package jalview.structures.models;
import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
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;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.BitSet;
import java.util.List;
/**
* @author gmcarstairs
*
*/
-public abstract class AAStructureBindingModel extends
- SequenceStructureBindingModel implements StructureListener,
- StructureSelectionManagerProvider
+public abstract class AAStructureBindingModel
+ extends SequenceStructureBindingModel
+ implements StructureListener, StructureSelectionManagerProvider
{
private StructureSelectionManager ssm;
* @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]
+ String[][] newchains = new String[pdbEntry.length][];
+ int pe = 0;
+ for (PDBEntry pdb : pdbEntry)
+ {
+ SequenceI[] seqsForPdb = sequence[pe];
+ if (seqsForPdb != null)
+ {
+ newchains[pe] = new String[seqsForPdb.length];
+ int se = 0;
+ for (SequenceI asq : seqsForPdb)
+ {
+ String chain = (chains != null && chains[pe] != null)
+ ? chains[pe][se]
+ : null;
+ 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)
+ {
+ chain = chaincode;
+ chainmaps++;
+ break;
+ }
+ }
+ }
+ }
+ newchains[pe][se] = chain;
+ se++;
+ }
+ pe++;
+ }
+ }
+
+ chains = newchains;
+ return chainmaps > 0;
+ }
public StructureSelectionManager getSsm()
{
return ssm;
{
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<String> c = new ArrayList<>();
if (getChains() == null)
{
setChains(new String[getPdbCount()][]);
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));
* Returns a readable description of all mappings for the wrapped pdbfile to
* any mapped sequences
*
- * @param pdbfile
- * @param seqs
- * @return
+ * @return
*/
public String printMappings()
{
* the sequence alignment which is the basis of structure
* superposition
* @param matched
- * an array of booleans, indexed by alignment column, where true
- * indicates that every structure has a mapped residue present in the
- * column (so the column can participate in structure alignment)
+ * a BitSet, where bit j is set to indicate that every structure has
+ * a mapped residue present in column j (so the column can
+ * participate in structure alignment)
* @param structures
* an array of data beans corresponding to pdb file index
* @return
*/
protected int findSuperposableResidues(AlignmentI alignment,
- boolean[] matched, SuperposeData[] structures)
+ BitSet matched, SuperposeData[] structures)
{
int refStructure = -1;
- String[] files = getPdbFile();
+ String[] files = getStructureFiles();
if (files == null)
{
return -1;
{
refStructure = pdbfnum;
}
- for (int r = 0; r < matched.length; r++)
+ for (int r = 0; r < alignment.getWidth(); r++)
{
- if (!matched[r])
+ if (!matched.get(r))
{
continue;
}
int pos = getMappedPosition(theSequence, r, mapping);
if (pos < 1 || pos == lastPos)
{
- matched[r] = false;
+ matched.clear(r);
continue;
}
lastPos = pos;
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;
}
public abstract void setJalviewColourScheme(ColourSchemeI cs);
- public abstract void superposeStructures(AlignmentI[] als, int[] alm,
- ColumnSelection[] alc);
-
- public abstract void setBackgroundColour(Color col);
-
- protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment);
-
/**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @param alignment
+ * Constructs and sends a command to align structures against a reference
+ * structure, based on one or more sequence alignments. May optionally return
+ * an error or warning message for the alignment command.
*
+ * @param alignments
+ * an array of alignments to process
+ * @param structureIndices
+ * an array of corresponding reference structures (index into pdb
+ * file array); if a negative value is passed, the first PDB file
+ * mapped to an alignment sequence is used as the reference for
+ * superposition
+ * @param hiddenCols
+ * an array of corresponding hidden columns for each alignment
* @return
*/
- public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment);
+ public abstract String superposeStructures(AlignmentI[] alignments,
+ int[] structureIndices, HiddenColumns[] hiddenCols);
+
+ public abstract void setBackgroundColour(Color col);
+
+ protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
/**
* returns the current sequenceRenderer that should be used to colour the
*
* @return
*/
- public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+ public abstract SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment);
protected abstract void colourBySequence(
StructureMappingcommandSet[] colourBySequenceCommands);
*/
public void colourBySequence(AlignmentViewPanel alignmentv)
{
- boolean showFeatures = alignmentv.getAlignViewport()
- .isShowSequenceFeatures();
if (!colourBySequence || !isLoadingFinished())
{
return;
{
return;
}
- String[] files = getPdbFile();
-
+ String[] files = getStructureFiles();
+
SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
- {
- fr = getFeatureRenderer(alignmentv);
- }
- AlignmentI alignment = alignmentv.getAlignment();
-
+
StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
- files, sr, fr, alignment);
+ files, sr, alignmentv);
colourBySequence(colourBySequenceCommands);
}
{
return fileLoadingError != null && fileLoadingError.length() > 0;
}
+
+ public abstract jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment);
}
git://source.jalview.org / jalview.git / blobdiff