import java.awt.Dimension;
import java.awt.Font;
import java.awt.Rectangle;
-import java.io.File;
-import java.util.ArrayDeque;
import java.util.ArrayList;
-import java.util.Deque;
import java.util.Hashtable;
import java.util.Set;
import java.util.Vector;
* @version $Revision: 1.141 $
*/
public class AlignViewport extends AlignmentViewport implements
- SelectionSource, VamsasSource, AlignViewportI, CommandListener
+ SelectionSource, AlignViewportI, CommandListener
{
int startRes;
boolean antiAlias = false;
- Rectangle explodedPosition;
+ private Rectangle explodedGeometry;
String viewName;
- boolean gatherViewsHere = false;
-
- private Deque<CommandI> historyList = new ArrayDeque<CommandI>();
-
- private Deque<CommandI> redoList = new ArrayDeque<CommandI>();
+ private boolean gatherViewsHere = false;
private AnnotationColumnChooser annotationColumnSelectionState;
/**
}
}
+ /**
+ * Returns the (Desktop) instance of the StructureSelectionManager
+ */
+ @Override
public StructureSelectionManager getStructureSelectionManager()
{
return StructureSelectionManager
StructureSelectionManager ssm, VamsasSource source)
{
/*
- * ...work in progress... do nothing unless we are a 'complement' of the
- * source May replace this with direct calls not via SSM.
+ * Do nothing unless we are a 'complement' of the source. May replace this
+ * with direct calls not via SSM.
*/
if (source instanceof AlignViewportI
&& ((AlignViewportI) source).getCodingComplement() == this)
}
}
- @Override
- public VamsasSource getVamsasSource()
- {
- return this;
- }
-
- /**
- * Add one command to the command history list.
- *
- * @param command
- */
- public void addToHistoryList(CommandI command)
- {
- if (this.historyList != null)
- {
- this.historyList.push(command);
- broadcastCommand(command, false);
- }
- }
-
- protected void broadcastCommand(CommandI command, boolean undo)
- {
- getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource());
- }
-
- /**
- * Add one command to the command redo list.
- *
- * @param command
- */
- public void addToRedoList(CommandI command)
- {
- if (this.redoList != null)
- {
- this.redoList.push(command);
- }
- broadcastCommand(command, true);
- }
-
- /**
- * Clear the command redo list.
- */
- public void clearRedoList()
- {
- if (this.redoList != null)
- {
- this.redoList.clear();
- }
- }
-
- public void setHistoryList(Deque<CommandI> list)
- {
- this.historyList = list;
- }
-
- public Deque<CommandI> getHistoryList()
- {
- return this.historyList;
- }
-
- public void setRedoList(Deque<CommandI> list)
- {
- this.redoList = list;
- }
-
- public Deque<CommandI> getRedoList()
- {
- return this.redoList;
- }
-
/**
* Add the sequences from the given alignment to this viewport. Optionally,
* may give the user the option to open a new frame, or split panel, with cDNA
* added to the protein alignment.
*/
MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna);
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
if (mapped != MappingResult.Mapped)
{
/*
if (openSplitPane)
{
- // TODO: move this kind of constructor stuff to a factory/controller
- // method ?
- /*
- * Open in split pane. DNA sequence above, protein below.
- */
- AlignFrame copyMe = new AlignFrame(thisAlignment,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
- final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
- : newAlignFrame;
- final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
- : copyMe;
- protein = proteinFrame.viewport.getAlignment();
-
- cdnaFrame.setVisible(true);
- proteinFrame.setVisible(true);
- String sep = String.valueOf(File.separatorChar);
- String proteinShortName = proteinFrame.getTitle().substring(
- proteinFrame.getTitle().lastIndexOf(sep) + 1);
- String dnaShortName = cdnaFrame.getTitle().substring(
- cdnaFrame.getTitle().lastIndexOf(sep) + 1);
- String linkedTitle = MessageManager.formatMessage(
- "label.linked_view_title", dnaShortName, proteinShortName);
- JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
- Desktop.addInternalFrame(splitFrame, linkedTitle,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
-
- /*
- * Set the frames to listen for each other's edit and sort commands.
- */
- ssm.addCommandListener(cdnaFrame.getViewport());
- ssm.addCommandListener(proteinFrame.getViewport());
-
- /*
- * 'Coding complement' (dna/protein) views will mirror each others' edits,
- * selections, sorting etc as decided from time to time by the relevant
- * authorities.
- */
- proteinFrame.getViewport().setCodingComplement(cdnaFrame.getViewport());
+ 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;
}
+ /**
+ * Helper method to open a new SplitFrame holding linked dna and protein
+ * alignments.
+ *
+ * @param newAlignFrame
+ * containing a new alignment to be shown
+ * @param existingAlignment
+ * an existing alignment to be copied for display in the split frame
+ * @return the protein alignment in the split frame
+ */
+ protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
+ AlignmentI existingAlignment)
+ {
+ // TODO: move this to a factory/controller method ?
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ AlignFrame copyMe = new AlignFrame(existingAlignment,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+
+ AlignmentI al = newAlignFrame.viewport.getAlignment();
+ final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+ : newAlignFrame;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
+ : copyMe;
+ AlignmentI protein = proteinFrame.viewport.getAlignment();
+
+ cdnaFrame.setVisible(true);
+ proteinFrame.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+
+ /*
+ * Set the frames to listen for each other's edit and sort commands.
+ */
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.addCommandListener(cdnaFrame.getViewport());
+ ssm.addCommandListener(proteinFrame.getViewport());
+
+ /*
+ * 'Coding complement' (dna/protein) views will mirror each others' edits,
+ * selections, sorting etc as decided from time to time by the relevant
+ * authorities.
+ */
+ proteinFrame.getViewport().setCodingComplement(cdnaFrame.getViewport());
+ return protein;
+ }
+
public AnnotationColumnChooser getAnnotationColumnSelectionState()
{
return annotationColumnSelectionState;
getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
}
}
+
+ public Rectangle getExplodedGeometry()
+ {
+ return explodedGeometry;
+ }
+
+ public void setExplodedGeometry(Rectangle explodedPosition)
+ {
+ this.explodedGeometry = explodedPosition;
+ }
+
+ public boolean isGatherViewsHere()
+ {
+ return gatherViewsHere;
+ }
+
+ public void setGatherViewsHere(boolean gatherViewsHere)
+ {
+ this.gatherViewsHere = gatherViewsHere;
+ }
}
git://source.jalview.org / jalview.git / blobdiff