())
{
-
// false if any annotation present from this structure
// JBPNote this fails for jmol/chimera view because the *file* is
// passed, not the structure data ID -
// false if any annotation present from this structure
// JBPNote this fails for jmol/chimera view because the *file* is
// passed, not the structure data ID -
- if (MCview.PDBfile.isCalcIdForFile(ala.getCalcId(),
+ if (MCview.PDBfile.isCalcIdForFile(ala,
findIdForPDBFile(pdbFile)))
{
parseSecStr = false;
findIdForPDBFile(pdbFile)))
{
parseSecStr = false;
@@
-277,7
+276,7
@@
public class StructureSelectionManager
{
pdb = new MCview.PDBfile(true, parseSecStr, pdbFile, protocol);
if (pdb.id != null && pdb.id.trim().length() > 0
{
pdb = new MCview.PDBfile(true, parseSecStr, pdbFile, protocol);
if (pdb.id != null && pdb.id.trim().length() > 0
- && FormatAdapter.FILE.equals(protocol))
+ && AppletFormatAdapter.FILE.equals(protocol))
{
registerPDBFile(pdb.id.trim(), pdbFile);
}
{
registerPDBFile(pdb.id.trim(), pdbFile);
}
@@
-361,11
+360,13
@@
public class StructureSelectionManager
+ maxChain.residues.size() + "\n\n");
PrintStream ps = new PrintStream(System.out)
{
+ maxChain.residues.size() + "\n\n");
PrintStream ps = new PrintStream(System.out)
{
+ @Override
public void print(String x)
{
mappingDetails.append(x);
}
public void print(String x)
{
mappingDetails.append(x);
}
+ @Override
public void println()
{
mappingDetails.append("\n");
public void println()
{
mappingDetails.append("\n");
@@
-381,7
+382,10
@@
public class StructureSelectionManager
+ (maxAlignseq.seq1end + sequence[s].getEnd() - 1));
maxChain.makeExactMapping(maxAlignseq, sequence[s]);
+ (maxAlignseq.seq1end + sequence[s].getEnd() - 1));
maxChain.makeExactMapping(maxAlignseq, sequence[s]);
-
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
+ sqmpping.getMap().getInverse());
maxChain.transferRESNUMFeatures(sequence[s], null);
// allocate enough slots to store the mapping from positions in
maxChain.transferRESNUMFeatures(sequence[s], null);
// allocate enough slots to store the mapping from positions in
@@
-427,7
+431,7
@@
public class StructureSelectionManager
mappings[mappings.length - 1] = newMapping;
}
mappings[mappings.length - 1] = newMapping;
}
- maxChain.transferResidueAnnotation(newMapping);
+ maxChain.transferResidueAnnotation(newMapping, sqmpping);
}
// ///////
}
// ///////