import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.List;
import java.util.Set;
import java.util.Vector;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
+import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewportI;
+import jalview.api.FeatureRenderer;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
private Rectangle explodedGeometry;
+ private FeatureRenderer featureRenderer;
+
+ private boolean includeHiddenRegion = true;
+
+ private AlignExportSettingI exportSettings;
+
String viewName;
/*
/**
*
* @param pdbEntries
- * @return a series of SequenceI arrays, one for each PDBEntry, listing which
- * sequence in the alignment holds a reference to it
+ * @return an array of SequenceI arrays, one for each PDBEntry, listing which
+ * sequences in the alignment hold a reference to it
*/
public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
{
- ArrayList<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
for (PDBEntry pdb : pdbEntries)
{
- ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
- for (int i = 0; i < alignment.getHeight(); i++)
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+ for (SequenceI sq : alignment.getSequences())
{
- Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
- .getPDBId();
+ Vector<PDBEntry> pdbs = sq
+ .getDatasetSequence().getPDBId();
if (pdbs == null)
{
continue;
}
- SequenceI sq;
- for (int p = 0; p < pdbs.size(); p++)
+ for (PDBEntry p1 : pdbs)
{
- PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
if (p1.getId().equals(pdb.getId()))
{
- if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ if (!seqs.contains(sq))
{
seqs.add(sq);
+ continue;
}
-
- continue;
}
}
}
complementPanel.scrollToCentre(sr, seqOffset);
}
}
+
+ @Override
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return featureRenderer;
+ }
+
+ @Override
+ public void setFeatureRenderer(FeatureRenderer featureRenderer)
+ {
+ this.featureRenderer = featureRenderer;
+ }
+
+ public AlignExportSettingI getExportSettings()
+ {
+ return exportSettings;
+ }
+
+ public void setExportSettings(AlignExportSettingI exportSettings)
+ {
+ this.exportSettings = exportSettings;
+ }
}