import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
-import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
-import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.DBRefSource;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
+import jalview.io.FileParse;
import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
+import jalview.io.ScoreMatrixFile;
import jalview.io.TCoffeeScoreFile;
-import jalview.io.gff.SequenceOntologyI;
import jalview.jbgui.GAlignFrame;
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAHelicesColourChooser;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.StrandColourScheme;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
-import jalview.ws.SequenceFetcher;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.StringSelection;
import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
import java.awt.dnd.DropTargetDragEvent;
import java.awt.dnd.DropTargetDropEvent;
import java.awt.dnd.DropTargetEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.print.PageFormat;
import java.awt.print.PrinterJob;
import java.beans.PropertyChangeEvent;
import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JRadioButtonMenuItem;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator, AlignViewControllerGuiI
+ IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
public static final int DEFAULT_WIDTH = 700;
AlignViewport viewport;
+ ViewportRanges vpRanges;
+
public AlignViewControllerI avc;
- List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
+ List<AlignmentPanel> alignPanels = new ArrayList<>();
/**
* Last format used to load or save alignments in this window
*/
- String currentFileFormat = null;
+ FileFormatI currentFileFormat = null;
/**
* Current filename for this alignment
* @param height
* height of frame.
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
int width, int height)
{
this(al, hiddenColumns, width, height, null);
* @param sequenceSetId
* (may be null)
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
int width, int height, String sequenceSetId)
{
this(al, hiddenColumns, width, height, sequenceSetId, null);
* @param viewId
* (may be null)
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
int width, int height, String sequenceSetId, String viewId)
{
setSize(width, height);
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- ColumnSelection hiddenColumns, int width, int height)
+ HiddenColumns hiddenColumns, int width, int height)
{
setSize(width, height);
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
+ vpRanges = viewport.getRanges();
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
- BLOSUM62Colour.setEnabled(false);
+ // BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
modifyConservation.setEnabled(false);
// PIDColour.setEnabled(false);
sortPairwiseMenuItem_actionPerformed(null);
}
- if (Desktop.desktop != null)
- {
- this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- addServiceListeners();
- setGUINucleotide(viewport.getAlignment().isNucleotide());
- }
-
this.alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
- buildTreeMenu();
+ calculateTree.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ openTreePcaDialog();
+ }
+ });
+ buildColourMenu();
+
+ if (Desktop.desktop != null)
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+ addServiceListeners();
+ setGUINucleotide();
+ }
if (viewport.getWrapAlignment())
{
addKeyListener();
- final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
- final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
+ final List<AlignmentPanel> selviews = new ArrayList<>();
+ final List<AlignmentPanel> origview = new ArrayList<>();
final String menuLabel = MessageManager
.getString("label.copy_format_from");
ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
origview.clear();
origview.add(alignPanel);
// make an array of all alignment panels except for this one
- List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
+ List<AlignmentPanel> aps = new ArrayList<>(
Arrays.asList(Desktop.getAlignmentPanels(null)));
aps.remove(AlignFrame.this.alignPanel);
return aps.toArray(new AlignmentPanel[aps.size()]);
* @param format
* format of file
*/
- public void setFileName(String file, String format)
+ public void setFileName(String file, FileFormatI format)
{
fileName = file;
setFileFormat(format);
new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
- alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
+ .getStartRes();
+ alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
+ .getStartSeq();
}
alignPanel.getSeqPanel().seqCanvas.repaint();
break;
toggleHiddenRegions(toggleSeqs, toggleCols);
break;
}
+ case KeyEvent.VK_B:
+ {
+ boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
+ boolean modifyExisting = true; // always modify, don't clear
+ // evt.isShiftDown();
+ boolean invertHighlighted = evt.isAltDown();
+ avc.markHighlightedColumns(invertHighlighted, modifyExisting,
+ toggleSel);
+ break;
+ }
case KeyEvent.VK_PAGE_UP:
- if (viewport.getWrapAlignment())
- {
- alignPanel.scrollUp(true);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
- }
+ vpRanges.pageUp();
break;
case KeyEvent.VK_PAGE_DOWN:
- if (viewport.getWrapAlignment())
- {
- alignPanel.scrollUp(false);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
- }
+ vpRanges.pageDown();
break;
}
}
/**
* Configure menu items that vary according to whether the alignment is
* nucleotide or protein
- *
- * @param nucleotide
*/
- public void setGUINucleotide(boolean nucleotide)
+ public void setGUINucleotide()
{
+ AlignmentI al = getViewport().getAlignment();
+ boolean nucleotide = al.isNucleotide();
+
showTranslation.setVisible(nucleotide);
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
- modifyConservation.setEnabled(!nucleotide);
+ modifyConservation.setEnabled(!nucleotide
+ && conservationMenuItem.isSelected());
showGroupConservation.setEnabled(!nucleotide);
- rnahelicesColour.setEnabled(nucleotide);
- purinePyrimidineColour.setEnabled(nucleotide);
- showComplementMenuItem.setText(MessageManager
- .getString(nucleotide ? "label.protein" : "label.nucleotide"));
- setColourSelected(jalview.bin.Cache.getDefault(
- nucleotide ? Preferences.DEFAULT_COLOUR_NUC
- : Preferences.DEFAULT_COLOUR_PROT, "None"));
+
+ showComplementMenuItem.setText(nucleotide ? MessageManager
+ .getString("label.protein") : MessageManager
+ .getString("label.nucleotide"));
}
/**
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+ modifyPID.setEnabled(abovePIDThreshold.isSelected());
conservationMenuItem.setSelected(av.getConservationSelected());
+ modifyConservation.setEnabled(conservationMenuItem.isSelected());
seqLimits.setSelected(av.getShowJVSuffix());
idRightAlign.setSelected(av.isRightAlignIds());
centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
- setColourSelected(ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
+ ColourMenuHelper.setColourSelected(colourMenu,
+ av.getGlobalColourScheme());
showSeqFeatures.setSelected(av.isShowSequenceFeatures());
hiddenMarkers.setState(av.getShowHiddenMarkers());
autoCalculate.setSelected(av.autoCalculateConsensus);
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
- rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
- rnahelicesColour
- .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
showProducts.setEnabled(canShowProducts());
setGroovyEnabled(Desktop.getGroovyConsole() != null);
// originating file's format
// TODO: work out how to recover feature settings for correct view(s) when
// file is reloaded.
