+
+ public boolean isFinishedInit()
+ {
+ return finishedInit;
+ }
+
+ public void setFinishedInit(boolean fi)
+ {
+ 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, HiddenColumns[] 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();
+
+ /**
+ * 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 (!isLoadingFinished())
+ {
+ return;
+ }
+ // todo: property change event for visibleAlignment
+ // to avoid unnecessary redraws here
+ if (!colourBySequence && !isShowAlignmentOnly())
+ {
+ return;
+ }
+ if (getSsm() == null)
+ {
+ return;
+ }
+ String[] files = getStructureFiles();
+
+ 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);
+
+ /**
+ * 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 mapped visible residues in the alignment should be
+ * visible in the structure viewer, else false
+ *
+ * @return
+ */
+ public boolean isShowAlignmentOnly()
+ {
+ return showAlignmentOnly;
+ }
+
+ /**
+ * 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
+ */
+ public void showStructures(AlignViewportI alignViewportI)
+ {
+ // 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);
+ }
+ }
+}