import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueColourScheme;
import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.Font;
+import java.awt.FontMetrics;
import java.awt.Rectangle;
-import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
-import java.util.Vector;
import javax.swing.JInternalFrame;
* @author $author$
* @version $Revision: 1.141 $
*/
-public class AlignViewport extends AlignmentViewport implements
- SelectionSource, CommandListener
+public class AlignViewport extends AlignmentViewport
+ implements SelectionSource
{
Font font;
- NJTree currentTree = null;
-
boolean cursorMode = false;
boolean antiAlias = false;
private Rectangle explodedGeometry;
- String viewName;
+ private String viewName;
/*
* Flag set true on the view that should 'gather' multiple views of the same
*/
public AlignViewport(AlignmentI al)
{
- setAlignment(al);
+ super(al);
init();
}
public AlignViewport(AlignmentI al, String seqsetid, String viewid)
{
+ super(al);
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
{
- Cache.log.debug("Setting viewport's sequence set id : "
- + sequenceSetID);
+ Cache.log.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
init();
+
}
/**
* @param hiddenColumns
* ColumnSelection
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
{
- setAlignment(al);
+ super(al);
if (hiddenColumns != null)
{
- colSel = hiddenColumns;
+ al.setHiddenColumns(hiddenColumns);
}
init();
}
* @param seqsetid
* (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
String seqsetid)
{
this(al, hiddenColumns, seqsetid, null);
* @param viewid
* (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
String seqsetid, String viewid)
{
+ super(al);
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
{
- Cache.log.debug("Setting viewport's sequence set id : "
- + sequenceSetID);
+ Cache.log.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
+
if (hiddenColumns != null)
{
- colSel = hiddenColumns;
+ al.setHiddenColumns(hiddenColumns);
}
init();
}
*/
private void applyViewProperties()
{
- antiAlias = Cache.getDefault("ANTI_ALIAS", false);
-
- viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
- setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
- setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
- setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
- autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
-
- setPadGaps(Cache.getDefault("PAD_GAPS", true));
- setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
- setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
- viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
- viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
- viewStyle.setShowUnconserved(Cache
- .getDefault("SHOW_UNCONSERVED", false));
- sortByTree = Cache.getDefault("SORT_BY_TREE", false);
- followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
- sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
- Preferences.SORT_ANNOTATIONS,
- SequenceAnnotationOrder.NONE.name()));
- showAutocalculatedAbove = Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE, false);
- viewStyle.setScaleProteinAsCdna(Cache.getDefault(
- Preferences.SCALE_PROTEIN_TO_CDNA, true));
+ antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, false);
+
+ viewStyle.setShowJVSuffix(
+ Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
+ setShowAnnotation(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true));
+
+ setRightAlignIds(Cache.getDefault(Preferences.RIGHT_ALIGN_IDS, false));
+ setCentreColumnLabels(Cache.getDefault(Preferences.CENTRE_COLUMN_LABELS, false));
+ autoCalculateConsensusAndConservation = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true);
+
+ setPadGaps(Cache.getDefault(Preferences.PAD_GAPS, true));
+ setShowNPFeats(Cache.getDefault(Preferences.SHOW_NPFEATS_TOOLTIP, true));
+ setShowDBRefs(Cache.getDefault(Preferences.SHOW_DBREFS_TOOLTIP, true));
+ viewStyle.setSeqNameItalics(Cache.getDefault(Preferences.ID_ITALICS, true));
+ viewStyle.setWrapAlignment(
+ Cache.getDefault(Preferences.WRAP_ALIGNMENT, false));
+ viewStyle.setShowUnconserved(
+ Cache.getDefault(Preferences.SHOW_UNCONSERVED, false));
+ sortByTree = Cache.getDefault(Preferences.SORT_BY_TREE, false);
+ followSelection = Cache.getDefault(Preferences.FOLLOW_SELECTIONS, true);
+ sortAnnotationsBy = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache
+ .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
+ viewStyle.setScaleProteinAsCdna(
+ Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true));
}
void init()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
applyViewProperties();
- String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
- String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
- String fontSize = Cache.getDefault("FONT_SIZE", "10");
+ String fontName = Cache.getDefault(Preferences.FONT_NAME, "SansSerif");
+ String fontStyle = Cache.getDefault(Preferences.FONT_STYLE,
+ Font.PLAIN + "");
+ String fontSize = Cache.getDefault(Preferences.FONT_SIZE, "10");
int style = 0;
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
alignment
- .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+ .setGapCharacter(Cache.getDefault(Preferences.GAP_SYMBOL, "-")
+ .charAt(0));
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
{
if (!alignment.isNucleotide())
{
- showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
- showQuality = Cache.getDefault("SHOW_QUALITY", true);
- showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
- false);
+ showConservation = Cache.getDefault(Preferences.SHOW_CONSERVATION,
+ true);
+ showQuality = Cache.getDefault(Preferences.SHOW_QUALITY, true);
+ showGroupConservation = Cache
+ .getDefault(Preferences.SHOW_GROUP_CONSERVATION, false);
}
- showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
- true);
- showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
- normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+ showConsensusHistogram = Cache
+ .getDefault(Preferences.SHOW_CONSENSUS_HISTOGRAM, true);
+ showSequenceLogo = Cache.getDefault(Preferences.SHOW_CONSENSUS_LOGO,
false);
- showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
- showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+ normaliseSequenceLogo = Cache
+ .getDefault(Preferences.NORMALISE_CONSENSUS_LOGO, false);
+ showGroupConsensus = Cache
+ .getDefault(Preferences.SHOW_GROUP_CONSENSUS, false);
+ showConsensus = Cache.getDefault(Preferences.SHOW_IDENTITY, true);
+
+ showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
- String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
+ String colourProperty = alignment.isNucleotide()
+ ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
- String propertyValue = Cache.getProperty(colourProperty);
- if (propertyValue == null)
+ String schemeName = Cache.getProperty(colourProperty);
+ if (schemeName == null)
{
- // fall back on this property for backwards compatibility
- propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+ // only DEFAULT_COLOUR available in Jalview before 2.9
+ schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
}
- if (propertyValue != null)
- {
- ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
- alignment, propertyValue);
- globalColourScheme = new ResidueShader(colourScheme);
+ ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this,
+ alignment, schemeName);
+ residueShading = new ResidueShader(colourScheme);
- if (colourScheme instanceof UserColourScheme)
- {
- globalColourScheme = new ResidueShader(
- UserDefinedColours.loadDefaultColours());
- globalColourScheme.setThreshold(0, isIgnoreGapsConsensus());
- }
-
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
- }
- }
-
- /**
- * get the consensus sequence as displayed under the PID consensus annotation
- * row.
- *
- * @return consensus sequence as a new sequence object
- */
- public SequenceI getConsensusSeq()
- {
- if (consensus == null)
+ if (colourScheme instanceof UserColourScheme)
{
- updateConsensus(null);
+ residueShading = new ResidueShader(
+ UserDefinedColours.loadDefaultColours());
+ residueShading.setThreshold(0, isIgnoreGapsConsensus());
}
- if (consensus == null)
- {
- return null;
- }
- StringBuffer seqs = new StringBuffer();
- for (int i = 0; i < consensus.annotations.length; i++)
+
+ if (residueShading != null)
{
- if (consensus.annotations[i] != null)
- {
- if (consensus.annotations[i].description.charAt(0) == '[')
- {
- seqs.append(consensus.annotations[i].description.charAt(1));
- }
- else
- {
- seqs.append(consensus.annotations[i].displayCharacter);
- }
- }
+ residueShading.setConsensus(hconsensus);
}
-
- SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus "
- + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
- return sq;
+ setColourAppliesToAllGroups(true);
}
boolean validCharWidth;
/**
- * update view settings with the given font. You may need to call
- * alignPanel.fontChanged to update the layout geometry
- *
- * @param setGrid
- * when true, charWidth/height is set according to font mentrics
+ * {@inheritDoc}
*/
+ @Override
public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
- java.awt.FontMetrics fm = c.getFontMetrics(font);
- int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
- .getCharHeight();
if (setGrid)
{
+ FontMetrics fm = c.getFontMetrics(font);
+ int ww = fm.charWidth('M');
setCharHeight(fm.getHeight());
setCharWidth(ww);
}
super.setViewStyle(settingsForView);
setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
viewStyle.getFontSize()), false);
- if (globalColourScheme != null)
- {
- globalColourScheme.setConservationApplied(settingsForView
- .isConservationColourSelected());
- }
}
/**
*/
if (align != null)
{
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- ssm.registerMappings(align.getCodonFrames());
+ Desktop.getInstance().getStructureSelectionManager()
+ .registerMappings(align.getCodonFrames());
}
/*
List<AlignedCodonFrame> mappings = al.getCodonFrames();
if (mappings != null)
{
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ StructureSelectionManager ssm = Desktop.getInstance()
+ .getStructureSelectionManager();
for (AlignedCodonFrame acf : mappings)
{
if (noReferencesTo(acf))
}
/**
- * DOCUMENT ME!
- *
- * @param tree
- * DOCUMENT ME!
- */
- public void setCurrentTree(NJTree tree)
- {
- currentTree = tree;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public NJTree getCurrentTree()
- {
- return currentTree;
- }
-
- /**
* returns the visible column regions of the alignment
*
* @param selectedRegionOnly
* area
* @return
*/
- public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
{
- int[] viscontigs = null;
- int start = 0, end = 0;
+ int start = 0;
+ int end = 0;
if (selectedRegionOnly && selectionGroup != null)
{
start = selectionGroup.getStartRes();
{
end = alignment.getWidth();
}
- viscontigs = colSel.getVisibleContigs(start, end);
- return viscontigs;
+ return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+ false));
}
/**
@Override
public void sendSelection()
{
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance).sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
+ Desktop.getInstance().getStructureSelectionManager().sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()),
+ new HiddenColumns(getAlignment().getHiddenColumns()), this);
}
/**
*/
public AlignmentPanel getAlignPanel()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
- .getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher
+ .getAssociatedPanels(this.getSequenceSetId());
for (int p = 0; aps != null && p < aps.length; p++)
{
if (aps[p].av == this)
@Override
public StructureSelectionManager getStructureSelectionManager()
{
- return StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- }
-
- /**
- *
- * @param pdbEntries
- * @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)
- {
- List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
- for (PDBEntry pdb : pdbEntries)
- {
- List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
- for (SequenceI sq : alignment.getSequences())
- {
- Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
- .getAllPDBEntries();
- if (pdbRefEntries == null)
- {
- continue;
- }
- for (PDBEntry pdbRefEntry : pdbRefEntries)
- {
- if (pdbRefEntry.getId().equals(pdb.getId()))
- {
- if (pdbRefEntry.getChainCode() != null
- && pdb.getChainCode() != null)
- {
- if (pdbRefEntry.getChainCode().equalsIgnoreCase(
- pdb.getChainCode())
- && !choosenSeqs.contains(sq))
- {
- choosenSeqs.add(sq);
- continue;
- }
- }
- else
- {
- if (!choosenSeqs.contains(sq))
- {
- choosenSeqs.add(sq);
- continue;
- }
- }
-
- }
- }
- }
- seqvectors
- .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
- }
- return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+ return Desktop.getInstance().getStructureSelectionManager();
}
@Override
return validCharWidth;
}
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
* <ul>
* <li>compute the equivalent edit on the mapped sequences</li>
* <li>apply the mapped edit</li>
- * <li>'apply' the source edit to the working copy of the source sequences</li>
+ * <li>'apply' the source edit to the working copy of the source
+ * sequences</li>
* </ul>
*
* @param command
{
if (AlignmentUtils.isMappable(toAdd, getAlignment()))
{
- if (openLinkedAlignment(toAdd, title))
- {
- return;
- }
+ openLinkedAlignment(toAdd, title);
+ return;
}
}
+ addDataToAlignment(toAdd);
+ }
- /*
- * No mappings, or offer declined - add sequences to this alignment
- */
+ /**
+ * adds sequences to this alignment
+ *
+ * @param toAdd
+ */
+ void addDataToAlignment(AlignmentI toAdd)
+ {
// TODO: JAL-407 regardless of above - identical sequences (based on ID and
// provenance) should share the same dataset sequence
}
}
- setEndSeq(getAlignment().getHeight());
+ ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
firePropertyChange("alignment", null, getAlignment().getSequences());
}
+ public final static int NO_SPLIT = 0;
+
+ public final static int SPLIT_FRAME = 1;
+
+ public final static int NEW_WINDOW = 2;
+
/**
* Show a dialog with the option to open and link (cDNA <-> protein) as a new
* alignment, either as a standalone alignment or in a split frame. Returns
* @param al
* @param title
*/
- protected boolean openLinkedAlignment(AlignmentI al, String title)
+ protected void 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,
MessageManager.getString("label.open_split_window?"));
- int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
+
+ /*
+ * options No, Split Window, New Window correspond to
+ * dialog responses 0, 1, 2 (even though JOptionPane shows them
+ * in reverse order)
+ */
+ JvOptionPane dialog = JvOptionPane
+ .newOptionDialog(Desktop.getDesktopPane())
+ .setResponseHandler(NO_SPLIT, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ addDataToAlignment(al);
+ }
+ }).setResponseHandler(SPLIT_FRAME, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ openLinkedAlignmentAs(getAlignPanel().alignFrame,
+ new Alignment(getAlignment()), al, title,
+ SPLIT_FRAME);
+ }
+ }).setResponseHandler(NEW_WINDOW, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ openLinkedAlignmentAs(null, getAlignment(), al, title,
+ NEW_WINDOW);
+ }
+ });
+ dialog.showDialog(question,
MessageManager.getString("label.open_split_window"),
JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
+ }
- if (response != 1 && response != 2)
- {
- return false;
- }
- final boolean openSplitPane = (response == 1);
- final boolean openInNewWindow = (response == 2);
-
+ /**
+ * Open a split frame or a new window
+ *
+ * @param al
+ * @param title
+ * @param mode
+ * SPLIT_FRAME or NEW_WINDOW
+ */
+ public static void openLinkedAlignmentAs(AlignFrame thisFrame,
+ AlignmentI thisAlignment, AlignmentI al, String title, int mode)
+ {
/*
* Identify protein and dna alignments. Make a copy of this one if opening
* in a new split pane.
*/
- AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
- : getAlignment();
AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
- final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+ AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
/*
* Map sequences. At least one should get mapped as we have already passed
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 }));
+ newAlignFrame.setStatus(MessageManager
+ .formatMessage("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.
// alignFrame.setFileName(file, format);
// }
- if (openInNewWindow)
+ if (mode == NEW_WINDOW)
{
Desktop.addInternalFrame(newAlignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
try
{
- newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
+ newAlignFrame.setMaximum(jalview.bin.Cache
+ .getDefault(Preferences.SHOW_FULLSCREEN, false));
} catch (java.beans.PropertyVetoException ex)
{
}
- if (openSplitPane)
+ if (mode == SPLIT_FRAME)
{
al.alignAs(thisAlignment);
- protein = openSplitFrame(newAlignFrame, thisAlignment);
+ openSplitFrame(thisFrame, newAlignFrame, thisAlignment);
}
-
- return true;
}
/**
* cdna/protein complement alignment to show in the other split half
* @return the protein alignment in the split frame
*/
- protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
- AlignmentI complement)
+ static protected AlignmentI openSplitFrame(AlignFrame thisFrame,
+ AlignFrame newAlignFrame, AlignmentI complement)
{
/*
* Make a new frame with a copy of the alignment we are adding to. If this
* 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);
- copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+ AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ copyMe.setTitle(thisFrame.getTitle());
AlignmentI al = newAlignFrame.viewport.getAlignment();
final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();
- complementPanel.setDontScrollComplement(true);
+ complementPanel.setToScrollComplementPanel(false);
complementPanel.scrollToCentre(sr, verticalOffset);
+ complementPanel.setToScrollComplementPanel(true);
}
}
fr.setTransparency(featureSettings.getTransparency());
}
+ public String getViewName()
+ {
+ return viewName;
+ }
+
+ public void setViewName(String viewName)
+ {
+ this.viewName = viewName;
+ }
}
git://source.jalview.org / jalview.git / blobdiff