*/
package jalview.structures.models;
+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.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+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.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/*
* datasource protocol for access to PDBEntrylatest
*/
- String protocol = null;
+ DataSourceType protocol = null;
protected boolean colourBySequence = true;
*/
protected String[] modelFileNames = null;
+ public String fileLoadingError;
+
/**
* Data bean class to simplify parameterisation in superposeStructures
*/
*/
public AAStructureBindingModel(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
- String protocol)
+ DataSourceType protocol)
{
this.ssm = ssm;
this.sequence = sequenceIs;
return chains;
}
- public String getProtocol()
+ public DataSourceType getProtocol()
{
return protocol;
}
*/
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);
+
+ public abstract void superposeStructures(AlignmentI[] als, int[] alm,
+ ColumnSelection[] alc);
+
+ public abstract void setBackgroundColour(Color col);
+
+ protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, FeatureRenderer fr,
+ AlignmentI alignment);
+
+ /**
+ * returns the current featureRenderer that should be used to colour the
+ * structures
+ *
+ * @param alignment
+ *
+ * @return
+ */
+ public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment);
+
+ /**
+ * 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();
+
+ /**
+ * 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)
+ {
+ boolean showFeatures = alignmentv.getAlignViewport()
+ .isShowSequenceFeatures();
+ if (!colourBySequence || !isLoadingFinished())
+ {
+ return;
+ }
+ if (getSsm() == null)
+ {
+ return;
+ }
+ String[] files = getPdbFile();
+
+ SequenceRenderer sr = getSequenceRenderer(alignmentv);
+
+ FeatureRenderer fr = null;
+ if (showFeatures)
+ {
+ fr = getFeatureRenderer(alignmentv);
+ }
+ AlignmentI alignment = alignmentv.getAlignment();
+
+ StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
+ files, sr, fr, alignment);
+ colourBySequence(colourBySequenceCommands);
+ }
+
+ public boolean hasFileLoadingError()
+ {
+ return fileLoadingError != null && fileLoadingError.length() > 0;
+ }
}