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Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
[jalview.git]
/
src
/
jalview
/
ws
/
sifts
/
SiftsClient.java
diff --git
a/src/jalview/ws/sifts/SiftsClient.java
b/src/jalview/ws/sifts/SiftsClient.java
index
50cf5cb
..
e04bbb7
100644
(file)
--- a/
src/jalview/ws/sifts/SiftsClient.java
+++ b/
src/jalview/ws/sifts/SiftsClient.java
@@
-26,6
+26,7
@@
import jalview.api.SiftsClientI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
+import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
import jalview.util.Format;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
import jalview.util.Format;
@@
-77,7
+78,7
@@
public class SiftsClient implements SiftsClientI
{
private Entry siftsEntry;
{
private Entry siftsEntry;
- private PDBfile pdb;
+ private StructureFile pdb;
private String pdbId;
private String pdbId;
@@
-147,10
+148,10
@@
public class SiftsClient implements SiftsClientI
* @param pdbId
* @throws SiftsException
*/
* @param pdbId
* @throws SiftsException
*/
- public SiftsClient(PDBfile pdb) throws SiftsException
+ public SiftsClient(StructureFile pdb) throws SiftsException
{
this.pdb = pdb;
{
this.pdb = pdb;
- this.pdbId = pdb.id;
+ this.pdbId = pdb.getId();
File siftsFile = getSiftsFile(pdbId);
siftsEntry = parseSIFTs(siftsFile);
}
File siftsFile = getSiftsFile(pdbId);
siftsEntry = parseSIFTs(siftsFile);
}
@@
-167,7
+168,7
@@
public class SiftsClient implements SiftsClientI
public SiftsClient(PDBfile pdb, File siftsFile) throws SiftsException
{
this.pdb = pdb;
public SiftsClient(PDBfile pdb, File siftsFile) throws SiftsException
{
this.pdb = pdb;
- this.pdbId = pdb.id;
+ this.pdbId = pdb.getId();
siftsEntry = parseSIFTs(siftsFile);
}
siftsEntry = parseSIFTs(siftsFile);
}
@@
-456,7
+457,7
@@
public class SiftsClient implements SiftsClientI
{
ArrayList<Integer> omitNonObserved = new ArrayList<Integer>();
int nonObservedShiftIndex = 0;
{
ArrayList<Integer> omitNonObserved = new ArrayList<Integer>();
int nonObservedShiftIndex = 0;
- System.out.println("Generating mappings for : " + entityId);
+ // System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
String originalSeq = AlignSeq.extractGaps(
Entity entity = null;
entity = getEntityById(entityId);
String originalSeq = AlignSeq.extractGaps(
@@
-491,8
+492,8
@@
public class SiftsClient implements SiftsClientI
for (Segment segment : segments)
{
segStartEnd = segment.getStart() + " - " + segment.getEnd();
for (Segment segment : segments)
{
segStartEnd = segment.getStart() + " - " + segment.getEnd();
- System.out.println("Mappging segments : " + segment.getSegId() + "\\"
- + segStartEnd);
+ // System.out.println("Mapping segments : " + segment.getSegId() + "\\"
+ // + segStartEnd);
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
{
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
{
@@
-519,6
+520,7
@@
public class SiftsClient implements SiftsClientI
{
currSeqIndex = Integer.valueOf(resNumIndexString
.split("[a-zA-Z]")[0]);
{
currSeqIndex = Integer.valueOf(resNumIndexString
.split("[a-zA-Z]")[0]);
+ continue;
}
if (pdbRefDb != null)
{
}
if (pdbRefDb != null)
{
@@
-647,18
+649,25
@@
public class SiftsClient implements SiftsClientI
void populateAtomPositions(String chainId,
HashMap<Integer, int[]> mapping) throws IllegalArgumentException
{
void populateAtomPositions(String chainId,
HashMap<Integer, int[]> mapping) throws IllegalArgumentException
{
- PDBChain chain = pdb.findChain(chainId);
- if (chain == null || mapping == null)
- {
- throw new IllegalArgumentException(
- "Chain id or mapping must not be null.");
- }
- for (int[] map : mapping.values())
+ try
{
{
- if (map[PDB_RES_POS] != UNASSIGNED)
+ PDBChain chain = pdb.findChain(chainId);
+
+ if (chain == null || mapping == null)
{
{
- map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
+ throw new IllegalArgumentException(
+ "Chain id or mapping must not be null.");
}
}
+ for (int[] map : mapping.values())
+ {
+ if (map[PDB_RES_POS] != UNASSIGNED)
+ {
+ map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
+ }
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
}
}
}
}
@@
-763,8
+772,8
@@
public class SiftsClient implements SiftsClientI
Arrays.sort(keys);
int firstIndex = keys[0];
int lastIndex = keys[keys.length - 1];
Arrays.sort(keys);
int firstIndex = keys[0];
int lastIndex = keys[keys.length - 1];
- System.out.println("Min value " + firstIndex);
- System.out.println("Max value " + lastIndex);
+ // System.out.println("Min value " + firstIndex);
+ // System.out.println("Max value " + lastIndex);
for (int x = firstIndex; x <= lastIndex; x++)
{
if (!resNumMap.containsKey(x) && !omitNonObserved.contains(x))
for (int x = firstIndex; x <= lastIndex; x++)
{
if (!resNumMap.containsKey(x) && !omitNonObserved.contains(x))
@@
-853,8
+862,8
@@
public class SiftsClient implements SiftsClientI
++count;
}
Arrays.sort(sPojo, Collections.reverseOrder());
++count;
}
Arrays.sort(sPojo, Collections.reverseOrder());
- System.out.println("highest matched entity : " + sPojo[0].entityId);
- System.out.println("highest matched pid : " + sPojo[0].pid);
+ // System.out.println("highest matched entity : " + sPojo[0].entityId);
+ // System.out.println("highest matched pid : " + sPojo[0].pid);
if (sPojo[0].entityId != null)
{
if (sPojo[0].entityId != null)
{