import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
* @author gmcarstairs
*
*/
-public abstract class AAStructureBindingModel extends
- SequenceStructureBindingModel implements StructureListener,
- StructureSelectionManagerProvider
+public abstract class AAStructureBindingModel
+ extends SequenceStructureBindingModel
+ implements StructureListener, StructureSelectionManagerProvider
{
private StructureSelectionManager ssm;
private SequenceI[][] sequence;
/*
- * array of target chains for sequences - tied to pdbentry and sequence[]
+ * array of list of target chains for sequences - tied to pdbentry and sequence[]
*/
- private String[][] chains;
+ private List<String>[][] chains;
/*
* datasource protocol for access to PDBEntrylatest
* @param ssm
* @param pdbentry
* @param sequenceIs
- * @param chains
* @param protocol
*/
public AAStructureBindingModel(StructureSelectionManager ssm,
this.nucleotide = Comparison.isNucleotide(sequenceIs);
this.pdbEntry = pdbentry;
this.protocol = protocol;
+ resolveChains();
}
+ private boolean resolveChains()
+ {
+ /**
+ * final count of chain mappings discovered
+ */
+ int chainmaps = 0;
+ // JBPNote: JAL-2693 - this should be a list of chain mappings per
+ // [pdbentry][sequence]
+ List<String>[][] newchains = new List[pdbEntry.length][];
+ int pe = 0;
+ for (PDBEntry pdb : pdbEntry)
+ {
+ SequenceI[] seqsForPdb = sequence[pe];
+ if (seqsForPdb != null)
+ {
+ newchains[pe] = new List[seqsForPdb.length];
+ int se = 0;
+ for (SequenceI asq : seqsForPdb)
+ {
+ List<String> chain = (chains != null && chains[pe] != null)
+ ? chains[pe][se]
+ : null;
+ if (chain == null)
+ {
+ chain = new ArrayList<>();
+ }
+ newchains[pe][se] = chain;
+
+ SequenceI sq = (asq.getDatasetSequence() == null) ? asq
+ : asq.getDatasetSequence();
+ if (sq.getAllPDBEntries() != null)
+ {
+ for (PDBEntry pdbentry : sq.getAllPDBEntries())
+ {
+ if (pdb.getFile() != null && pdbentry.getFile() != null
+ && pdb.getFile().equals(pdbentry.getFile()))
+ {
+ String chaincode = pdbentry.getChainCode();
+ if (chaincode != null && chaincode.length() > 0)
+ {
+ newchains[pe][se].add(chaincode);
+ chainmaps++;
+ }
+ }
+ }
+ }
+ se++;
+ }
+ pe++;
+ }
+ }
+
+ chains = newchains;
+ return chainmaps > 0;
+ }
public StructureSelectionManager getSsm()
{
return ssm;
return sequence;
}
- public String[][] getChains()
+ public List<String>[][] getChains()
{
return chains;
}
this.sequence = sequence;
}
- protected void setChains(String[][] chains)
+ protected void setChains(List<String>[][] chains)
{
this.chains = chains;
}
{
throw new Error(MessageManager.formatMessage(
"error.implementation_error_no_pdbentry_from_index",
- new Object[] { Integer.valueOf(pe).toString() }));
+ new Object[]
+ { Integer.valueOf(pe).toString() }));
}
- final String nullChain = "TheNullChain";
- List<SequenceI> s = new ArrayList<SequenceI>();
- List<String> c = new ArrayList<String>();
+ List<SequenceI> s = new ArrayList<>();
+ List<List<String>> c = new ArrayList<>();
if (getChains() == null)
{
- setChains(new String[getPdbCount()][]);
+ setChains(new List[getPdbCount()][]);
}
if (getSequence()[pe] != null)
{
}
else
{
- c.add(nullChain);
+ c.add(new ArrayList());
}
}
else
{
if (tchain != null && tchain.length > 0)
{
- c.add(nullChain);
+ c.add(new ArrayList());
}
}
}
s.add(seq[i]);
if (tchain != null && i < tchain.length)
{
- c.add(tchain[i] == null ? nullChain : tchain[i]);
+ List<String> clist = new ArrayList();
+ c.add(clist);
+ if (tchain[i] != null)
+ {
+ clist.add(tchain[i]);
+ }
}
}
}
getSequence()[pe] = tmp;
if (c.size() > 0)
{
- String[] tch = c.toArray(new String[c.size()]);
- for (int i = 0; i < tch.length; i++)
- {
- if (tch[i] == nullChain)
- {
- tch[i] = null;
- }
- }
+ List<String>[] tch = c.toArray(new List[c.size()]);
getChains()[pe] = tch;
}
else
public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
SequenceI[][] seq, String[][] chns)
{
- List<PDBEntry> v = new ArrayList<PDBEntry>();
- List<int[]> rtn = new ArrayList<int[]>();
+ List<PDBEntry> v = new ArrayList<>();
+ List<int[]> rtn = new ArrayList<>();
for (int i = 0; i < getPdbCount(); i++)
{
v.add(getPdbEntry(i));
{
// expand the tied sequence[] and string[] arrays
SequenceI[][] sqs = new SequenceI[getPdbCount()][];
- String[][] sch = new String[getPdbCount()][];
+ List<String>[][] sch = new List[getPdbCount()][];
System.arraycopy(getSequence(), 0, sqs, 0, getSequence().length);
System.arraycopy(getChains(), 0, sch, 0, this.getChains().length);
setSequence(sqs);
if (waiting)
{
- System.err
- .println("Timed out waiting for structure viewer to load file "
+ System.err.println(
+ "Timed out waiting for structure viewer to load file "
+ notLoaded);
return false;
}
{
for (SequenceI s : seqs)
{
- if (s == seq
- || (s.getDatasetSequence() != null && s
- .getDatasetSequence() == seq
- .getDatasetSequence()))
+ if (s == seq || (s.getDatasetSequence() != null
+ && s.getDatasetSequence() == seq.getDatasetSequence()))
{
return true;
}
* an array of corresponding hidden columns for each alignment
* @return
*/
- public abstract String superposeStructures(AlignmentI[] alignments, int[] structureIndices,
- ColumnSelection[] hiddenCols);
+ public abstract String superposeStructures(AlignmentI[] alignments,
+ int[] structureIndices, HiddenColumns[] hiddenCols);
public abstract void setBackgroundColour(Color col);
*
* @return
*/
- public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+ public abstract SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment);
protected abstract void colourBySequence(
StructureMappingcommandSet[] colourBySequenceCommands);
return;
}
String[] files = getStructureFiles();
-
+
SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
+
StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
files, sr, alignmentv);
colourBySequence(colourBySequenceCommands);
git://source.jalview.org / jalview.git / blobdiff