/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
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.List;
-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.AlignViewportI;
-import jalview.api.FeatureRenderer;
+import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
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.Set;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
/**
* DOCUMENT ME!
*
private Rectangle explodedGeometry;
- private FeatureRenderer featureRenderer;
-
- private boolean includeHiddenRegion = true;
String viewName;
/*
private boolean gatherViewsHere = false;
private AnnotationColumnChooser annotationColumnSelectionState;
+
/**
* Creates a new AlignViewport object.
*
viewStyle.getFontSize()), false);
}
+
/**
* DOCUMENT ME!
*
*/
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)
+ {
+
+ /*
+ * Deregister current mappings (if any)
+ */
+ deregisterMappings();
+
+ /*
+ * Register new mappings (if any)
+ */
+ if (align != null)
{
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).removeMappings(alignment.getCodonFrames());
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerMappings(align.getCodonFrames());
}
- this.alignment = align;
- if (alignment != null && alignment.getCodonFrames() != null)
+
+ /*
+ * replace mappings on our alignment
+ */
+ if (alignment != null && align != null)
{
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).addMappings(alignment.getCodonFrames());
+ alignment.setCodonFrames(align.getCodonFrames());
+ }
+ }
+
+ protected void deregisterMappings()
+ {
+ AlignmentI al = getAlignment();
+ if (al != null)
+ {
+ Set<AlignedCodonFrame> mappings = al.getCodonFrames();
+ if (mappings != null)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ for (AlignedCodonFrame acf : mappings)
+ {
+ if (noReferencesTo(acf))
+ {
+ ssm.deregisterMapping(acf);
+ }
+ }
+ }
}
}
// TODO: JAL-1126
if (historyList == null || redoList == null)
{
- return new long[]
- { -1, -1 };
+ return new long[] { -1, -1 };
}
- return new long[]
- { historyList.hashCode(), this.redoList.hashCode() };
+ return new long[] { historyList.hashCode(), this.redoList.hashCode() };
}
/**
List<SequenceI> seqs = new ArrayList<SequenceI>();
for (SequenceI sq : alignment.getSequences())
{
- Vector<PDBEntry> pdbs = sq
- .getDatasetSequence().getPDBId();
+ Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
if (pdbs == null)
{
continue;
*/
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))
*/
protected boolean openLinkedAlignment(AlignmentI al, String title)
{
- String[] options = new String[]
- { MessageManager.getString("action.no"),
+ String[] options = new String[] {
+ MessageManager.getString("action.no"),
MessageManager.getString("label.split_window"),
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
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);
newAlignFrame.setTitle(title);
newAlignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new Object[]
- { title }));
+ "label.successfully_loaded_file", new Object[] { title }));
// TODO if we want this (e.g. to enable reload of the alignment from file),
// we will need to add parameters to the stack.
if (openInNewWindow)
{
Desktop.addInternalFrame(newAlignFrame, title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
try
{
newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN",
- false));
+ "SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
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);
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);
-
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
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();
+ final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
+ .getAlignPanel();
complementPanel.setFollowingComplementScroll(true);
- complementPanel.scrollToCentre(sr, seqOffset);
+ complementPanel.scrollToCentre(sr, verticalOffset);
}
}
- @Override
- public FeatureRenderer getFeatureRenderer()
- {
- return featureRenderer;
- }
-
- @Override
- public void setFeatureRenderer(FeatureRenderer featureRenderer)
- {
- this.featureRenderer = featureRenderer;
- }
-
- public boolean isIncludeHiddenRegion()
+ /**
+ * Answers true if no alignment holds a reference to the given mapping
+ *
+ * @param acf
+ * @return
+ */
+ protected boolean noReferencesTo(AlignedCodonFrame acf)
{
- return includeHiddenRegion;
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames == null)
+ {
+ return true;
+ }
+ for (AlignFrame af : frames)
+ {
+ if (!af.isClosed())
+ {
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ AlignmentI al = ap.getAlignment();
+ if (al != null && al.getCodonFrames().contains(acf))
+ {
+ return false;
+ }
+ }
+ }
+ }
+ return true;
}
- public void setIncludeHiddenRegion(boolean includeHiddenRegion)
- {
- this.includeHiddenRegion = includeHiddenRegion;
- }
}
git://source.jalview.org / jalview.git / blobdiff