- if (currentFileFormat.equals("Jalview"))
+ if (FileFormat.Jalview.equals(currentFileFormat))
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
for (int i = 0; i < frames.length; i++)
Desktop.instance.closeAssociatedWindows();
FileLoader loader = new FileLoader();
- String protocol = fileName.startsWith("http:") ? "URL" : "File";
+ DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
+ : DataSourceType.FILE;
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
else
Rectangle bounds = this.getBounds();
FileLoader loader = new FileLoader();
- String protocol = fileName.startsWith("http:") ? "URL" : "File";
+ DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
+ : DataSourceType.FILE;
AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
protocol, currentFileFormat);
@Override
public void save_actionPerformed(ActionEvent e)
{
- if (fileName == null
- || (currentFileFormat == null || !jalview.io.FormatAdapter
- .isValidIOFormat(currentFileFormat, true))
+ if (fileName == null || (currentFileFormat == null)
|| fileName.startsWith("http"))
{
saveAs_actionPerformed(null);
@Override
public void saveAs_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
- jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
- jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
- currentFileFormat, false);
+ String format = currentFileFormat == null ? null : currentFileFormat
+ .getName();
+ JalviewFileChooser chooser = JalviewFileChooser.forWrite(
+ Cache.getProperty("LAST_DIRECTORY"), format);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
currentFileFormat = chooser.getSelectedFormat();
while (currentFileFormat == null)
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager
.getString("label.select_file_format_before_saving"),
MessageManager
.getString("label.file_format_not_specified"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
currentFileFormat = chooser.getSelectedFormat();
value = chooser.showSaveDialog(this);
if (value != JalviewFileChooser.APPROVE_OPTION)
fileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
- currentFileFormat);
+ Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
- if (currentFileFormat.indexOf(" ") > -1)
- {
- currentFileFormat = currentFileFormat.substring(0,
- currentFileFormat.indexOf(" "));
- }
+ Cache.setProperty("LAST_DIRECTORY", fileName);
saveAlignment(fileName, currentFileFormat);
}
}
- public boolean saveAlignment(String file, String format)
+ public boolean saveAlignment(String file, FileFormatI format)
{
boolean success = true;
- if (format.equalsIgnoreCase("Jalview"))
+ if (FileFormat.Jalview.equals(format))
{
String shortName = title;
}
else
{
- if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
- {
- warningMessage("Cannot save file " + fileName + " using format "
- + format, "Alignment output format not supported");
- if (!Jalview.isHeadlessMode())
- {
- saveAs_actionPerformed(null);
- }
- return false;
- }
-
AlignmentExportData exportData = getAlignmentForExport(format,
viewport, null);
if (exportData.getSettings().isCancelled())
exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
exportData.getOmitHidden(), exportData.getStartEndPostions(),
- f.getCacheSuffixDefault(format),
- viewport.getColumnSelection());
+ f.getCacheSuffixDefault(format), viewport.getAlignment()
+ .getHiddenColumns());
if (output == null)
{
{
try
{
- java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter(file));
+ PrintWriter out = new PrintWriter(new FileWriter(file));
out.print(output);
out.close();
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
- new Object[] { fileName, format }));
+ new Object[] { fileName, format.getName() }));
} catch (Exception ex)
{
success = false;
if (!success)
{
- JOptionPane.showInternalMessageDialog(this, MessageManager
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
.formatMessage("label.couldnt_save_file",
new Object[] { fileName }), MessageManager
.getString("label.error_saving_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
return success;
}
else
{
- JOptionPane.showInternalMessageDialog(this, warning, title,
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(this, warning, title,
+ JvOptionPane.WARNING_MESSAGE);
}
return;
}
@Override
protected void outputText_actionPerformed(ActionEvent e)
{
-
- AlignmentExportData exportData = getAlignmentForExport(
- e.getActionCommand(), viewport, null);
+ FileFormatI fileFormat = FileFormats.getInstance().forName(
+ e.getActionCommand());
+ AlignmentExportData exportData = getAlignmentForExport(fileFormat,
+ viewport, null);
if (exportData.getSettings().isCancelled())
{
return;
cap.setForInput(null);
try
{
+ FileFormatI format = fileFormat;
cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
- .formatSequences(e.getActionCommand(),
- exportData.getAlignment(),
+ .formatSequences(format, exportData.getAlignment(),
exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- viewport.getColumnSelection()));
+ exportData
+ .getStartEndPostions(), viewport
+ .getAlignment().getHiddenColumns()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
"label.alignment_output_command",
new Object[] { e.getActionCommand() }), 600, 500);
}
public static AlignmentExportData getAlignmentForExport(
- String exportFormat, AlignViewportI viewport,
+ FileFormatI format, AlignViewportI viewport,
AlignExportSettingI exportSettings)
{
AlignmentI alignmentToExport = null;
if (settings == null)
{
settings = new AlignExportSettings(hasHiddenSeqs,
- viewport.hasHiddenColumns(), exportFormat);
+ viewport.hasHiddenColumns(), format);
}
// settings.isExportAnnotations();
{
alignmentToExport = viewport.getAlignment();
}
- alignmentStartEnd = alignmentToExport
- .getVisibleStartAndEndIndex(viewport.getColumnSelection()
- .getHiddenColumns());
+ alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
+ .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HtmlSvgOutput(null, alignPanel);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
+ htmlSVG.exportHTML(null);
}
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
- bjs.exportJalviewAlignmentAsBioJsHtmlFile();
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+ bjs.exportHTML(null);
}
public void createImageMap(File file, String image)
synchronized void slideSequences(boolean right, int size)
{
- List<SequenceI> sg = new ArrayList<SequenceI>();
+ List<SequenceI> sg = new ArrayList<>();
if (viewport.cursorMode)
{
sg.add(viewport.getAlignment().getSequenceAt(
return;
}
- List<SequenceI> invertGroup = new ArrayList<SequenceI>();
+ List<SequenceI> invertGroup = new ArrayList<>();
for (SequenceI seq : viewport.getAlignment().getSequences())
{
omitHidden = viewport.getViewAsString(true);
}
- String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden, null);
+ String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
+ seqs, omitHidden, null);
StringSelection ss = new StringSelection(output);
ArrayList<int[]> hiddenColumns = null;
if (viewport.hasHiddenColumns())
{
- hiddenColumns = new ArrayList<int[]>();
- int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
- .getSelectionGroup().getEndRes();
- for (int[] region : viewport.getColumnSelection().getHiddenColumns())
+ hiddenColumns = new ArrayList<>();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+ ArrayList<int[]> hiddenRegions = viewport.getAlignment()
+ .getHiddenColumns().getHiddenColumnsCopy();
+ for (int[] region : hiddenRegions)
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
return;
}
- String str, format;
+ String str;
+ FileFormatI format;
try
{
str = (String) contents.getTransferData(DataFlavor.stringFlavor);
return;
}
- format = new IdentifyFile().identify(str, "Paste");
+ format = new IdentifyFile().identify(str, DataSourceType.PASTE);
} catch (OutOfMemoryError er)
{
else
{
// parse the clipboard as an alignment.
