*/
package jalview.structures.models;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.AtomSpecModel;
+import jalview.ext.rbvi.chimera.ChimeraCommands;
import jalview.io.DataSourceType;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
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.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Map;
/**
*
public String fileLoadingError;
+ private boolean showAlignmentOnly;
+
+ /*
+ * a list of chains "pdbid:chainid" to show in the viewer;
+ * empty means show all
+ */
+ // TODO make private once showStructures() deals with this
+ protected List<String> chainsToShow;
+
+ private boolean hideHiddenRegions;
+
/**
* Data bean class to simplify parameterisation in superposeStructures
*/
{
this.ssm = ssm;
this.sequence = seqs;
+ chainsToShow = new ArrayList<>();
}
/**
this.nucleotide = Comparison.isNucleotide(sequenceIs);
this.pdbEntry = pdbentry;
this.protocol = protocol;
+ chainsToShow = new ArrayList<>();
+
resolveChains();
}
{ 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));
public abstract void setBackgroundColour(Color col);
- protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
+ protected abstract String[] getColourBySequenceCommands(
+ String[] files, AlignmentViewPanel avp);
/**
* returns the current sequenceRenderer that should be used to colour the
AlignmentViewPanel alignment);
protected abstract void colourBySequence(
- StructureMappingcommandSet[] colourBySequenceCommands);
+ String[] 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.
+ * Recolours the displayed structures, if they are coloured by sequence, or
+ * 'show only visible alignment' is selected. This supports updating structure
+ * colours on either change of alignment colours, or change to the visible
+ * region of the alignment.
*/
- public void colourBySequence(AlignmentViewPanel alignmentv)
+ public void updateStructureColours(AlignmentViewPanel alignmentv)
{
- if (!colourBySequence || !isLoadingFinished())
+ if (!isLoadingFinished())
{
return;
}
+
+ /*
+ * if structure is not coloured by sequence, but restricted to the alignment,
+ * then redraw it (but don't recolour it) in case hidden regions have changed
+ * (todo: specific messaging for change of hidden region only)
+ */
+ if (!colourBySequence)
+ {
+ if (isShowAlignmentOnly())
+ {
+ showStructures(alignmentv.getAlignViewport(), false);
+ }
+ return;
+ }
if (getSsm() == null)
{
return;
}
String[] files = getStructureFiles();
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
- files, sr, alignmentv);
+ String[] colourBySequenceCommands = getColourBySequenceCommands(
+ files, alignmentv);
colourBySequence(colourBySequenceCommands);
}
public abstract jalview.api.FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment);
+
+ /**
+ * Sets the flag for whether only mapped visible residues in the alignment
+ * should be visible in the structure viewer
+ *
+ * @param b
+ */
+ public void setShowAlignmentOnly(boolean b)
+ {
+ showAlignmentOnly = b;
+ }
+
+ /**
+ * Answers true if only residues mapped to the alignment should be shown in the
+ * structure viewer, else false
+ *
+ * @return
+ */
+ public boolean isShowAlignmentOnly()
+ {
+ return showAlignmentOnly;
+ }
+
+ /**
+ * Sets the flag for hiding regions of structure which are hidden in the
+ * alignment (only applies when the structure viewer is restricted to the
+ * alignment only)
+ *
+ * @param b
+ */
+ public void setHideHiddenRegions(boolean b)
+ {
+ hideHiddenRegions = b;
+ }
+
+ /**
+ * Answers true if regions hidden in the alignment should also be hidden in the
+ * structure viewer, else false (only applies when the structure viewer is
+ * restricted to the alignment only)
+ *
+ * @return
+ */
+ public boolean isHideHiddenRegions()
+ {
+ return hideHiddenRegions;
+ }
+
+ /**
+ * Shows the structures in the viewer, without changing their colouring. This is
+ * to support toggling of whether the whole structure is shown, or only residues
+ * mapped to visible regions of the alignment.
