*/
package jalview.gui;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
-import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
/**
* DOCUMENT ME!
*
* @version $Revision: 1.141 $
*/
public class AlignViewport extends AlignmentViewport implements
- SelectionSource, AlignViewportI, CommandListener
+ SelectionSource, CommandListener
{
Font font;
*/
public void setAlignment(AlignmentI align)
{
- if (alignment != null && alignment.getCodonFrames() != null)
+ replaceMappings(align);
+ this.alignment = align;
+ }
+
+ /**
+ * Replace any codon mappings for this viewport with those for the given
+ * viewport
+ *
+ * @param align
+ */
+ public void replaceMappings(AlignmentI align)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+
+ /*
+ * Deregister current mappings (if any)
+ */
+ if (alignment != null)
{
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).removeMappings(alignment.getCodonFrames());
+ ssm.removeMappings(alignment.getCodonFrames());
}
- this.alignment = align;
- if (alignment != null && alignment.getCodonFrames() != null)
+
+ /*
+ * Register new mappings (if any)
+ */
+ if (align != null)
+ {
+ ssm.addMappings(align.getCodonFrames());
+ }
+
+ /*
+ * replace mappings on our alignment
+ */
+ if (alignment != null && align != null)
{
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).addMappings(alignment.getCodonFrames());
+ alignment.setCodonFrames(align.getCodonFrames());
}
}
/**
*
* @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().getAllPDBEntries();
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;
}
}
}
* If any cDNA/protein mappings can be made between the alignments, offer to
* open a linked alignment with split frame option.
*/
- if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
+ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
+ if (al.getDataset() == null)
+ {
+ // need to create ds seqs
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() == null)
+ {
+ sq.createDatasetSequence();
+ }
+ }
+ }
if (AlignmentUtils.isMappable(al, getAlignment()))
{
if (openLinkedAlignment(al, title))
AlignmentUtils.mapProteinToCdna(protein, cdna);
/*
- * Create the AlignFrame for the added alignment. Note this will include the
- * cDNA consensus annotation if it is protein (because the alignment holds
- * mappings to nucleotide)
+ * Create the AlignFrame for the added alignment. If it is protein, mappings
+ * are registered with StructureSelectionManager as a side-effect.
*/
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
if (openSplitPane)
{
- protein = openSplitFrame(newAlignFrame, thisAlignment,
- protein.getCodonFrames());
+ al.alignAs(thisAlignment);
+ protein = openSplitFrame(newAlignFrame, thisAlignment);
}
- /*
- * Register the mappings (held on the protein alignment) with the
- * StructureSelectionManager (for mouseover linking).
- */
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- ssm.addMappings(protein.getCodonFrames());
-
return true;
}
* containing a new alignment to be shown
* @param complement
* cdna/protein complement alignment to show in the other split half
- * @param mappings
* @return the protein alignment in the split frame
*/
protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
- AlignmentI complement, Set<AlignedCodonFrame> mappings)
+ AlignmentI complement)
{
/*
* Make a new frame with a copy of the alignment we are adding to. If this
- * is protein, the new frame will have a cDNA consensus annotation row
- * added.
+ * is protein, the mappings to cDNA will be registered with StructureSelectionManager as a side-effect.
*/
AlignFrame copyMe = new AlignFrame(complement,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
: newAlignFrame;
final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
: copyMe;
- AlignmentI protein = proteinFrame.viewport.getAlignment();
- protein.setCodonFrames(mappings);
-
cdnaFrame.setVisible(true);
proteinFrame.setVisible(true);
String linkedTitle = MessageManager
JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
- return protein;
+ return proteinFrame.viewport.getAlignment();
}
public AnnotationColumnChooser getAnnotationColumnSelectionState()
* is found, the result will be empty.
*/
SearchResults sr = new SearchResults();
- int seqOffset = findComplementScrollTarget(sr);
+ int verticalOffset = findComplementScrollTarget(sr);
if (!sr.isEmpty())
{
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
complementPanel.setFollowingComplementScroll(true);
- complementPanel.scrollToCentre(sr, seqOffset);
+ complementPanel.scrollToCentre(sr, verticalOffset);
}
}
+
}
git://source.jalview.org / jalview.git / blobdiff