- alignment = new FormatAdapter().readFile(str, "Paste", format);
+ alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
+ format);
sequences = alignment.getSequencesArray();
}
int alwidth = 0;
- ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
+ ArrayList<Integer> newGraphGroups = new ArrayList<>();
int fgroup = -1;
if (newAlignment)
{
// propagate alignment changed.
- viewport.setEndSeq(alignment.getHeight());
+ vpRanges.setEndSeq(alignment.getHeight());
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
.getAlignment().getWidth()) ? true : false;
if (isEntireAlignWidth)
{
- int confirm = JOptionPane.showConfirmDialog(this,
+ int confirm = JvOptionPane.showConfirmDialog(this,
MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JOptionPane.OK_CANCEL_OPTION);
+ JvOptionPane.OK_CANCEL_OPTION);
- if (confirm == JOptionPane.CANCEL_OPTION
- || confirm == JOptionPane.CLOSED_OPTION)
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
{
return;
}
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
column, viewport.getAlignment());
- viewport.setStartRes(0);
+ vpRanges.setStartRes(0);
}
else
{
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(vpRanges.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
- viewport.setStartRes(seq.findIndex(startRes) - 1);
+ vpRanges.setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(vpRanges.getStartRes());
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
- viewport.setStartRes(seq.findIndex(startRes) - 1);
+ vpRanges.setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
*/
newap.av.replaceMappings(viewport.getAlignment());
+ /*
+ * start up cDNA consensus (if applicable) now mappings are in place
+ */
+ if (newap.av.initComplementConsensus())
+ {
+ newap.refresh(true); // adjust layout of annotations
+ }
+
newap.av.viewName = getNewViewName(viewTitle);
addAlignmentPanel(newap, true);
*/
protected List<String> getExistingViewNames(List<Component> comps)
{
- List<String> existingNames = new ArrayList<String>();
+ List<String> existingNames = new ArrayList<>();
for (Component comp : comps)
{
if (comp instanceof AlignmentPanel)
viewport.setFollowHighlight(state);
if (state)
{
- alignPanel.scrollToPosition(
- alignPanel.getSeqPanel().seqCanvas.searchResults, false);
+ alignPanel.scrollToPosition(viewport.getSearchResults(), false);
}
}
public void showAllColumns_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
- repaint();
+ alignPanel.paintAlignment(true);
viewport.sendSelection();
}
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
- // alignPanel.paintAlignment(true);
}
/**
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if ((viewport.getColumnSelection() != null
- && viewport.getColumnSelection().getSelected() != null && viewport
- .getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns()
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
{
hideSelSequences_actionPerformed(null);
hide = true;
}
- else if (!(toggleCols && viewport.getColumnSelection().getSelected()
- .size() > 0))
+ else if (!(toggleCols && viewport.hasSelectedColumns()))
{
showAllSeqs_actionPerformed(null);
}
if (toggleCols)
{
- if (viewport.getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns())
{
hideSelColumns_actionPerformed(null);
if (!toggleSeqs)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
alignPanel.paintAlignment(true);
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
- }
-
- /**
- * Set or clear 'Show Sequence Features'
- *
- * @param evt
- * DOCUMENT ME!
- */
- @Override
- public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
- {
- viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
- .isSelected());
- if (viewport.isShowSequenceFeaturesHeight())
- {
- // ensure we're actually displaying features
- viewport.setShowSequenceFeatures(true);
- showSeqFeatures.setSelected(true);
- }
- alignPanel.paintAlignment(true);
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
}
/**
}
JInternalFrame frame = new JInternalFrame();
- OverviewPanel overview = new OverviewPanel(alignPanel);
+ final OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, MessageManager.formatMessage(
"label.overview_params", new Object[] { this.getTitle() }),
- frame.getWidth(), frame.getHeight());
+ true, frame.getWidth(), frame.getHeight(), true, true);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
+ overview.dispose();
alignPanel.setOverviewPanel(null);
};
});
}
@Override
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
new TextColourChooser().chooseColour(alignPanel, null);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ /*
+ * public void covariationColour_actionPerformed() {
+ * changeColour(new
+ * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
+ * ()[0])); }
*/
@Override
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
- changeColour(null);
+ new AnnotationColourChooser(viewport, alignPanel);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
@Override
- public void clustalColour_actionPerformed(ActionEvent e)
+ public void annotationColumn_actionPerformed(ActionEvent e)
{
- changeColour(new ClustalxColourScheme(viewport.getAlignment(),
- viewport.getHiddenRepSequences()));
+ new AnnotationColumnChooser(viewport, alignPanel);
}
/**
- * DOCUMENT ME!
+ * Action on the user checking or unchecking the option to apply the selected
+ * colour scheme to all groups. If unchecked, groups may have their own
+ * independent colour schemes.
*
- * @param e
- * DOCUMENT ME!
+ * @param selected
*/
@Override
- public void zappoColour_actionPerformed(ActionEvent e)
+ public void applyToAllGroups_actionPerformed(boolean selected)
{
- changeColour(new ZappoColourScheme());
+ viewport.setColourAppliesToAllGroups(selected);
}
/**
- * DOCUMENT ME!
+ * Action on user selecting a colour from the colour menu
*
- * @param e
- * DOCUMENT ME!
+ * @param name
+ * the name (not the menu item label!) of the colour scheme
*/
@Override
- public void taylorColour_actionPerformed(ActionEvent e)
+ public void changeColour_actionPerformed(String name)
{
- changeColour(new TaylorColourScheme());
- }
+ /*
+ * 'User Defined' opens a panel to configure or load a
+ * user-defined colour scheme
+ */
+ if (ResidueColourScheme.USER_DEFINED.equals(name))
+ {
+ new UserDefinedColours(alignPanel);
+ return;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HydrophobicColourScheme());
+ /*
+ * otherwise set the chosen colour scheme (or null for 'None')
+ */
+ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+ viewport.getAlignment(), viewport.getHiddenRepSequences());
+ changeColour(cs);
}
/**
- * DOCUMENT ME!
+ * Actions on setting or changing the alignment colour scheme
*
- * @param e
- * DOCUMENT ME!
+ * @param cs
*/
@Override
- public void helixColour_actionPerformed(ActionEvent e)
+ public void changeColour(ColourSchemeI cs)
{
- changeColour(new HelixColourScheme());
- }
+ // TODO: pull up to controller method
+ ColourMenuHelper.setColourSelected(colourMenu, cs);
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void strandColour_actionPerformed(ActionEvent e)
- {
- changeColour(new StrandColourScheme());
+ viewport.setGlobalColourScheme(cs);
+
+ alignPanel.paintAlignment(true);
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Show the PID threshold slider panel
*/
@Override
- public void turnColour_actionPerformed(ActionEvent e)
+ protected void modifyPID_actionPerformed()
{
- changeColour(new TurnColourScheme());
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ SliderPanel.showPIDSlider();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Show the Conservation slider panel
*/
@Override
- public void buriedColour_actionPerformed(ActionEvent e)
+ protected void modifyConservation_actionPerformed()
{
- changeColour(new BuriedColourScheme());
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ SliderPanel.showConservationSlider();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on selecting or deselecting (Colour) By Conservation
*/
@Override
- public void nucleotideColour_actionPerformed(ActionEvent e)
+ public void conservationMenuItem_actionPerformed(boolean selected)
{
- changeColour(new NucleotideColourScheme());
- }
+ modifyConservation.setEnabled(selected);
+ viewport.setConservationSelected(selected);
+ viewport.getResidueShading().setConservationApplied(selected);
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PurinePyrimidineColourScheme());
+ changeColour(viewport.getGlobalColourScheme());
+ if (selected)
+ {
+ modifyConservation_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hideConservationSlider();
+ }
}
- /*
- * public void covariationColour_actionPerformed(ActionEvent e) {
- * changeColour(new
- * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
- * ()[0])); }
+ /**
+ * Action on selecting or deselecting (Colour) Above PID Threshold
*/
@Override
- public void annotationColour_actionPerformed(ActionEvent e)
- {
- new AnnotationColourChooser(viewport, alignPanel);
- }
-
- @Override
- public void annotationColumn_actionPerformed(ActionEvent e)
+ public void abovePIDThreshold_actionPerformed(boolean selected)
{
- new AnnotationColumnChooser(viewport, alignPanel);
- }
+ modifyPID.setEnabled(selected);
+ viewport.setAbovePIDThreshold(selected);
+ if (!selected)
+ {
+ viewport.getResidueShading().setThreshold(0,
+ viewport.isIgnoreGapsConsensus());
+ }
- @Override
- public void rnahelicesColour_actionPerformed(ActionEvent e)
- {
- new RNAHelicesColourChooser(viewport, alignPanel);
+ changeColour(viewport.getGlobalColourScheme());
+ if (selected)
+ {
+ modifyPID_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hidePIDSlider();
+ }
}
/**
* DOCUMENT ME!
*/
@Override
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
- {
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param cs
- * DOCUMENT ME!
- */
- @Override
- public void changeColour(ColourSchemeI cs)
+ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
- // TODO: pull up to controller method
-
- if (cs != null)
- {
- // Make sure viewport is up to date w.r.t. any sliders
- if (viewport.getAbovePIDThreshold())
- {
- int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
- viewport.setThreshold(threshold);
- }
-
- if (viewport.getConservationSelected())
- {
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
- }
- if (cs instanceof TCoffeeColourScheme)
- {
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
- }
- }
-
- viewport.setGlobalColourScheme(cs);
-
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
+ .getAlignment().getSequenceAt(0));
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
* DOCUMENT ME!
*/
@Override
- protected void modifyPID_actionPerformed(ActionEvent e)
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
- if (viewport.getAbovePIDThreshold()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showPIDSlider();
- }
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByID(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
*/
@Override
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ public void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
- if (viewport.getConservationSelected()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showConservationSlider();
- }
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
*/
@Override
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
- viewport.setConservationSelected(conservationMenuItem.isSelected());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setSelected(false);
-
- changeColour(viewport.getGlobalColourScheme());
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByGroup(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
- modifyConservation_actionPerformed(null);
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
*/
@Override
- public void abovePIDThreshold_actionPerformed(ActionEvent e)
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
- conservationMenuItem.setSelected(false);
- viewport.setConservationSelected(false);
-
- changeColour(viewport.getGlobalColourScheme());
-
- modifyPID_actionPerformed(null);
+ new RedundancyPanel(alignPanel, this);
}
/**
* DOCUMENT ME!
*/
@Override
- public void userDefinedColour_actionPerformed(ActionEvent e)
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals(
- MessageManager.getString("action.user_defined")))
+ if ((viewport.getSelectionGroup() == null)
+ || (viewport.getSelectionGroup().getSize() < 2))
{
- new UserDefinedColours(alignPanel, null);
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .getString("label.you_must_select_least_two_sequences"),
+ MessageManager.getString("label.invalid_selection"),
+ JvOptionPane.WARNING_MESSAGE);
}
else
{
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- changeColour(udc);
+ JInternalFrame frame = new JInternalFrame();
+ frame.setContentPane(new PairwiseAlignPanel(viewport));
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
+ 500);
}
}
- public void updateUserColourMenu()
+ @Override
+ public void autoCalculate_actionPerformed(ActionEvent e)
{
-
- Component[] menuItems = colourMenu.getMenuComponents();
- int iSize = menuItems.length;
- for (int i = 0; i < iSize; i++)
- {
- if (menuItems[i].getName() != null
- && menuItems[i].getName().equals("USER_DEFINED"))
- {
- colourMenu.remove(menuItems[i]);
- iSize--;
- }
- }
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger())
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop,
- MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
-
- colourMenu.insert(radioItem, 15);
- colours.add(radioItem);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void PIDColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PIDColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- changeColour(new Blosum62ColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
- .getAlignment().getSequenceAt(0), null);
- addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortIDMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortLengthMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByLength(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Length Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByGroup(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Group Sort", oldOrder,
- viewport.getAlignment()));
-
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
- {
- new RedundancyPanel(alignPanel, this);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
- {
- if ((viewport.getSelectionGroup() == null)
- || (viewport.getSelectionGroup().getSize() < 2))
- {
- JOptionPane.showInternalMessageDialog(this, MessageManager
- .getString("label.you_must_select_least_two_sequences"),
- MessageManager.getString("label.invalid_selection"),
- JOptionPane.WARNING_MESSAGE);
- }
- else
- {
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(new PairwiseAlignPanel(viewport));
- Desktop.addInternalFrame(frame,
- MessageManager.getString("action.pairwise_alignment"), 600,
- 500);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void PCAMenuItem_actionPerformed(ActionEvent e)
- {
- if (((viewport.getSelectionGroup() != null)
- && (viewport.getSelectionGroup().getSize() < 4) && (viewport
- .getSelectionGroup().getSize() > 0))
- || (viewport.getAlignment().getHeight() < 4))
- {
- JOptionPane
- .showInternalMessageDialog(
- this,
- MessageManager
- .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
- MessageManager
- .getString("label.sequence_selection_insufficient"),
- JOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
- new PCAPanel(alignPanel);
- }
-
- @Override
- public void autoCalculate_actionPerformed(ActionEvent e)
- {
- viewport.autoCalculateConsensus = autoCalculate.isSelected();
- if (viewport.autoCalculateConsensus)
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();
+ if (viewport.autoCalculateConsensus)
{
viewport.firePropertyChange("alignment", null, viewport
.getAlignment().getSequences());
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("AV", "PID", "Average distance tree using PID");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
- }
-
- /**
- * DOCUMENT ME!
+ * Constructs a tree panel and adds it to the desktop
*
* @param type
- * DOCUMENT ME!
- * @param pwType
- * DOCUMENT ME!
- * @param title
- * DOCUMENT ME!
+ * tree type (NJ or AV)
+ * @param modelName
+ * name of score model used to compute the tree
+ * @param options
+ * parameters for the distance or similarity calculation
*/
- void newTreePanel(String type, String pwType, String title)
+ void newTreePanel(String type, String modelName, SimilarityParamsI options)
{
+ String frameTitle = "";
TreePanel tp;
+ boolean onSelection = false;
if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() > 0)
{
- if (viewport.getSelectionGroup().getSize() < 3)
- {
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.you_need_more_two_sequences_selected_build_tree"),
- MessageManager
- .getString("label.not_enough_sequences"),
- JOptionPane.WARNING_MESSAGE);
- return;
- }
-
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
{
if (_s.getLength() < sg.getEndRes())
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
MessageManager
.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
MessageManager
.getString("label.sequences_selection_not_aligned"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
}
-
- title = title + " on region";
- tp = new TreePanel(alignPanel, type, pwType);
+ onSelection = true;
}
else
{
- // are the visible sequences aligned?
- if (!viewport.getAlignment().isAligned(false))
- {
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.sequences_must_be_aligned_before_creating_tree"),
- MessageManager
- .getString("label.sequences_not_aligned"),
- JOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
if (viewport.getAlignment().getHeight() < 2)
{
return;
}
-
- tp = new TreePanel(alignPanel, type, pwType);
}
- title += " from ";
+ tp = new TreePanel(alignPanel, type, modelName, options);
+ frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
+
+ frameTitle += " from ";
if (viewport.viewName != null)
{
- title += viewport.viewName + " of ";
+ frameTitle += viewport.viewName + " of ";
}
- title += this.title;
+ frameTitle += this.title;
- Desktop.addInternalFrame(tp, title, 600, 500);
+ Desktop.addInternalFrame(tp, frameTitle, 600, 500);
}
/**
* call. Listeners are added to remove the menu item when the treePanel is
* closed, and adjust the tree leaf to sequence mapping when the alignment is
* modified.
- *
- * @param treePanel
- * Displayed tree window.
- * @param title
- * SortBy menu item title.
*/
@Override
- public void buildTreeMenu()
+ public void buildTreeSortMenu()
{
- calculateTree.removeAll();
- // build the calculate menu
-
- for (final String type : new String[] { "NJ", "AV" })
- {
- String treecalcnm = MessageManager.getString("label.tree_calc_"
- + type.toLowerCase());
- for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
- {
- JMenuItem tm = new JMenuItem();
- ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
- if (sm.isDNA() == viewport.getAlignment().isNucleotide()
- || sm.isProtein() == !viewport.getAlignment()
- .isNucleotide())
- {
- String smn = MessageManager.getStringOrReturn(
- "label.score_model_", sm.getName());
- final String title = MessageManager.formatMessage(
- "label.treecalc_title", treecalcnm, smn);
- tm.setText(title);//
- tm.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- newTreePanel(type, pwtype, title);
- }
- });
- calculateTree.add(tm);
- }
-
- }
- }
sortByTreeMenu.removeAll();
List<Component> comps = PaintRefresher.components.get(viewport
.getSequenceSetId());
- List<TreePanel> treePanels = new ArrayList<TreePanel>();
+ List<TreePanel> treePanels = new ArrayList<>();
for (Component comp : comps)
{
if (comp instanceof TreePanel)
else if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() == 1)
{
- int option = JOptionPane.showConfirmDialog(this,
+ int option = JvOptionPane.showConfirmDialog(this,
MessageManager.getString("warn.oneseq_msainput_selection"),
MessageManager.getString("label.invalid_selection"),
- JOptionPane.OK_CANCEL_OPTION);
- if (option == JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION);
+ if (option == JvOptionPane.OK_OPTION)
{
msa = viewport.getAlignmentView(false);
}
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- jalview.io.NewickFile fin = null;
+ String filePath = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", filePath);
+ NewickFile fin = null;
try
{
- fin = new jalview.io.NewickFile(choice, "File");
- viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
+ fin = new NewickFile(filePath, DataSourceType.FILE);
+ viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
ex.getMessage(),
MessageManager
.getString("label.problem_reading_tree_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
if (fin != null && fin.hasWarningMessage())
{
- JOptionPane.showMessageDialog(Desktop.desktop, fin
+ JvOptionPane.showMessageDialog(Desktop.desktop, fin
.getWarningMessage(), MessageManager
.getString("label.possible_problem_with_tree_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
}
- @Override
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
- {
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
- }
-
- public TreePanel ShowNewickTree(NewickFile nf, String title)
- {
- return ShowNewickTree(nf, title, 600, 500, 4, 5);
- }
-
- public TreePanel ShowNewickTree(NewickFile nf, String title,
- AlignmentView input)
+ public TreePanel showNewickTree(NewickFile nf, String treeTitle)
{
- return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
+ return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
}
- public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
+ public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
int h, int x, int y)
{
- return ShowNewickTree(nf, title, null, w, h, x, y);
+ return showNewickTree(nf, treeTitle, null, w, h, x, y);
}
/**
- * Add a treeviewer for the tree extracted from a newick file object to the
+ * Add a treeviewer for the tree extracted from a Newick file object to the
* current alignment view
*
* @param nf
* position
* @return TreePanel handle
*/
- public TreePanel ShowNewickTree(NewickFile nf, String title,
+ public TreePanel showNewickTree(NewickFile nf, String treeTitle,
AlignmentView input, int w, int h, int x, int y)
{
TreePanel tp = null;
if (nf.getTree() != null)
{
- tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
+ tp = new TreePanel(alignPanel, nf, treeTitle, input);
tp.setSize(w, h);
tp.setLocation(x, y);
}
- Desktop.addInternalFrame(tp, title, w, h);
+ Desktop.addInternalFrame(tp, treeTitle, w, h);
}
} catch (Exception ex)
{
@Override
public void run()
{
- final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
+ final List<JMenuItem> legacyItems = new ArrayList<>();
try
{
// System.err.println("Building ws menu again "
// TODO: group services by location as well as function and/or
// introduce
// object broker mechanism.
- final Vector<JMenu> wsmenu = new Vector<JMenu>();
+ final Vector<JMenu> wsmenu = new Vector<>();
final IProgressIndicator af = me;
+
+ /*
+ * do not i18n these strings - they are hard-coded in class
+ * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
+ * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
+ */
final JMenu msawsmenu = new JMenu("Alignment");
final JMenu secstrmenu = new JMenu(
"Secondary Structure Prediction");
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
final JMenu dismenu = new JMenu("Protein Disorder");
- // final JMenu msawsmenu = new
- // JMenu(MessageManager.getString("label.alignment"));
- // final JMenu secstrmenu = new
- // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
- // final JMenu seqsrchmenu = new
- // JMenu(MessageManager.getString("label.sequence_database_search"));
- // final JMenu analymenu = new
- // JMenu(MessageManager.getString("label.analysis"));
- // final JMenu dismenu = new
- // JMenu(MessageManager.getString("label.protein_disorder"));
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
{
SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
AlignmentI dataset = viewport.getAlignment().getDataset();
+
+ showProducts.removeAll();
+ final boolean dna = viewport.getAlignment().isNucleotide();
+
+ if (seqs == null || seqs.length == 0)
+ {
+ // nothing to see here.
+ return false;
+ }
+
boolean showp = false;
try
{
- showProducts.removeAll();
- final boolean dna = viewport.getAlignment().isNucleotide();
- List<String> ptypes = (seqs == null || seqs.length == 0) ? null
- : new CrossRef(seqs, dataset)
- .findXrefSourcesForSequences(dna);
+ List<String> ptypes = new CrossRef(seqs, dataset)
+ .findXrefSourcesForSequences(dna);
for (final String source : ptypes)
{
protected void showProductsFor(final SequenceI[] sel,
final boolean _odna, final String source)
{
- Runnable foo = new Runnable()
- {
-
- @Override
- public void run()
- {
- final long sttime = System.currentTimeMillis();
- AlignFrame.this.setProgressBar(MessageManager.formatMessage(
- "status.searching_for_sequences_from",
- new Object[] { source }), sttime);
- try
- {
- AlignmentI alignment = AlignFrame.this.getViewport()
- .getAlignment();
- AlignmentI dataset = alignment.getDataset() == null ? alignment
- : alignment.getDataset();
- boolean dna = alignment.isNucleotide();
- if (_odna != dna)
- {
- System.err
- .println("Conflict: showProducts for alignment originally "
- + "thought to be "
- + (_odna ? "DNA" : "Protein")
- + " now searching for "
- + (dna ? "DNA" : "Protein") + " Context.");
- }
- AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
- source, dna);
- if (xrefs == null)
- {
- return;
- }
- /*
- * get display scheme (if any) to apply to features
- */
- FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
- .getFeatureColourScheme(source);
-
- AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
- xrefs);
- if (!dna)
- {
- xrefsAlignment = AlignmentUtils.makeCdsAlignment(
- xrefsAlignment.getSequencesArray(), dataset, sel);
- xrefsAlignment.alignAs(alignment);
- }
-
- /*
- * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
- * sequences). If we are DNA, drop introns and update mappings
- */
- AlignmentI copyAlignment = null;
-
- if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
- {
- boolean copyAlignmentIsAligned = false;
- if (dna)
- {
- copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
- xrefsAlignment.getSequencesArray());
- if (copyAlignment.getHeight() == 0)
- {
- JOptionPane.showMessageDialog(AlignFrame.this,
- MessageManager.getString("label.cant_map_cds"),
- MessageManager.getString("label.operation_failed"),
- JOptionPane.OK_OPTION);
- System.err.println("Failed to make CDS alignment");
- }
-
- /*
- * pending getting Embl transcripts to 'align',
- * we are only doing this for Ensembl
- */
- // TODO proper criteria for 'can align as cdna'
- if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
- || AlignmentUtils.looksLikeEnsembl(alignment))
- {
- copyAlignment.alignAs(alignment);
- copyAlignmentIsAligned = true;
- }
- }
- else
- {
- copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
- xrefs.getSequencesArray(), dataset);
- }
- copyAlignment.setGapCharacter(AlignFrame.this.viewport
- .getGapCharacter());
-
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
-
- /*
- * register any new mappings for sequence mouseover etc
- * (will not duplicate any previously registered mappings)
- */
- ssm.registerMappings(dataset.getCodonFrames());
-
- if (copyAlignment.getHeight() <= 0)
- {
- System.err.println("No Sequences generated for xRef type "
- + source);
- return;
- }
- /*
- * align protein to dna
- */
- if (dna && copyAlignmentIsAligned)
- {
- xrefsAlignment.alignAs(copyAlignment);
- }
- else
- {
- /*
- * align cdna to protein - currently only if
- * fetching and aligning Ensembl transcripts!
