*/
package jalview.structures.models;
+import jalview.api.AlignViewportI;
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.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
* @author gmcarstairs
*
*/
-public abstract class AAStructureBindingModel extends
- SequenceStructureBindingModel implements StructureListener,
- StructureSelectionManagerProvider
+public abstract class AAStructureBindingModel
+ extends SequenceStructureBindingModel
+ implements StructureListener, StructureSelectionManagerProvider
{
private StructureSelectionManager ssm;
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<>();
}
/**
* @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;
+ 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)
+ {
+ 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;
{
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>();
- 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));
BitSet matched, SuperposeData[] structures)
{
int refStructure = -1;
- String[] files = getPdbFile();
+ String[] files = getStructureFiles();
if (files == null)
{
return -1;
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;
}
* an array of corresponding hidden columns for each alignment
* @return
*/
- public abstract String superposeStructures(AlignmentI[] alignments, int[] structureIndices,
- ColumnSelection[] hiddenCols);
+ public abstract String superposeStructures(AlignmentI[] alignments,
+ int[] structureIndices, HiddenColumns[] hiddenCols);
public abstract void setBackgroundColour(Color col);
protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
+ String[] files, AlignmentViewPanel avp);
/**
* returns the current sequenceRenderer that should be used to colour the
*
* @return
*/
- public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+ public abstract SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment);
protected abstract void colourBySequence(
StructureMappingcommandSet[] colourBySequenceCommands);
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)
{
- if (!colourBySequence || !isLoadingFinished())
+ if (!isLoadingFinished())
+ {
+ return;
+ }
+ // todo: property change event for visibleAlignment
+ // to avoid unnecessary redraws here
+ if (!colourBySequence && !isShowAlignmentOnly())
{
return;
}
{
return;
}
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
+ String[] files = getStructureFiles();
+
StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
- files, sr, alignmentv);
+ 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())
+ {
+ colourBySequence(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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff