import java.awt.*;
import jalview.analysis.*;
+import jalview.api.StructureSelectionManagerProvider;
import jalview.bin.*;
* DOCUMENT ME!
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.141 $
*/
public class AlignViewport implements SelectionSource, VamsasSource
{
}
/**
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ *
+ * @return null or the currently selected sequence region
*/
public SequenceGroup getSelectionGroup()
{
}
/**
- * DOCUMENT ME!
+ * Set the selection group for this window.
*
- * @param sg
- * DOCUMENT ME!
+ * @param sg - group holding references to sequences in this alignment view
+ *
*/
public void setSelectionGroup(SequenceGroup sg)
{
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * GUI state
+ * @return true if conservation based shading is enabled
*/
public boolean getConservationSelected()
{
}
/**
- * DOCUMENT ME!
- *
+ * GUI state
* @param b
- * DOCUMENT ME!
+ * enable conservation based shading
*/
public void setConservationSelected(boolean b)
{
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * GUI state
+ * @return true if percent identity threshold is applied to shading
*/
public boolean getAbovePIDThreshold()
{
}
/**
- * DOCUMENT ME!
+ * GUI state
*
- * @param b
- * DOCUMENT ME!
+ *
+ * @param b indicate if percent identity threshold is applied to shading
*/
public void setAbovePIDThreshold(boolean b)
{
{
if (alignment != null && alignment.getCodonFrames() != null)
{
- StructureSelectionManager.getStructureSelectionManager()
+ StructureSelectionManager.getStructureSelectionManager(Desktop.instance)
.removeMappings(alignment.getCodonFrames());
}
this.alignment = align;
if (alignment.getCodonFrames() != null)
{
- StructureSelectionManager.getStructureSelectionManager().addMappings(
+ StructureSelectionManager.getStructureSelectionManager(Desktop.instance).addMappings(
alignment.getCodonFrames());
}
}
/**
* checks current SelectionGroup against record of last hash value, and
* updates record.
+ * @param b update the record of last hash value
*
- * @return true if SelectionGroup changed since last call
+ * @return true if SelectionGroup changed since last call (when b is true)
*/
- boolean isSelectionGroupChanged()
+ boolean isSelectionGroupChanged(boolean b)
{
- int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode();
- if (hc != sgrouphash)
+ int hc = (selectionGroup == null || selectionGroup.getSize()==0) ? -1 : selectionGroup.hashCode();
+ if (hc!=-1 && hc != sgrouphash)
{
- sgrouphash = hc;
+ if (b) {sgrouphash = hc;}
return true;
}
return false;
}
/**
- * checks current colsel against record of last hash value, and updates
+ * checks current colsel against record of last hash value, and optionally updates
* record.
- *
- * @return true if colsel changed since last call
+
+ * @param b update the record of last hash value
+ * @return true if colsel changed since last call (when b is true)
*/
- boolean isColSelChanged()
+ boolean isColSelChanged(boolean b)
{
- int hc = (colSel == null) ? -1 : colSel.hashCode();
- if (hc != colselhash)
+ int hc = (colSel == null || colSel.size()==0) ? -1 : colSel.hashCode();
+ if (hc!=-1 && hc != colselhash)
{
- colselhash = hc;
+ if (b) {colselhash = hc;}
return true;
}
return false;
public void sendSelection()
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().sendSelection(
+ .getStructureSelectionManager(Desktop.instance).sendSelection(
new SequenceGroup(getSelectionGroup()),
new ColumnSelection(getColumnSelection()), this);
}
}
}
}
+
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+ }
+
+ /**
+ *
+ * @param pdbEntries
+ * @return a series of SequenceI arrays, one for each PDBEntry, listing which sequence in the alignment holds a reference to it
+ */
+ public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
+ {
+ ArrayList<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ for (PDBEntry pdb: pdbEntries) {
+ ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ Vector pdbs = alignment.getSequenceAt(i)
+ .getDatasetSequence().getPDBId();
+ if (pdbs == null)
+ continue;
+ SequenceI sq;
+ for (int p = 0; p < pdbs.size(); p++)
+ {
+ PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq=alignment.getSequenceAt(i)))
+ seqs.add(sq);
+
+ continue;
+ }
+ }
+ }
+ seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+ }
+ return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+ }
}