- */
- // TODO: generalise for other sources of locus/transcript/cds data
- if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
- {
- copyAlignment.alignAs(xrefsAlignment);
- }
- }
- }
- /*
- * build AlignFrame(s) according to available alignment data
- */
- AlignFrame newFrame = new AlignFrame(xrefsAlignment,
- DEFAULT_WIDTH, DEFAULT_HEIGHT);
- if (Cache.getDefault("HIDE_INTRONS", true))
- {
- newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
- }
- String newtitle = String.format("%s %s %s", MessageManager
- .getString(dna ? "label.proteins" : "label.nucleotides"),
- MessageManager.getString("label.for"), getTitle());
- newFrame.setTitle(newtitle);
-
- if (copyAlignment == null)
- {
- /*
- * split frame display is turned off in preferences file
- */
- Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- return; // via finally clause
- }
- AlignFrame copyThis = new AlignFrame(copyAlignment,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- copyThis.setTitle(AlignFrame.this.getTitle());
-
- boolean showSequenceFeatures = viewport.isShowSequenceFeatures();
- newFrame.setShowSeqFeatures(showSequenceFeatures);
- copyThis.setShowSeqFeatures(showSequenceFeatures);
- FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer();
-
- /*
- * copy feature rendering settings to split frame
- */
- newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
- .transferSettings(myFeatureStyling);
- copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
- .transferSettings(myFeatureStyling);
-
- /*
- * apply 'database source' feature configuration
- * if any was found
- */
- // TODO is this the feature colouring for the original
- // alignment or the fetched xrefs? either could be Ensembl
- newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
- copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
-
- SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
- dna ? newFrame : copyThis);
- newFrame.setVisible(true);
- copyThis.setVisible(true);
- String linkedTitle = MessageManager
- .getString("label.linked_view_title");
- Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
- sf.adjustDivider();
- } catch (OutOfMemoryError e)
- {
- new OOMWarning("whilst fetching crossreferences", e);
- } catch (Throwable e)
- {
- Cache.log.error("Error when finding crossreferences", e);
- } finally
- {
- AlignFrame.this.setProgressBar(MessageManager.formatMessage(
- "status.finished_searching_for_sequences_from",
- new Object[] { source }), sttime);
- }
- }
-
- /**
- * Makes an alignment containing the given sequences, and adds them to the
- * given dataset, which is also set as the dataset for the new alignment
- *
- * TODO: refactor to DatasetI method
- *
- * @param dataset
- * @param seqs
- * @return
- */
- protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
- AlignmentI seqs)
- {
- SequenceI[] sprods = new SequenceI[seqs.getHeight()];
- for (int s = 0; s < sprods.length; s++)
- {
- sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
- if (dataset.getSequences() == null
- || !dataset.getSequences().contains(
- sprods[s].getDatasetSequence()))
- {
- dataset.addSequence(sprods[s].getDatasetSequence());
- }
- sprods[s].updatePDBIds();
- }
- Alignment al = new Alignment(sprods);
- al.setDataset(dataset);
- return al;
- }
-
- };
- Thread frunner = new Thread(foo);
- frunner.start();
+ new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+ .start();
}
/**
final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("label.translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ JvOptionPane.ERROR_MESSAGE);
return;
}
if (al == null || al.getHeight() == 0)
.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
final String errorTitle = MessageManager
.getString("label.translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ JvOptionPane.WARNING_MESSAGE);
}
else
{
/**
* Set the file format
*
- * @param fileFormat
+ * @param format
*/
- public void setFileFormat(String fileFormat)
+ public void setFileFormat(FileFormatI format)
{
- this.currentFileFormat = fileFormat;
+ this.currentFileFormat = format;
}
/**
*
* @param file
* contents or path to retrieve file
- * @param type
+ * @param sourceType
* access mode of file (see jalview.io.AlignFile)
* @return true if features file was parsed correctly.
*/
- public boolean parseFeaturesFile(String file, String type)
+ public boolean parseFeaturesFile(String file, DataSourceType sourceType)
{
- return avc.parseFeaturesFile(file, type,
- jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+ return avc.parseFeaturesFile(file, sourceType,
+ Cache.getDefault("RELAXEDSEQIDMATCHING", false));
}
@Override
public void drop(DropTargetDropEvent evt)
{
+ // JAL-1552 - acceptDrop required before getTransferable call for
+ // Java's Transferable for native dnd
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
- java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
+ List<String> files = new ArrayList<>();
+ List<DataSourceType> protocols = new ArrayList<>();
try
{
/**
* Object[] { String,SequenceI}
*/
- ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
- ArrayList<String> filesnotmatched = new ArrayList<String>();
+ ArrayList<Object[]> filesmatched = new ArrayList<>();
+ ArrayList<String> filesnotmatched = new ArrayList<>();
for (int i = 0; i < files.size(); i++)
{
String file = files.get(i).toString();
String pdbfn = "";
- String protocol = FormatAdapter.checkProtocol(file);
- if (protocol == jalview.io.FormatAdapter.FILE)
+ DataSourceType protocol = FormatAdapter.checkProtocol(file);
+ if (protocol == DataSourceType.FILE)
{
File fl = new File(file);
pdbfn = fl.getName();
}
- else if (protocol == jalview.io.FormatAdapter.URL)
+ else if (protocol == DataSourceType.URL)
{
URL url = new URL(file);
pdbfn = url.getFile();
}
if (mtch != null)
{
- String type = null;
+ FileFormatI type = null;
try
{
type = new IdentifyFile().identify(file, protocol);
{
type = null;
}
- if (type != null)
+ if (type != null && type.isStructureFile())
{
- if (type.equalsIgnoreCase("PDB"))
- {
- filesmatched.add(new Object[] { file, protocol, mtch });
- continue;
- }
+ filesmatched.add(new Object[] { file, protocol, mtch });
+ continue;
}
}
// File wasn't named like one of the sequences or wasn't a PDB file.
if (filesmatched.size() > 0)
{
if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
- || JOptionPane
+ || JvOptionPane
.showConfirmDialog(
this,
MessageManager
.formatMessage(
- "label.automatically_associate_pdb_files_with_sequences_same_name",
+ "label.automatically_associate_structure_files_with_sequences_same_name",
new Object[] { Integer
.valueOf(
filesmatched
.size())
.toString() }),
MessageManager
- .getString("label.automatically_associate_pdb_files_by_name"),
- JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
+ .getString("label.automatically_associate_structure_files_by_name"),
+ JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
{
for (Object[] fm : filesmatched)
{
PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq((String) fm[0],
- (String) fm[1], toassoc, false,
+ (DataSourceType) fm[1], toassoc, false,
Desktop.instance);
if (pe != null)
{
{
if (assocfiles > 0
&& (Cache.getDefault(
- "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
+ "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
.showConfirmDialog(
this,
"<html>"
+ "</html>",
MessageManager
.getString("label.ignore_unmatched_dropped_files"),
- JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
+ JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
{
return;
}
}
/**
- * Attempt to load a "dropped" file or URL string: First by testing whether
- * it's an Annotation file, then a JNet file, and finally a features file. If
- * all are false then the user may have dropped an alignment file onto this
- * AlignFrame.
+ * Attempt to load a "dropped" file or URL string, by testing in turn for
+ * <ul>
+ * <li>an Annotation file</li>
+ * <li>a JNet file</li>
+ * <li>a features file</li>
+ * <li>else try to interpret as an alignment file</li>
+ * </ul>
*
* @param file
* either a filename or a URL string.
*/
- public void loadJalviewDataFile(String file, String protocol,
- String format, SequenceI assocSeq)
+ public void loadJalviewDataFile(String file, DataSourceType sourceType,
+ FileFormatI format, SequenceI assocSeq)
{
try
{
- if (protocol == null)
+ if (sourceType == null)
{
- protocol = FormatAdapter.checkProtocol(file);
+ sourceType = FormatAdapter.checkProtocol(file);
}
// if the file isn't identified, or not positively identified as some
// other filetype (PFAM is default unidentified alignment file type) then
// try to parse as annotation.
- boolean isAnnotation = (format == null || format
- .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
- .annotateAlignmentView(viewport, file, protocol) : false;
+ boolean isAnnotation = (format == null || FileFormat.Pfam
+ .equals(format)) ? new AnnotationFile()
+ .annotateAlignmentView(viewport, file, sourceType) : false;
if (!isAnnotation)
{
TCoffeeScoreFile tcf = null;
try
{
- tcf = new TCoffeeScoreFile(file, protocol);
+ tcf = new TCoffeeScoreFile(file, sourceType);
if (tcf.isValid())
{
if (tcf.annotateAlignment(viewport.getAlignment(), true))
{
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
+ buildColourMenu();
changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
statusBar
{
// some problem - if no warning its probable that the ID matching
// process didn't work
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
tcf.getWarningMessage() == null ? MessageManager
: tcf.getWarningMessage(),
MessageManager
.getString("label.problem_reading_tcoffee_score_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
else
// try to parse it as a features file
if (format == null)
{
- format = new IdentifyFile().identify(file, protocol);
+ format = new IdentifyFile().identify(file, sourceType);
+ }
+ if (FileFormat.ScoreMatrix == format)
+ {
+ ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
+ sourceType));
+ sm.parse();
+ // todo: i18n this message
+ statusBar
+ .setText(MessageManager.formatMessage(
+ "label.successfully_loaded_matrix",
+ sm.getMatrixName()));
}
- if (format.equalsIgnoreCase("JnetFile"))
+ else if (FileFormat.Jnet.equals(format))
{
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(
- file, protocol);
+ JPredFile predictions = new JPredFile(file, sourceType);
new JnetAnnotationMaker();
JnetAnnotationMaker.add_annotation(predictions,
viewport.getAlignment(), 0, false);
SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
viewport.getAlignment().setSeqrep(repseq);
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
cs.hideInsertionsFor(repseq);
- viewport.setColumnSelection(cs);
+ viewport.getAlignment().setHiddenColumns(cs);
isAnnotation = true;
}
- else if (IdentifyFile.FeaturesFile.equals(format))
+ // else if (IdentifyFile.FeaturesFile.equals(format))
+ else if (FileFormat.Features.equals(format))
{
- if (parseFeaturesFile(file, protocol))
+ if (parseFeaturesFile(file, sourceType))
{
alignPanel.paintAlignment(true);
}
}
else
{
- new FileLoader().LoadFile(viewport, file, protocol, format);
+ new FileLoader().LoadFile(viewport, file, sourceType, format);
}
}
}
}
new OOMWarning(
"loading data "
- + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
- : "using " + protocol + " from " + file)
+ + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
+ : "using " + sourceType + " from " + file)
: ".")
+ (format != null ? "(parsing as '" + format
+ "' file)" : ""), oom, Desktop.desktop);
}
/*
+ * 'focus' any colour slider that is open to the selected viewport
+ */
+ if (viewport.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ }
+ else
+ {
+ SliderPanel.hideConservationSlider();
+ }
+ if (viewport.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ }
+ else
+ {
+ SliderPanel.hidePIDSlider();
+ }
+
+ /*
* If there is a frame linked to this one in a SplitPane, switch it to the
* same view tab index. No infinite recursion of calls should happen, since
* tabSelectionChanged() should not get invoked on setting the selected
if (e.isPopupTrigger())
{
String msg = MessageManager.getString("label.enter_view_name");
- String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
- JOptionPane.QUESTION_MESSAGE);
+ String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
+ JvOptionPane.QUESTION_MESSAGE);
if (reply != null)
{
{
return;
}
- List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
+ List<SequenceI> cdnaSeqs = new ArrayList<>();
for (SequenceI aaSeq : alignment.getSequences())
{
for (AlignedCodonFrame acf : mappings)
}
AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
.size()]));
- AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
+ GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
cdna.alignAs(alignment);
String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
} catch (Exception ex)
{
System.err.println((ex.toString()));
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("label.couldnt_run_groovy_script"),
MessageManager
.getString("label.groovy_support_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
else
}
return false;
}
+
+ @Override
+ protected void selectHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ // include key modifier check in case user selects from menu
+ avc.markHighlightedColumns(
+ (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
+ true,
+ (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
+ }
+
+ /**
+ * Rebuilds the Colour menu, including any user-defined colours which have
+ * been loaded either on startup or during the session
+ */
+ public void buildColourMenu()
+ {
+ colourMenu.removeAll();
+
+ colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+
+ ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
+
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
+
+ ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
+ ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
+ }
+
+ /**
+ * Open a dialog (if not already open) that allows the user to select and
+ * calculate PCA or Tree analysis
+ */
+ protected void openTreePcaDialog()
+ {
+ if (alignPanel.getCalculationDialog() == null)
+ {
+ new CalculationChooser(AlignFrame.this);
+ }
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff