*/
package jalview.structures.models;
-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;
BitSet matched, SuperposeData[] structures)
{
int refStructure = -1;
- String[] files = getPdbFile();
+ String[] files = getStructureFiles();
if (files == null)
{
return -1;
* move on to next pdb file (ignore sequences for other chains
* for the same structure)
*/
- s = seqCountForPdbFile;
- break;
+ // s = seqCountForPdbFile;
+ // break;
}
}
}
public abstract void setBackgroundColour(Color col);
protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI alignViewportI);
-
- /**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment);
+ String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
/**
* returns the current sequenceRenderer that should be used to colour the
{
return;
}
- String[] files = getPdbFile();
+ String[] files = getStructureFiles();
SequenceRenderer sr = getSequenceRenderer(alignmentv);
- FeatureRenderer fr = null;
- boolean showFeatures = alignmentv.getAlignViewport()
- .isShowSequenceFeatures();
- if (showFeatures)
- {
- fr = getFeatureRenderer(alignmentv);
- }
-
StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
- files, sr, fr, alignmentv.getAlignViewport());
+ files, sr, alignmentv);
colourBySequence(colourBySequenceCommands);
}
{
return fileLoadingError != null && fileLoadingError.length() > 0;
}
+
+ public abstract jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment);
}