+/*
+ * 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.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.io.DataSourceType;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
+import jalview.structure.StructureCommandsI;
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.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.SwingUtilities;
+
/**
*
* 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 static final String COLOURING_STRUCTURES = MessageManager
+ .getString("status.colouring_structures");
+
+ /*
+ * the Jalview panel through which the user interacts
+ * with the structure viewer
+ */
+ private JalviewStructureDisplayI viewer;
+
+ /*
+ * helper that generates command syntax
+ */
+ private StructureCommandsI commandGenerator;
private StructureSelectionManager ssm;
+ /*
+ * modelled chains, formatted as "pdbid:chainCode"
+ */
+ private List<String> chainNames;
+
+ /*
+ * lookup of pdb file name by key "pdbid:chainCode"
+ */
+ private Map<String, String> chainFile;
+
+ /*
+ * 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;
+
+ /**
+ * 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;
+ chainNames = new ArrayList<>();
+ chainFile = new HashMap<>();
}
/**
* @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(ssm, sequenceIs);
this.nucleotide = Comparison.isNucleotide(sequenceIs);
- this.chains = chains;
this.pdbEntry = pdbentry;
this.protocol = protocol;
- if (chains == null)
+ 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()
+ {
+ 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)
+ {
+ waiting = false;
+ for (String file : files)
+ {
+ 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;
+ }
+
+ @Override
+ public boolean isListeningFor(SequenceI seq)
{
- if (atoms != null)
+ if (sequence != null)
{
- for (AtomSpec atom : atoms)
+ for (SequenceI[] seqs : sequence)
{
- highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
- atom.getChain(), atom.getPdbFile());
+ if (seqs != null)
+ {
+ for (SequenceI s : seqs)
+ {
+ if (s == seq || (s.getDatasetSequence() != null
+ && s.getDatasetSequence() == seq.getDatasetSequence()))
+ {
+ return true;
+ }
+ }
+ }
}
}
+ return false;
}
- protected abstract void highlightAtom(int atomIndex, int pdbResNum,
- String chain, String pdbFile);
+ public boolean isFinishedInit()
+ {
+ return finishedInit;
+ }
- protected boolean isNucleotide()
+ public void setFinishedInit(boolean fi)
{
- return this.nucleotide;
+ this.finishedInit = fi;
+ }
+
+ /**
+ * Returns a list of chains mapped in this viewer, formatted as
+ * "pdbid:chainCode"
+ *
+ * @return
+ */
+ public List<String> getChainNames()
+ {
+ return chainNames;
+ }
+
+ /**
+ * Returns the Jalview panel hosting the structure viewer (if any)
+ *
+ * @return
+ */
+ public JalviewStructureDisplayI getViewer()
+ {
+ return viewer;
+ }
+
+ public void setViewer(JalviewStructureDisplayI v)
+ {
+ viewer = v;
+ }
+
+ /**
+ * 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);
+
+ /**
+ * returns the current sequenceRenderer that should be used to colour the
+ * structures
+ *
+ * @param alignment
+ *
+ * @return
+ */
+ public abstract SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment);
+
+ /**
+ * Sends a command to the structure viewer to colour each chain with a
+ * distinct colour (to the extent supported by the viewer)
+ */
+ public void colourByChain()
+ {
+ colourBySequence = false;
+
+ // TODO: JAL-628 colour chains distinctly across all visible models
+
+ executeCommand(commandGenerator.colourByChain(), false,
+ COLOURING_STRUCTURES);
+ }
+
+ /**
+ * Sends a command to the structure viewer to colour each chain with a
+ * distinct colour (to the extent supported by the viewer)
+ */
+ public void colourByCharge()
+ {
+ colourBySequence = false;
+
+ executeCommand(commandGenerator.colourByCharge(), false,
+ COLOURING_STRUCTURES);
+ }
+
+ /**
+ * Sends a command to the structure to apply a colour scheme (defined in
+ * Jalview but not necessarily applied to the alignment), which defines a
+ * colour per residue letter. More complex schemes (e.g. that depend on
+ * consensus) cannot be used here and are ignored.
+ *
+ * @param cs
+ */
+ public void colourByJalviewColourScheme(ColourSchemeI cs)
+ {
+ colourBySequence = false;
+
+ if (cs == null || !cs.isSimple())
+ {
+ return;
+ }
+
+ /*
+ * build a map of {Residue3LetterCode, Color}
+ */
+ Map<String, Color> colours = new HashMap<>();
+ List<String> residues = ResidueProperties.getResidues(isNucleotide(),
+ false);
+ for (String resName : residues)
+ {
+ char res = resName.length() == 3
+ ? ResidueProperties.getSingleCharacterCode(resName)
+ : resName.charAt(0);
+ Color colour = cs.findColour(res, 0, null, null, 0f);
+ colours.put(resName, colour);
+ }
+
+ /*
+ * pass to the command constructor, and send the command
+ */
+ String cmd = commandGenerator.colourByResidues(colours);
+ executeCommand(cmd, false, COLOURING_STRUCTURES);
+ }
+
+ public void setBackgroundColour(Color col)
+ {
+ String cmd = commandGenerator.setBackgroundColour(col);
+ executeCommand(cmd, false, null);
+ }
+
+ /**
+ * Sends one command to the structure viewer. If {@code getReply} is true, the
+ * command is sent synchronously, otherwise in a deferred thread.
+ * <p>
+ * If a progress message is supplied, this is displayed before command
+ * execution, and removed afterwards.
+ *
+ * @param cmd
+ * @param getReply
+ * @param msg
+ * @return
+ */
+ private List<String> executeCommand(String cmd, boolean getReply,
+ String msg)
+ {
+ if (getReply)
+ {
+ return executeSynchronous(cmd, msg, getReply);
+ }
+ else
+ {
+ executeAsynchronous(cmd, msg);
+ return null;
+ }
+ }
+
+ /**
+ * Sends the command in the current thread. If a message is supplied, this is
+ * shown before the thread is started, and removed when it completes. May
+ * return a reply to the command if requested.
+ *
+ * @param cmd
+ * @param msg
+ * @param getReply
+ * @return
+ */
+ private List<String> executeSynchronous(String cmd, String msg, boolean getReply)
+ {
+ final JalviewStructureDisplayI theViewer = getViewer();
+ final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
+ try
+ {
+ return executeCommand(cmd, getReply);
+ } finally
+ {
+ if (msg != null)
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
+ }
+ }
+
+ /**
+ * Sends the command in a separate thread. If a message is supplied, this is
+ * shown before the thread is started, and removed when it completes. No value
+ * is returned.
+ *
+ * @param cmd
+ * @param msg
+ */
+ private void executeAsynchronous(String cmd, String msg)
+ {
+ final JalviewStructureDisplayI theViewer = getViewer();
+ final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
+
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ executeCommand(cmd, false);
+ } finally
+ {
+ if (msg != null)
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
+ }
+ }
+ });
+ }
+
+ protected abstract List<String> executeCommand(String command,
+ boolean getReply);
+
+ protected List<String> executeCommands(boolean getReply,
+ String... commands)
+ {
+ List<String> response = null;
+ for (String cmd : commands)
+ {
+ response = executeCommand(cmd, getReply);
+ }
+ return response;
+ }
+
+ /**
+ * 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 = getStructureFiles();
+
+ SequenceRenderer sr = getSequenceRenderer(alignmentv);
+
+ String[] colourBySequenceCommands = commandGenerator
+ .colourBySequence(getSsm(), files, getSequence(), sr,
+ alignmentv);
+ executeCommands(false, colourBySequenceCommands);
+ }
+
+ /**
+ * Centre the display in the structure viewer
+ */
+ public void focusView()
+ {
+ executeCommand(commandGenerator.focusView(), false);
+ }
+
+ /**
+ * Generates and executes a command to show only specified chains in the
+ * structure viewer. The list of chains to show should contain entries
+ * formatted as "pdbid:chaincode".
+ *
+ * @param toShow
+ */
+ public void showChains(List<String> toShow)
+ {
+ // todo or reformat toShow list entries as modelNo:pdbId:chainCode ?
+
+ /*
+ * Reformat the pdbid:chainCode values as modelNo:chainCode
+ * since this is what is needed to construct the viewer command
+ * todo: find a less messy way to do this
+ */
+ List<String> showThese = new ArrayList<>();
+ for (String chainId : toShow)
+ {
+ String[] tokens = chainId.split("\\:");
+ if (tokens.length == 2)
+ {
+ String pdbFile = getFileForChain(chainId);
+ int modelNo = getModelNoForFile(pdbFile);
+ String model = modelNo == -1 ? "" : String.valueOf(modelNo);
+ showThese.add(model + ":" + tokens[1]);
+ }
+ }
+ executeCommand(commandGenerator.showChains(showThese), false);
+ }
+
+ /**
+ * Answers the structure viewer's model number given a PDB file name. Returns
+ * -1 if model number is not found.
+ *
+ * @param chainId
+ * @return
+ */
+ protected abstract int getModelNoForFile(String chainId);
+
+ public boolean hasFileLoadingError()
+ {
+ return fileLoadingError != null && fileLoadingError.length() > 0;
+ }
+
+ /**
+ * Returns the FeatureRenderer for the given alignment view, or null if
+ * feature display is turned off in the view.
+ *
+ * @param avp
+ * @return
+ */
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel avp)
+ {
+ AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel()
+ : avp;
+ return ap.getAlignViewport().isShowSequenceFeatures()
+ ? ap.getFeatureRenderer()
+ : null;
+ }
+
+ protected void setStructureCommands(StructureCommandsI cmd)
+ {
+ commandGenerator = cmd;
+ }
+
+ /**
+ * Records association of one chain id (formatted as "pdbid:chainCode") with
+ * the corresponding PDB file name
+ *
+ * @param chainId
+ * @param fileName
+ */
+ public void addChainFile(String chainId, String fileName)
+ {
+ chainFile.put(chainId, fileName);
+ }
+
+ /**
+ * Returns the PDB filename for the given chain id (formatted as
+ * "pdbid:chainCode"), or null if not found
+ *
+ * @param chainId
+ * @return
+ */
+ protected String getFileForChain(String chainId)
+ {
+ return chainFile.get(chainId);
}
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / blobdiff