+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.structures.models;
-import java.util.ArrayList;
-import java.util.List;
-
+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.AlignmentI;
+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.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.Collections;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
/**
*
* 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
{
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 nucleotide;
+ private boolean finishedInit = false;
+
+ /**
+ * current set of model filenames loaded in the Jmol instance
+ */
+ protected String[] modelFileNames = null;
+
+ 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 deprecated JalviewJmolBinding.centerViewer removed
+ protected List<String> chainsToShow;
+
+ private boolean hideHiddenRegions;
+
+ protected List<String> chainNames = new ArrayList<>();
+
+ /**
+ * Data bean class to simplify parameterisation in superposeStructures
+ */
+ protected class SuperposeData
+ {
+ /**
+ * Constructor with alignment width argument
+ *
+ * @param width
+ */
+ public SuperposeData(int width)
+ {
+ pdbResNo = new int[width];
+ }
+
+ public String filename;
+
+ public String pdbId;
+
+ public String chain = "";
+
+ public boolean isRna;
+
+ /*
+ * The pdb residue number (if any) mapped to each column of the alignment
+ */
+ public int[] pdbResNo;
+ }
+
/**
* Constructor
*
{
this.ssm = ssm;
this.sequence = seqs;
+ chainsToShow = new ArrayList<>();
}
/**
* @param ssm
* @param pdbentry
* @param sequenceIs
- * @param chains
* @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)
+ chainsToShow = new ArrayList<>();
+
+ 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)
{
- this.chains = new String[pdbentry.length][];
+ 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;
}
/**
+ * Answers true if this binding includes the given PDB id, else false
+ *
+ * @param pdbId
+ * @return
+ */
+ public boolean hasPdbId(String pdbId)
+ {
+ if (pdbEntry != null)
+ {
+ for (PDBEntry pdb : pdbEntry)
+ {
+ if (pdb.getId().equals(pdbId))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
* Returns the number of modelled PDB file entries.
*
* @return
return chains;
}
- public String getProtocol()
+ public DataSourceType getProtocol()
{
return protocol;
}
/**
* Construct a title string for the viewer window based on the data Jalview
* knows about
- * @param viewerName TODO
+ *
+ * @param viewerName
+ * TODO
* @param verbose
*
* @return
public String getViewerTitle(String viewerName, boolean verbose)
{
if (getSequence() == null || getSequence().length < 1
- || getPdbCount() < 1
- || getSequence()[0].length < 1)
+ || getPdbCount() < 1 || getSequence()[0].length < 1)
{
return ("Jalview " + viewerName + " Window");
}
// 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();
{ 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()][]);
*
* @returns the pdb entries added to the current set.
*/
- public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, SequenceI[][] seq,
- String[][] chns)
+ 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));
int r = v.indexOf(pdbe[i]);
if (r == -1 || r >= getPdbCount())
{
- rtn.add(new int[]
- { v.size(), i });
+ rtn.add(new int[] { v.size(), i });
v.add(pdbe[i]);
}
else
}
@Override
- public void highlightAtoms(List<AtomSpec> atoms)
+ public abstract void highlightAtoms(List<AtomSpec> atoms);
+
+ protected boolean isNucleotide()
{
- if (atoms != null)
+ return this.nucleotide;
+ }
+
+ /**
+ * Returns a readable description of all mappings for the wrapped pdbfile to
+ * any mapped sequences
+ *
+ * @param pdbfile
+ * @param seqs
+ * @return
+ */
+ public String printMappings()
+ {
+ if (pdbEntry == null)
+ {
+ return "";
+ }
+ StringBuilder sb = new StringBuilder(128);
+ for (int pdbe = 0; pdbe < getPdbCount(); pdbe++)
+ {
+ String pdbfile = getPdbEntry(pdbe).getFile();
+ List<SequenceI> seqs = Arrays.asList(getSequence()[pdbe]);
+ sb.append(getSsm().printMappings(pdbfile, seqs));
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Returns the mapped structure position for a given aligned column of a given
+ * sequence, or -1 if the column is gapped, beyond the end of the sequence, or
+ * not mapped to structure.
+ *
+ * @param seq
+ * @param alignedPos
+ * @param mapping
+ * @return
+ */
+ protected int getMappedPosition(SequenceI seq, int alignedPos,
+ StructureMapping mapping)
+ {
+ if (alignedPos >= seq.getLength())
+ {
+ return -1;
+ }
+
+ if (Comparison.isGap(seq.getCharAt(alignedPos)))
+ {
+ return -1;
+ }
+ int seqPos = seq.findPosition(alignedPos);
+ int pos = mapping.getPDBResNum(seqPos);
+ return pos;
+ }
+
+ /**
+ * Helper method to identify residues that can participate in a structure
+ * superposition command. For each structure, identify a sequence in the
+ * alignment which is mapped to the structure. Identify non-gapped columns in
+ * the sequence which have a mapping to a residue in the structure. Returns
+ * the index of the first structure that has a mapping to the alignment.
+ *
+ * @param alignment
+ * the sequence alignment which is the basis of structure
+ * superposition
+ * @param matched
+ * 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,
+ BitSet matched, SuperposeData[] structures)
+ {
+ int refStructure = -1;
+ String[] files = getStructureFiles();
+ if (files == null)
+ {
+ return -1;
+ }
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
+ int lastPos = -1;
+
+ /*
+ * 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)
+ {
+ if (refStructure < 0)
+ {
+ refStructure = pdbfnum;
+ }
+ for (int r = 0; r < alignment.getWidth(); r++)
+ {
+ if (!matched.get(r))
+ {
+ continue;
+ }
+ int pos = getMappedPosition(theSequence, r, mapping);
+ if (pos < 1 || pos == lastPos)
+ {
+ matched.clear(r);
+ continue;
+ }
+ lastPos = pos;
+ structures[pdbfnum].pdbResNo[r] = pos;
+ }
+ String chain = mapping.getChain();
+ if (chain != null && chain.trim().length() > 0)
+ {
+ structures[pdbfnum].chain = chain;
+ }
+ structures[pdbfnum].pdbId = mapping.getPdbId();
+ structures[pdbfnum].isRna = theSequence.getRNA() != null;
+
+ /*
+ * move on to next pdb file (ignore sequences for other chains
+ * for the same structure)
+ */
+ s = seqCountForPdbFile;
+ break;
+ }
+ }
+ }
+ }
+ return refStructure;
+ }
+
+ /**
+ * Returns true if the structure viewer has loaded all of the files of
+ * interest (identified by the file mapping having been set up), or false if
+ * any are still not loaded after a timeout interval.
+ *
+ * @param files
+ */
+ protected boolean waitForFileLoad(String[] files)
+ {
+ /*
+ * give up after 10 secs plus 1 sec per file
+ */
+ long starttime = System.currentTimeMillis();
+ long endTime = 10000 + 1000 * files.length + starttime;
+ String notLoaded = null;
+
+ boolean waiting = true;
+ while (waiting && System.currentTimeMillis() < endTime)
{
- for (AtomSpec atom : atoms)
+ waiting = false;
+ for (String file : files)
{
- highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
- atom.getChain(), atom.getPdbFile());
+ notLoaded = file;
+ if (file == null)
+ {
+ continue;
+ }
+ try
+ {
+ StructureMapping[] sm = getSsm().getMapping(file);
+ if (sm == null || sm.length == 0)
+ {
+ waiting = true;
+ }
+ } catch (Throwable x)
+ {
+ waiting = true;
+ }
}
}
+
+ if (waiting)
+ {
+ System.err.println(
+ "Timed out waiting for structure viewer to load file "
+ + notLoaded);
+ return false;
+ }
+ return true;
}
- protected abstract void highlightAtom(int atomIndex, int pdbResNum,
- String chain, String pdbFile);
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ if (sequence != null)
+ {
+ for (SequenceI[] seqs : sequence)
+ {
+ if (seqs != null)
+ {
+ for (SequenceI s : seqs)
+ {
+ if (s == seq || (s.getDatasetSequence() != null
+ && s.getDatasetSequence() == seq.getDatasetSequence()))
+ {
+ return true;
+ }
+ }
+ }
+ }
+ }
+ return false;
+ }
- protected boolean isNucleotide()
+ public boolean isFinishedInit()
{
- return this.nucleotide;
+ return finishedInit;
+ }
+
+ public void setFinishedInit(boolean fi)
+ {
+ this.finishedInit = fi;
+ }
+
+ /**
+ * 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, HiddenColumns[] hiddenCols);
+
+ public abstract void setBackgroundColour(Color col);
+
+ protected abstract String[] getColourBySequenceCommands(
+ String[] files, 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(
+ String[] colourBySequenceCommands);
+
+ public abstract void colourByChain();
+
+ public abstract void colourByCharge();
+
+ /**
+ * 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 updateStructureColours(AlignmentViewPanel alignmentv)
+ {
+ 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();
+
+ String[] colourBySequenceCommands = getColourBySequenceCommands(
+ files, alignmentv);
+ colourBySequence(colourBySequenceCommands);
+ }
+
+ public boolean hasFileLoadingError()
+ {
+ return fileLoadingError != null && fileLoadingError.length() > 0;
+ }
+
+ 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;
+ }
+
+ /**
+ * Returns a list of chains mapped in this viewer. Note this list is not
+ * currently scoped per structure.
+ *
+ * @return
+ */
+ public List<String> getChainNames()
+ {
+ return chainNames;
}
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / blobdiff