+ *
+ * @param alignViewportI
+ * @param refocus
+ * if true, refit the display to the viewer
+ */
+ public void showStructures(AlignViewportI alignViewportI, boolean refocus)
+ {
+ // override with implementation
+ }
+
+ @Override
+ public void updateColours(Object source)
+ {
+ AlignmentViewPanel ap = (AlignmentViewPanel) source;
+ // ignore events from panels not used to colour this view
+ if (!getViewer().isUsedforcolourby(ap))
+ {
+ return;
+ }
+ if (!isLoadingFromArchive())
+ {
+ updateStructureColours(ap);
+ }
+ }
+
+ /**
+ * Sets the list of chains to display (as "pdbid:chain"), where an empty list
+ * means show all
+ *
+ * @param chains
+ */
+ public void setChainsToShow(List<String> chains)
+ {
+ chainsToShow = chains;
+ }
+
+ /**
+ * Answers true if the specified structure and chain are selected to be shown in
+ * the viewer, else false
+ *
+ * @param pdbId
+ * @param chainId
+ * @return
+ */
+ protected boolean isShowChain(String pdbId, String chainId)
+ {
+ if (chainsToShow.isEmpty())
+ {
+ return true;
+ }
+ return chainsToShow.contains(pdbId + ":" + chainId);
+ }
+
+ @Override
+ public abstract String[] getStructureFiles();
+
+ /**
+ * Builds a model of residues mapped from sequences to show on structure, taking
+ * into account user choices of
+ * <ul>
+ * <li>which chains are shown</li>
+ * <li>whether all structure is shown, or only that mapped to the alignment</li>
+ * <li>whether hidden regions of the alignment are hidden (excluded) or grayed
+ * out (included)</li>
+ * </ul>
+ *
+ * @param av
+ * @return
+ */
+ protected AtomSpecModel getShownResidues(AlignViewportI av)
+ {
+ AlignmentI alignment = av.getAlignment();
+ final int width = alignment.getWidth();
+
+ String[] files = getStructureFiles();
+
+ AtomSpecModel model = new AtomSpecModel();
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
+
+ /*
+ * Find the first mapped sequence (if any) for this PDB entry which is in
+ * the alignment
+ */
+ final int seqCountForPdbFile = getSequence()[pdbfnum].length;
+ for (int s = 0; s < seqCountForPdbFile; s++)
+ {
+ for (StructureMapping mapping : mappings)
+ {
+ final SequenceI theSequence = getSequence()[pdbfnum][s];
+ if (mapping.getSequence() == theSequence
+ && alignment.findIndex(theSequence) > -1)
+ {
+ String chainCd = mapping.getChain();
+ if (!isShowChain(mapping.getPdbId(), chainCd))
+ {
+ continue;
+ }
+ Iterator<int[]> visible;
+ if (isShowAlignmentOnly() && isHideHiddenRegions())
+ {
+ visible = alignment.getHiddenColumns()
+ .getVisContigsIterator(0, width, true);
+ }
+ else
+ {
+ visible = Collections.singletonList(new int[] { 0, width })
+ .iterator();
+ }
+ while (visible.hasNext())
+ {
+ int[] visibleRegion = visible.next();
+ int seqStartPos = theSequence.findPosition(visibleRegion[0]);
+ int seqEndPos = theSequence.findPosition(visibleRegion[1]);
+ List<int[]> residueRanges = mapping
+ .getPDBResNumRanges(seqStartPos, seqEndPos);
+ if (!residueRanges.isEmpty())
+ {
+ for (int[] range : residueRanges)
+ {
+ model.addRange(pdbfnum, range[0], range[1], chainCd);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return model;
+ }
+
+ /**
+ * Answers a default structure model specification which is simply the string
+ * form of the model number. Override if needed to specify submodels.
+ *
+ * @param model
+ * @return
+ */
+ public String getModelSpec(int model)
+ {
+ return String.valueOf(model);
+ }
+
+ /**
+ * Build a data structure which records contiguous subsequences for each colour.
+ * From this we can easily generate the Chimera command for colour by sequence.
+ *
+ * <pre>
+ * Color
+ * Model number
+ * Chain
+ * list of start/end ranges
+ * </pre>
+ *
+ * Ordering is by order of addition (for colours and positions), natural
+ * ordering (for models and chains)
+ *
+ * @param viewPanel
+ * @return
+ */
+ public Map<Object, AtomSpecModel> buildColoursMap(
+ AlignmentViewPanel viewPanel)
+ {
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+ AlignViewportI viewport = viewPanel.getAlignViewport();
+ HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
+ AlignmentI al = viewport.getAlignment();
+ SequenceRenderer sr = getSequenceRenderer(viewPanel);
+ String[] files = getStructureFiles();
+
+ Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>();
+ Color lastColour = null;
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+
+ if (mapping == null || mapping.length < 1)
+ {
+ continue;
+ }
+
+ int startPos = -1, lastPos = -1;
+ String lastChain = "";
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
+ {
+ for (int sp, m = 0; m < mapping.length; m++)
+ {
+ final SequenceI seq = sequence[pdbfnum][s];
+ if (mapping[m].getSequence() == seq
+ && (sp = al.findIndex(seq)) > -1)
+ {
+ SequenceI asp = al.getSequenceAt(sp);
+ for (int r = 0; r < asp.getLength(); r++)
+ {
+ // no mapping to gaps in sequence
+ if (Comparison.isGap(asp.getCharAt(r)))
+ {
+ continue;
+ }
+ int pos = mapping[m].getPDBResNum(asp.findPosition(r));
+
+ if (pos < 1 || pos == lastPos)
+ {
+ continue;
+ }
+
+ Color colour = sr.getResidueColour(seq, r, finder);
+
+ /*
+ * hidden regions are shown gray or, optionally, ignored
+ */
+ if (!cs.isVisible(r))
+ {
+ if (hideHiddenRegions)
+ {
+ continue;
+ }
+ else
+ {
+ colour = Color.GRAY;
+ }
+ }
+
+ final String chain = mapping[m].getChain();
+
+ /*
+ * Just keep incrementing the end position for this colour range
+ * _unless_ colour, PDB model or chain has changed, or there is a
+ * gap in the mapped residue sequence
+ */
+ final boolean newColour = !colour.equals(lastColour);
+ final boolean nonContig = lastPos + 1 != pos;
+ final boolean newChain = !chain.equals(lastChain);
+ if (newColour || nonContig || newChain)
+ {
+ if (startPos != -1)
+ {
+ ChimeraCommands.addAtomSpecRange(colourMap, lastColour,
+ pdbfnum, startPos,
+ lastPos, lastChain);
+ }
+ startPos = pos;
+ }
+ lastColour = colour;
+ lastPos = pos;
+ lastChain = chain;
+ }
+ // final colour range
+ if (lastColour != null)
+ {
+ ChimeraCommands.addAtomSpecRange(colourMap, lastColour,
+ pdbfnum,
+ startPos, lastPos, lastChain);
+ }
+ // break;
+ }
+ }
+ }
+ }
+ return colourMap;
+ }
}
git://source.jalview.org / jalview.git / blobdiff