/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.gui;
import jalview.analysis.AlignmentUtils;
-import jalview.analysis.AlignmentUtils.MappingResult;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
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 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>();
+ /*
+ * Flag set true on the view that should 'gather' multiple views of the same
+ * sequence set id when a project is reloaded. Set false on all views when
+ * they are 'exploded' into separate windows. Set true on the current view
+ * when 'Gather' is performed, and also on the first tab when the first new
+ * view is created.
+ */
+ private boolean gatherViewsHere = false;
private AnnotationColumnChooser annotationColumnSelectionState;
/**
style = 2;
}
- setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
alignment
.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
}
initAutoAnnotation();
- if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+ String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT;
+ String propertyValue = Cache.getProperty(colourProperty);
+ if (propertyValue == null)
+ {
+ // fall back on this property for backwards compatibility
+ propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+ }
+ if (propertyValue != null)
{
globalColourScheme = ColourSchemeProperty.getColour(alignment,
- jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+ propertyValue);
if (globalColourScheme instanceof UserColourScheme)
{
boolean validCharWidth;
/**
- * DOCUMENT ME!
+ * update view settings with the given font. You may need to call
+ * alignPanel.fontChanged to update the layout geometry
*
- * @param f
- * DOCUMENT ME!
+ * @param setGrid
+ * when true, charWidth/height is set according to font mentrics
*/
- public void setFont(Font f)
+ public void setFont(Font f, boolean setGrid)
{
font = f;
java.awt.FontMetrics fm = c.getFontMetrics(font);
int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
.getCharHeight();
- // only update width/height if the new font won't fit
- if (h < fm.getHeight())
+ if (setGrid)
{
setCharHeight(fm.getHeight());
- }
- if (w < ww)
- {
setCharWidth(ww);
}
viewStyle.setFontName(font.getName());
{
super.setViewStyle(settingsForView);
setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
- viewStyle.getFontSize()));
+ viewStyle.getFontSize()), false);
}
/**
}
}
+ /**
+ * 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
* If one alignment is protein and one nucleotide, with at least one
* sequence name in common, offer to open a linked alignment.
*/
- if (getAlignment().isNucleotide() != al.isNucleotide())
+ if (AlignmentUtils.isMappable(al, getAlignment()))
{
- // TODO: JAL-845 try a bit harder to link up imported sequences
- final Set<String> sequenceNames = getAlignment().getSequenceNames();
- sequenceNames.retainAll(al.getSequenceNames());
- if (!sequenceNames.isEmpty()) // at least one sequence name in both
+ if (openLinkedAlignment(al, title))
{
- if (openLinkedAlignment(al, title))
- {
- return;
- }
+ return;
}
}
// TODO: JAL-407 regardless of above - identical sequences (based on ID and
MessageManager.getString("label.split_window"),
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.open_linked_alignment?"));
+ MessageManager.getString("label.open_split_window?"));
int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
- MessageManager.getString("label.open_linked_alignment"),
+ MessageManager.getString("label.open_split_window"),
JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
}
/*
- * Try to find mappings for at least one sequence. Any mappings made will be
- * added to the protein alignment.
+ * Map sequences. At least one should get mapped as we have already passed
+ * the test for 'mappability'. Any mappings made will be added to the
+ * protein alignment.
*/
- MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna);
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- if (mapped != MappingResult.Mapped)
- {
- /*
- * No mapping possible - warn the user, but leave window open.
- */
- final String msg = JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.mapping_failed"));
- JOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
- MessageManager.getString("label.no_mappings"),
- JOptionPane.WARNING_MESSAGE);
- }
+ AlignmentUtils.mapProteinToCdna(protein, cdna);
try
{
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,
+ protein.getCodonFrames());
}
/*
* 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 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)
+ {
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ AlignFrame copyMe = new AlignFrame(complement,
+ 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();
+ protein.setCodonFrames(mappings);
+ proteinFrame.viewport.initComplementConsensus();
+
+ 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);
+
+ 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