*/
package jalview.structures.models;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.schemes.ColourSchemeI;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
import jalview.util.MessageManager;
+import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.BitSet;
import java.util.List;
/**
private StructureSelectionManager ssm;
+ /*
+ * distinct PDB entries (pdb files) associated
+ * with sequences
+ */
private PDBEntry[] pdbEntry;
/*
/*
* datasource protocol for access to PDBEntrylatest
*/
- String protocol = null;
+ DataSourceType protocol = null;
protected boolean colourBySequence = true;
private boolean finishedInit = false;
/**
+ * current set of model filenames loaded in the Jmol instance
+ */
+ protected String[] modelFileNames = null;
+
+ public String fileLoadingError;
+
+ /**
* Data bean class to simplify parameterisation in superposeStructures
*/
protected class SuperposeData
* @param protocol
*/
public AAStructureBindingModel(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
this.ssm = ssm;
this.sequence = sequenceIs;
this.nucleotide = Comparison.isNucleotide(sequenceIs);
- this.chains = chains;
this.pdbEntry = pdbentry;
this.protocol = protocol;
- if (chains == null)
- {
- this.chains = new String[pdbentry.length][];
- }
}
public StructureSelectionManager getSsm()
return chains;
}
- public String getProtocol()
+ public DataSourceType getProtocol()
{
return protocol;
}
// TODO: give a more informative title when multiple structures are
// displayed.
StringBuilder title = new StringBuilder(64);
- final PDBEntry pdbEntry = getPdbEntry(0);
+ final PDBEntry pdbe = getPdbEntry(0);
title.append(viewerName + " view for " + getSequence()[0][0].getName()
- + ":" + pdbEntry.getId());
+ + ":" + pdbe.getId());
if (verbose)
{
- if (pdbEntry.getProperty() != null)
+ String method = (String) pdbe.getProperty("method");
+ if (method != null)
{
- if (pdbEntry.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbEntry.getProperty().get("method"));
- }
- if (pdbEntry.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbEntry.getProperty().get("chains"));
- }
+ title.append(" Method: ").append(method);
+ }
+ String chain = (String) pdbe.getProperty("chains");
+ if (chain != null)
+ {
+ title.append(" Chain:").append(chain);
}
}
return title.toString();
* 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();
+ if (files == null)
+ {
+ return -1;
+ }
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
{
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;
}
structures[pdbfnum].pdbId = mapping.getPdbId();
structures[pdbfnum].isRna = theSequence.getRNA() != null;
- // move on to next pdb file
+
+ /*
+ * move on to next pdb file (ignore sequences for other chains
+ * for the same structure)
+ */
s = seqCountForPdbFile;
break;
}
{
this.finishedInit = fi;
}
+
+ /**
+ * Returns a list of chains mapped in this viewer.
+ *
+ * @return
+ */
+ public abstract List<String> getChainNames();
+
+ /**
+ * Returns the Jalview panel hosting the structure viewer (if any)
+ *
+ * @return
+ */
+ public JalviewStructureDisplayI getViewer()
+ {
+ return null;
+ }
+
+ public abstract void setJalviewColourScheme(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 String superposeStructures(AlignmentI[] alignments, int[] structureIndices,
+ ColumnSelection[] 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
+ * structures
+ *
+ * @param alignment
+ *
+ * @return
+ */
+ public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+
+ protected abstract void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands);
+
+ public abstract void colourByChain();
+
+ public abstract void colourByCharge();
+
+ /**
+ * colour any structures associated with sequences in the given alignment
+ * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
+ * if colourBySequence is enabled.
+ */
+ public void colourBySequence(AlignmentViewPanel alignmentv)
+ {
+ if (!colourBySequence || !isLoadingFinished())
+ {
+ return;
+ }
+ if (getSsm() == null)
+ {
+ return;
+ }
+ String[] files = getPdbFile();
+
+ SequenceRenderer sr = getSequenceRenderer(alignmentv);
+
+ StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
+ files, sr, alignmentv);
+ colourBySequence(colourBySequenceCommands);
+ }
+
+ public boolean hasFileLoadingError()
+ {
+ return fileLoadingError != null && fileLoadingError.length() > 0;
+ }
+
+ public abstract jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment);
}
git://source.jalview.org / jalview.git / blobdiff