*/
package jalview.gui;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+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.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+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 java.util.Deque;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComponent;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
+import ext.vamsas.ServiceHandle;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.CrossRef;
import jalview.analysis.Dna;
+import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignExportSettingsI;
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.SimilarityParamsI;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.hmmer.HMMAlign;
+import jalview.hmmer.HMMBuild;
+import jalview.hmmer.HMMERParamStore;
+import jalview.hmmer.HMMERPreset;
+import jalview.hmmer.HMMSearch;
+import jalview.hmmer.HmmerCommand;
+import jalview.hmmer.JackHMMER;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
+import jalview.io.BackupFiles;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.TCoffeeScoreFile;
import jalview.io.vcf.VCFLoader;
import jalview.jbgui.GAlignFrame;
+import jalview.project.Jalview2XML;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
-import jalview.util.dialogrunner.RunResponse;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.WSDiscovererI;
+import jalview.ws.api.ServiceWithParameters;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.slivkaws.SlivkaWSDiscoverer;
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-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.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-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 java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JComponent;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
+@SuppressWarnings("serial")
public class AlignFrame extends GAlignFrame implements DropTargetListener,
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
-
public static final int DEFAULT_WIDTH = 700;
public static final int DEFAULT_HEIGHT = 500;
*/
String fileName = null;
+ /**
+ * TODO: remove reference to 'FileObject' in AlignFrame - not correct mapping
+ */
File fileObject;
/**
*/
void init()
{
+// setBackground(Color.white); // BH 2019
+
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
if (Desktop.desktop != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- /**
- * BH 2018 ignore service listeners
- *
- * @j2sNative
- *
- */
+ if (!Platform.isJS())
{
addServiceListeners();
}
case KeyEvent.VK_BACK_SPACE:
if (!viewport.cursorMode)
{
- cut_actionPerformed(null);
+ cut_actionPerformed();
}
else
{
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
ap.av.updateStrucConsensus(ap);
+ ap.av.initInformationWorker(ap);
}
}
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
- };
+ }
});
// Finally, build the menu once to get current service state
new Thread(new Runnable()
showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+ showInformationHistogram.setSelected(av.isShowInformationHistogram());
+ showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
+ normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
ColourMenuHelper.setColourSelected(colourMenu,
av.getGlobalColourScheme());
return progressBar.operationInProgress();
}
+ /**
+ * Sets the text of the status bar. Note that setting a null or empty value
+ * will cause the status bar to be hidden, with possibly undesirable flicker
+ * of the screen layout.
+ */
@Override
public void setStatus(String text)
{
- statusBar.setText(text);
+ statusBar.setText(text == null || text.isEmpty() ? " " : text);
}
/*
}
@Override
+ public void hmmBuild_actionPerformed(boolean withDefaults)
+ {
+ if (!alignmentIsSufficient(1))
+ {
+ return;
+ }
+
+ /*
+ * get default parameters, and optionally show a dialog
+ * to allow them to be modified
+ */
+ ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
+ {
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new HMMBuild(this, args)).start();
+ }
+
+ @Override
+ public void hmmAlign_actionPerformed(boolean withDefaults)
+ {
+ if (!(checkForHMM() && alignmentIsSufficient(2)))
+ {
+ return;
+ }
+
+ /*
+ * get default parameters, and optionally show a dialog
+ * to allow them to be modified
+ */
+ ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
+ {
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new HMMAlign(this, args)).start();
+ }
+
+ @Override
+ public void hmmSearch_actionPerformed(boolean withDefaults)
+ {
+ if (!checkForHMM())
+ {
+ return;
+ }
+
+ /*
+ * get default parameters, and (if requested) show
+ * dialog to allow modification
+ */
+ ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
+ {
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new HMMSearch(this, args)).start();
+ alignPanel.repaint();
+ }
+
+ @Override
+ public void jackhmmer_actionPerformed(boolean withDefaults)
+ {
+
+ /*
+ * get default parameters, and (if requested) show
+ * dialog to allow modification
+ */
+
+ ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
+ {
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new JackHMMER(this, args)).start();
+ alignPanel.repaint();
+
+ }
+
+ /**
+ * Checks if the alignment has at least one hidden Markov model, if not shows
+ * a dialog advising to run hmmbuild or load an HMM profile
+ *
+ * @return
+ */
+ private boolean checkForHMM()
+ {
+ if (viewport.getAlignment().getHmmSequences().isEmpty())
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.no_hmm"));
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ protected void filterByEValue_actionPerformed()
+ {
+ viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
+ }
+
+ @Override
+ protected void filterByScore_actionPerformed()
+ {
+ viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
+ }
+
+ private double inputDouble(String message)
+ {
+ String str = null;
+ Double d = null;
+ while(d == null || d <= 0)
+ {
+ str = JOptionPane.showInputDialog(this.alignPanel, message);
+ try
+ {
+ d = Double.valueOf(str);
+ }
+ catch (NumberFormatException e)
+ {
+ }
+ }
+ return d;
+ }
+
+ /**
+ * Checks if the alignment contains the required number of sequences.
+ *
+ * @param required
+ * @return
+ */
+ public boolean alignmentIsSufficient(int required)
+ {
+ if (getViewport().getSequenceSelection().length < required)
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("label.not_enough_sequences"));
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
+ * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
+ * comma-separated list)
+ */
+ @Override
+ public void addDatabase_actionPerformed() throws IOException
+ {
+ if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
+ {
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+ }
+
+ String path = openFileChooser(false);
+ if (path != null && new File(path).exists())
+ {
+ IdentifyFile identifier = new IdentifyFile();
+ FileFormatI format = identifier.identify(path, DataSourceType.FILE);
+ if (format == FileFormat.Fasta || format == FileFormat.Stockholm
+ || format == FileFormat.Pfam)
+ {
+ String currentDbPaths = Cache
+ .getProperty(Preferences.HMMSEARCH_DBS);
+ currentDbPaths += Preferences.COMMA + path;
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
+ }
+ else
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.invalid_format"));
+ }
+ }
+ }
+
+ /**
+ * Opens a file chooser, optionally restricted to selecting folders
+ * (directories) only. Answers the path to the selected file or folder, or
+ * null if none is chosen.
+ *
+ * @param
+ * @return
+ */
+ protected String openFileChooser(boolean forFolder)
+ {
+ // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
+ String choice = null;
+ JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ choice = chooser.getSelectedFile().getPath();
+ }
+ return choice;
+ }
+
+ @Override
public void reload_actionPerformed(ActionEvent e)
{
if (fileName != null)
*/
public void saveAlignment(String file, FileFormatI format)
{
- lastSaveSuccessful = false;
+ lastSaveSuccessful = true;
lastFilenameSaved = file;
lastFormatSaved = format;
shortName = shortName.substring(
shortName.lastIndexOf(File.separatorChar) + 1);
}
- lastSaveSuccessful = new jalview.project.Jalview2XML().saveAlignment(this, file,
- shortName);
+ lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
}
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
- RunResponse cancelAction = new RunResponse(JvOptionPane.CANCEL_OPTION)
+ Runnable cancelAction = new Runnable()
{
@Override
public void run()
lastSaveSuccessful = false;
}
};
- RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
+ Runnable outputAction = new Runnable()
{
@Override
public void run()
}
else
{
+ // create backupfiles object and get new temp filename destination
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
try
{
- PrintWriter out = new PrintWriter(new FileWriter(file));
+ String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
+ PrintWriter out = new PrintWriter(
+ new FileWriter(tempFilePath));
+
out.print(output);
out.close();
AlignFrame.this.setTitle(file);
- setStatus(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format",
- new Object[]
- { fileName, format.getName() }));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { fileName, format.getName() }));
+ lastSaveSuccessful = true;
} catch (Exception ex)
{
lastSaveSuccessful = false;
ex.printStackTrace();
}
+
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(lastSaveSuccessful);
+ // do the backup file roll and rename the temp file to actual file
+ lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ }
}
}
};
{
AlignExportOptions choices = new AlignExportOptions(
alignPanel.getAlignViewport(), format, options);
- choices.setResponseAction(outputAction);
- choices.setResponseAction(cancelAction);
+ choices.setResponseAction(0, outputAction);
+ choices.setResponseAction(1, cancelAction);
choices.showDialog();
}
else
FileFormatI fileFormat = FileFormats.getInstance()
.forName(fileFormatName);
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
- RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
+ Runnable outputAction = new Runnable()
{
@Override
public void run()
{
AlignExportOptions choices = new AlignExportOptions(
alignPanel.getAlignViewport(), fileFormat, options);
- choices.setResponseAction(outputAction);
+ choices.setResponseAction(0, outputAction);
choices.showDialog();
}
else
@Override
public void associatedData_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
final JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(
- MessageManager.getString("label.load_jalview_annotations"));
- chooser.setToolTipText(
- MessageManager.getString("label.load_jalview_annotations"));
- chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ String tooltip = MessageManager.getString("label.load_jalview_annotations");
+ chooser.setDialogTitle(tooltip);
+ chooser.setToolTipText(tooltip);
+ chooser.setResponseHandler(0, new Runnable()
{
-
@Override
public void run()
{
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
}
-
});
- chooser.openDialog(this);
+ chooser.showOpenDialog(this);
}
/**
closeView(alignPanel);
}
}
-
if (closeAllTabs)
{
+ if (featureSettings != null && featureSettings.isOpen())
+ {
+ featureSettings.close();
+ featureSettings = null;
+ }
/*
* this will raise an INTERNAL_FRAME_CLOSED event and this method will
* be called recursively, with the frame now in 'closed' state
* DOCUMENT ME!
*/
@Override
- protected void copy_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed()
{
if (viewport.getSelectionGroup() == null)
{
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
@Override
protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(true);
}
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
@Override
protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(false);
}
*
* @param newAlignment
* true to paste to a new alignment, otherwise add to this.
+ * @throws InterruptedException
+ * @throws IOException
*/
- void paste(boolean newAlignment)
+ void paste(boolean newAlignment) throws IOException, InterruptedException
{
boolean externalPaste = true;
try
&& Desktop.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
- Vector newDs = (importDs) ? new Vector() : null; // used to create
+ Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
+ // create
// minimum dataset set
for (int i = 0; i < sequences.length; i++)
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
{
// propagate alignment changed.
- viewport.getRanges().setEndSeq(alignment.getHeight());
+ viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
System.out.println("Exception whilst pasting: " + ex);
// could be anything being pasted in here
}
-
}
@Override
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action Cut (delete and copy) the selected region
*/
@Override
- protected void cut_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed()
{
- copy_actionPerformed(null);
- delete_actionPerformed(null);
+ copy_actionPerformed();
+ delete_actionPerformed();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Performs menu option to Delete the currently selected region
*/
@Override
- protected void delete_actionPerformed(ActionEvent evt)
+ protected void delete_actionPerformed()
{
SequenceGroup sg = viewport.getSelectionGroup();
return;
}
+ Runnable okAction = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
+
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
+
+ viewport.setSelectionGroup(null);
+ viewport.sendSelection();
+ viewport.getAlignment().deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }};
+
/*
- * If the cut affects all sequences, warn, remove highlighted columns
+ * If the cut affects all sequences, prompt for confirmation
*/
- if (sg.getSize() == viewport.getAlignment().getHeight())
- {
- boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
- + 1) == viewport.getAlignment().getWidth()) ? true : false;
- if (isEntireAlignWidth)
- {
- int confirm = JvOptionPane.showConfirmDialog(this,
- MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
- MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JvOptionPane.OK_CANCEL_OPTION);
-
- if (confirm == JvOptionPane.CANCEL_OPTION
- || confirm == JvOptionPane.CLOSED_OPTION)
- {
- return;
- }
- }
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
- SequenceI[] cut = sg.getSequences()
- .toArray(new SequenceI[sg.getSize()]);
-
- addHistoryItem(new EditCommand(
- MessageManager.getString("label.cut_sequences"), Action.CUT,
- cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
-
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- if (viewport.getAlignment().getHeight() < 1)
- {
- try
- {
- this.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
+ boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
+ boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
+ + 1) == viewport.getAlignment().getWidth()) ? true : false;
+ if (wholeHeight && wholeWidth)
+ {
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
+ dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
+ Object[] options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ dialog.showDialog(MessageManager.getString("warn.delete_all"),
+ MessageManager.getString("label.delete_all"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+ } else
+ {
+ okAction.run();
+ }
}
/**
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- SequenceGroup sg = new SequenceGroup();
-
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
- }
+ SequenceGroup sg = new SequenceGroup(
+ viewport.getAlignment().getSequences());
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
+ viewport.isSelectionGroupChanged(true);
viewport.sendSelection();
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
newap.av.setRedoList(viewport.getRedoList());
/*
+ * copy any visualisation settings that are not saved in the project
+ */
+ newap.av.setColourAppliesToAllGroups(
+ viewport.getColourAppliesToAllGroups());
+
+ /*
* Views share the same mappings; need to deregister any new mappings
* created by copyAlignPanel, and register the new reference to the shared
* mappings
viewport.setFollowHighlight(state);
if (state)
{
- alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+ alignPanel.scrollToPosition(viewport.getSearchResults());
}
}
* @param toggleSeqs
* @param toggleCols
*/
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- // TODO: do we actually need to update overview for scale above change ?
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
@Override
public void featureSettings_actionPerformed(ActionEvent e)
{
+ showFeatureSettingsUI();
+ }
+
+ @Override
+ public FeatureSettingsControllerI showFeatureSettingsUI()
+ {
if (featureSettings != null)
{
- featureSettings.close();
+ featureSettings.closeOldSettings();
featureSettings = null;
}
if (!showSeqFeatures.isSelected())
showSeqFeatures_actionPerformed(null);
}
featureSettings = new FeatureSettings(this);
+ return featureSettings;
}
/**
{ contents.toString() });
contents = null;
- if (Jalview.isJS())
+ if (Platform.isJS())
{
JLabel textLabel = new JLabel();
textLabel.setText(content);
((JPanel) pane).add(textLabel, BorderLayout.NORTH);
}
else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
JEditorPane editPane = new JEditorPane("text/html", "");
editPane.setEditable(false);
{
overview.dispose();
alignPanel.setOverviewPanel(null);
- };
+ }
});
if (getKeyListeners().length > 0)
{
* otherwise set the chosen colour scheme (or null for 'None')
*/
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+ viewport,
viewport.getAlignment(), viewport.getHiddenRepSequences());
changeColour(cs);
}
alignPanel.paintAlignment(true, false);
}
+ @Override
+ public void sortEValueMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByEValue(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+
+ @Override
+ public void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByBitScore(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+
/**
* DOCUMENT ME!
*
}
if (viewport.getAlignment().getAlignmentAnnotation()
- .hashCode() != _annotationScoreVectorHash)
+ .hashCode() == _annotationScoreVectorHash)
+ {
+ return;
+ }
+
+ sortByAnnotScore.removeAll();
+ Set<String> scoreSorts = new HashSet<>();
+ for (SequenceI sqa : viewport.getAlignment().getSequences())
{
- sortByAnnotScore.removeAll();
- // almost certainly a quicker way to do this - but we keep it simple
- Hashtable scoreSorts = new Hashtable();
- AlignmentAnnotation aann[];
- for (SequenceI sqa : viewport.getAlignment().getSequences())
+ AlignmentAnnotation[] anns = sqa.getAnnotation();
+ for (int i = 0; anns != null && i < anns.length; i++)
{
- aann = sqa.getAnnotation();
- for (int i = 0; aann != null && i < aann.length; i++)
+ AlignmentAnnotation aa = anns[i];
+ if (aa != null && aa.hasScore() && aa.sequenceRef != null)
{
- if (aann[i].hasScore() && aann[i].sequenceRef != null)
- {
- scoreSorts.put(aann[i].label, aann[i].label);
- }
+ scoreSorts.add(aa.label);
}
}
- Enumeration labels = scoreSorts.keys();
- while (labels.hasMoreElements())
- {
- addSortByAnnotScoreMenuItem(sortByAnnotScore,
- (String) labels.nextElement());
- }
- sortByAnnotScore.setVisible(scoreSorts.size() > 0);
- scoreSorts.clear();
-
- _annotationScoreVectorHash = viewport.getAlignment()
- .getAlignmentAnnotation().hashCode();
}
+ for (String label : scoreSorts)
+ {
+ addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
+ }
+ sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
+
+ _annotationScoreVectorHash = viewport.getAlignment()
+ .getAlignmentAnnotation().hashCode();
}
/**
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- chooser.response(new jalview.util.dialogrunner.RunResponse(
- JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0,new Runnable()
{
@Override
public void run()
JvOptionPane.WARNING_MESSAGE);
}
}
- }).openDialog(this);
+ });
+ chooser.showOpenDialog(this);
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services
+ Vector<ServiceHandle> secstrpr = Discoverer.services
.get("SecStrPred");
if (secstrpr != null)
{
// Add any secondary structure prediction services
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ final ext.vamsas.ServiceHandle sh = secstrpr
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
}
// TODO: move into separate menu builder class.
boolean new_sspred = false;
+
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ WSDiscovererI jws2servs = Jws2Discoverer.getDiscoverer();
if (jws2servs != null)
{
if (jws2servs.hasServices())
{
jws2servs.attachWSMenuEntry(webService, me);
- for (Jws2Instance sv : jws2servs.getServices())
+ for (ServiceWithParameters sv : jws2servs.getServices())
{
- if (sv.description.toLowerCase().contains("jpred"))
+ if (sv.getName().toLowerCase().contains("jpred"))
{
for (JMenuItem jmi : legacyItems)
{
}
}
}
+
+ if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
+ {
+ WSDiscovererI discoverer = SlivkaWSDiscoverer
+ .getInstance();
+ if (discoverer != null)
+ {
+ if (discoverer.hasServices())
+ {
+ discoverer.attachWSMenuEntry(webService, me);
+ }
+ if (discoverer.isRunning())
+ {
+ JMenuItem tm = new JMenuItem(
+ "Still discovering Slivka Services");
+ tm.setEnabled(false);
+ webService.add(tm);
+ }
+ }
+ }
+
build_urlServiceMenu(me.webService);
build_fetchdbmenu(webService);
for (JMenu item : wsmenu)
*
* @param webService
*/
- private void build_urlServiceMenu(JMenu webService)
+ protected void build_urlServiceMenu(JMenu webService)
{
// TODO: remove this code when 2.7 is released
// DEBUG - alignmentView
* frame's DNA sequences to their aligned protein (amino acid) equivalents.
*/
@Override
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
AlignmentI al = null;
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
- al = dna.translateCdna();
+ al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
jalview.bin.Cache.log.error(
af.setFileFormat(this.currentFileFormat);
final String newTitle = MessageManager
.formatMessage("label.translation_of_params", new Object[]
- { this.getTitle() });
+ { this.getTitle(), codeTable.getId() });
af.setTitle(newTitle);
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
: FormatAdapter.checkProtocol(fileName));
if (protocol == DataSourceType.FILE)
{
- File fl = (file instanceof File ? (File) file
- : new File(fileName));
+ File fl;
+ if (file instanceof File) {
+ fl = (File) file;
+ Platform.cacheFileData(fl);
+ } else {
+ fl = new File(fileName);
+ }
pdbfn = fl.getName();
}
else if (protocol == DataSourceType.URL)
*
* @param file
* either a filename or a URL string.
+ * @throws InterruptedException
+ * @throws IOException
*/
public void loadJalviewDataFile(Object file, DataSourceType sourceType,
FileFormatI format, SequenceI assocSeq)
{
if (parseFeaturesFile(file, sourceType))
{
- alignPanel.paintAlignment(true, true);
+ SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
+ if (splitFrame != null)
+ {
+ splitFrame.repaint();
+ }
+ else
+ {
+ alignPanel.paintAlignment(true, true);
+ }
}
}
else
}
if (isAnnotation)
{
-
alignPanel.adjustAnnotationHeight();
viewport.updateSequenceIdColours();
buildSortByAnnotationScoresMenu();
viewport = alignPanel.av;
avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
+ if (featureSettings != null && featureSettings.isOpen()
+ && featureSettings.fr.getViewport() != viewport)
+ {
+ if (viewport.isShowSequenceFeatures())
+ {
+ // refresh the featureSettings to reflect UI change
+ showFeatureSettingsUI();
+ }
+ else
+ {
+ // close feature settings for this view.
+ featureSettings.close();
+ }
+ }
+
}
/*
trimrs.setSelected(trimrs.isSelected());
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
- };
+ }
});
rfetch.add(trimrs);
JMenuItem fetchr = new JMenuItem(
@Override
public void finished()
{
+
+ for (FeatureSettingsModelI srcSettings : dbRefFetcher
+ .getFeatureSettingsModels())
+ {
+
+ alignPanel.av.mergeFeaturesStyle(srcSettings);
+ }
AlignFrame.this.setMenusForViewport();
}
});
@Override
public void finished()
{
+ FeatureSettingsModelI srcSettings = dassource[0]
+ .getFeatureColourScheme();
+ alignPanel.av.mergeFeaturesStyle(
+ srcSettings);
AlignFrame.this.setMenusForViewport();
}
});
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true, true);
+ alignPanel.paintAlignment(true,
+ viewport.needToUpdateStructureViews());
}
}
colourMenu.add(textColour);
colourMenu.addSeparator();
- ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
- false);
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
+ colourMenu.add(annotationColour);
+ bg.add(annotationColour);
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);
}
}
+ /**
+ * Sets the status of the HMMER menu
+ */
+ public void updateHMMERStatus()
+ {
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+ }
+
@Override
protected void loadVcf_actionPerformed()
{
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
final AlignFrame us = this;
- chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
@Override
public void run()
{
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, us);
+ }
+ });
+ chooser.showOpenDialog(null);
- {
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, us);
- }
-
- };
- }).openDialog(null);
+ }
+ private Rectangle lastFeatureSettingsBounds = null;
+ @Override
+ public void setFeatureSettingsGeometry(Rectangle bounds)
+ {
+ lastFeatureSettingsBounds = bounds;
}
+ @Override
+ public Rectangle getFeatureSettingsGeometry()
+ {
+ return lastFeatureSettingsBounds;
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff