package jalview.structures.models;
import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
+import jalview.api.SequenceRendererI;
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.gui.AlignmentPanel;
+import jalview.gui.SequenceRenderer;
import jalview.io.DataSourceType;
import jalview.schemes.ColourSchemeI;
import jalview.structure.AtomSpec;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.BitSet;
import java.util.List;
+import org.springframework.web.filter.ShallowEtagHeaderFilter;
+
/**
*
* A base class to hold common function for protein structure model binding.
* @author gmcarstairs
*
*/
-public abstract class AAStructureBindingModel extends
- SequenceStructureBindingModel implements StructureListener,
- StructureSelectionManagerProvider
+public abstract class AAStructureBindingModel
+ extends SequenceStructureBindingModel
+ implements StructureListener, StructureSelectionManagerProvider
{
+ public enum ColourBy
+ {
+ Sequence, Chain, ChargeAndCysteine, Jalview, Viewer
+ }
+
+ /*
+ * selected colour menu option
+ */
+ private ColourBy colourBy = ColourBy.Sequence;
+ /*
+ * selected colour scheme, if a Jalview colour scheme is selected
+ */
+ private ColourSchemeI colourScheme;
+
+ /*
+ * flag for whether to include feature colouring, if using a Jalview colour
+ * scheme (independently of whether features are shown on alignment)
+ */
+ private boolean showFeatures;
+
private StructureSelectionManager ssm;
/*
* datasource protocol for access to PDBEntrylatest
*/
DataSourceType protocol = null;
-
- protected boolean colourBySequence = true;
-
+
private boolean nucleotide;
private boolean finishedInit = false;
* @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;
}
+ public void setColourBy(ColourBy option)
+ {
+ colourBy = option;
+ }
+
public boolean isColourBySequence()
{
- return colourBySequence;
+ return colourBy == ColourBy.Sequence;
}
-
- public void setColourBySequence(boolean colourBySequence)
+
+ protected boolean isJalviewColourScheme()
{
- this.colourBySequence = colourBySequence;
+ return colourBy == ColourBy.Jalview;
}
protected void addSequenceAndChain(int pe, SequenceI[] seq,
{
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>();
* 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;
}
return null;
}
- 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
+ * Sets the selected colour scheme, possibly with reference to the given
+ * alignment view
*
- * @return
+ * @param cs
+ * @param ap
+ * @param showFeats
*/
- public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment);
+ public void setJalviewColourScheme(ColourSchemeI cs, AlignmentViewPanel ap,
+ boolean showFeats)
+ {
+ colourBy = ColourBy.Jalview;
+ colourScheme = cs;
+ showFeatures = showFeats;
+
+ if (!showFeats && (cs == null || cs.isSimple()))
+ {
+ setSimpleColourScheme(cs);
+ }
+ else
+ {
+ colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport(), cs), showFeatures);
+ }
+ }
/**
- * returns the current sequenceRenderer that should be used to colour the
- * structures
+ * Sets a colour scheme which is determined solely by the residue at each
+ * position
*
- * @param alignment
+ * @param cs
+ */
+ protected abstract void setSimpleColourScheme(ColourSchemeI cs);
+
+ /**
+ * 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 SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+ public abstract String superposeStructures(AlignmentI[] alignments,
+ int[] structureIndices, HiddenColumns[] hiddenCols);
+
+ public abstract void setBackgroundColour(Color col);
+
+ protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRendererI sr, AlignmentViewPanel avp, boolean showFeatures);
protected abstract void colourBySequence(
StructureMappingcommandSet[] colourBySequenceCommands);
- public abstract void colourByChain();
+ public void colourByChain()
+ {
+ colourBy = ColourBy.Chain;
+ }
+
+ public void colourByCharge()
+ {
+ colourBy = ColourBy.ChargeAndCysteine;
+ }
- public abstract void colourByCharge();
+ public void colourBySequence(AlignmentViewPanel alignmentv, boolean showFeatures)
+ {
+ colourBySequence(alignmentv, alignmentv.getSequenceRenderer(), showFeatures);
+ }
/**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * Colours any structures associated with sequences in the given alignment view
+ * using the getFeatureRenderer() and getSequenceRenderer() renderers
*/
- public void colourBySequence(AlignmentViewPanel alignmentv)
+ public void colourBySequence(AlignmentViewPanel alignmentv, SequenceRendererI sr, boolean showFeats)
{
- boolean showFeatures = alignmentv.getAlignViewport()
- .isShowSequenceFeatures();
- if (!colourBySequence || !isLoadingFinished())
+ showFeatures = showFeats;
+ if (!isLoadingFinished())
{
return;
}
{
return;
}
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
- {
- fr = getFeatureRenderer(alignmentv);
- }
- AlignmentI alignment = alignmentv.getAlignment();
-
+ String[] files = getStructureFiles();
+
StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
- files, sr, fr, alignment);
+ files, sr, alignmentv, showFeatures);
colourBySequence(colourBySequenceCommands);
}
{
return fileLoadingError != null && fileLoadingError.length() > 0;
}
+
+ public abstract jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment);
+
+@Override
+public void updateColours(Object source) {
+ AlignmentPanel ap = (AlignmentPanel) source;
+
+ /*
+ * ignore events from panels not used to colour this view
+ */
+ if (!getViewer().isUsedForColourBy(ap))
+ {
+ return;
+ }
+
+ /*
+ * no need to update colours if structure colouring is not
+ * viewport dependent
+ */
+ if (!isColourBySequence() && !isJalviewColourScheme())
+ {
+ return;
+ }
+ if (!showFeatures && (colourScheme == null || colourScheme.isSimple()))
+ {
+ return;
+ }
+
+ if (!isLoadingFromArchive())
+ {
+ if (isColourBySequence())
+ {
+ colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport()),
+ showFeatures);
+ }
+ else
+ {
+ colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport(),
+ colourScheme), showFeatures);
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff