/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import java.awt.BorderLayout;
-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.ItemEvent;
-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.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.Set;
-import java.util.Vector;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-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;
-
-import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
-import jalview.analysis.Conservation;
import jalview.analysis.CrossRef;
import jalview.analysis.Dna;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsControllerI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
-import jalview.io.FeaturesFile;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.seqfetcher.DbSourceProxy;
+import java.awt.BorderLayout;
+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.ItemEvent;
+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.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.Set;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+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;
+
/**
* DOCUMENT ME!
*
alignPanel = new AlignmentPanel(this, viewport);
+ addAlignmentPanel(alignPanel, true);
+ init();
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection hiddenColumns, int width, int height)
+ {
+ setSize(width, height);
+
+ if (al.getDataset() == null)
+ {
+ al.setDataset(null);
+ }
+ viewport = new AlignViewport(al, hiddenColumns);
+
+ if (hiddenSeqs != null && hiddenSeqs.length > 0)
+ {
+ viewport.hideSequence(hiddenSeqs);
+ }
+ alignPanel = new AlignmentPanel(this, viewport);
addAlignmentPanel(alignPanel, true);
init();
}
*/
void init()
{
- progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ if (!Jalview.isHeadlessMode())
+ {
+ progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ }
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
-
+
if (viewport.getWrapAlignment())
{
wrapMenuItem_actionPerformed(null);
}
}
});
- formatMenu.add(vsel);
+ if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ .indexOf("devel") > -1
+ || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ .indexOf("test") > -1)
+ {
+ formatMenu.add(vsel);
+ }
}
case KeyEvent.VK_SPACE:
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
- || evt.isShiftDown() || evt.isAltDown());
+ alignPanel.getSeqPanel().insertGapAtCursor(
+ evt.isControlDown() || evt.isShiftDown()
+ || evt.isAltDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown() || evt.isAltDown());
+ alignPanel.getSeqPanel().deleteGapAtCursor(
+ evt.isControlDown() || evt.isShiftDown()
+ || evt.isAltDown());
}
break;
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
statusBar.setText(MessageManager.formatMessage(
- "label.keyboard_editing_mode", new String[]
- { (viewport.cursorMode ? "on" : "off") }));
+ "label.keyboard_editing_mode",
+ new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
- System.out.println("deregistering discoverer listener");
+ // System.out.println("deregistering discoverer listener");
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
@Override
public void addFromText_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
+ .getAlignPanel());
}
@Override
currentFileFormat, false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_alignment_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
success = new Jalview2XML().saveAlignment(this, file, shortName);
statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format }));
+ "label.successfully_saved_to_file_in_format", new Object[] {
+ fileName, format }));
}
else
{
warningMessage("Cannot save file " + fileName + " using format "
+ format, "Alignment output format not supported");
- saveAs_actionPerformed(null);
- // JBPNote need to have a raise_gui flag here
+ if (!Jalview.isHeadlessMode())
+ {
+ saveAs_actionPerformed(null);
+ }
return false;
}
- ExportData exportData = getAlignmentForExport();
- FormatAdapter f = new FormatAdapter(viewport);
- String output = f.formatSequences(format,
+ AlignmentExportData exportData = getAlignmentForExport(format,
+ viewport, null);
+ if (exportData.getSettings().isCancelled())
+ {
+ return false;
+ }
+ FormatAdapter f = new FormatAdapter(alignPanel,
+ exportData.getSettings());
+ String output = f.formatSequences(
+ format,
exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
- exportData.getOmitHidden(), f.getCacheSuffixDefault(format),
+ exportData.getOmitHidden(), exportData.getStartEndPostions(),
+ f.getCacheSuffixDefault(format),
viewport.getColumnSelection());
if (output == null)
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
- new Object[]
- { fileName, format }));
+ new Object[] { fileName, format }));
} catch (Exception ex)
{
success = false;
if (!success)
{
JOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new Object[]
- { fileName }), MessageManager
+ .formatMessage("label.couldnt_save_file",
+ new Object[] { fileName }), MessageManager
.getString("label.error_saving_file"),
JOptionPane.WARNING_MESSAGE);
}
return success;
}
-
private void warningMessage(String warning, String title)
{
if (new jalview.util.Platform().isHeadless())
protected void outputText_actionPerformed(ActionEvent e)
{
- ExportData exportData = getAlignmentForExport();
+ AlignmentExportData exportData = getAlignmentForExport(
+ e.getActionCommand(), viewport, null);
+ if (exportData.getSettings().isCancelled())
+ {
+ return;
+ }
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
-
try
{
- cap.setText(new FormatAdapter(viewport).formatSequences(
- e.getActionCommand(),
- exportData.getAlignment(),
- exportData.getOmitHidden(),
- viewport.getColumnSelection()));
+ cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
+ .formatSequences(e.getActionCommand(),
+ exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getColumnSelection()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command", new Object[]
- { e.getActionCommand() }), 600, 500);
+ "label.alignment_output_command",
+ new Object[] { e.getActionCommand() }), 600, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
}
- public ExportData getAlignmentForExport()
+ public static AlignmentExportData getAlignmentForExport(
+ String exportFormat, AlignViewportI viewport,
+ AlignExportSettingI exportSettings)
{
AlignmentI alignmentToExport = null;
+ AlignExportSettingI settings = exportSettings;
String[] omitHidden = null;
- FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
- viewport.setFeatureRenderer(fr);
+ int[] alignmentStartEnd = new int[2];
+
HiddenSequences hiddenSeqs = viewport.getAlignment()
.getHiddenSequences();
- if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
+
+ alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
+
+ boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
+ if (settings == null)
{
- int reply = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.alignment_contains_hidden_columns"),
- MessageManager
- .getString("action.save_omit_hidden_columns"),
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
+ settings = new AlignExportSettings(hasHiddenSeqs,
+ viewport.hasHiddenColumns(), exportFormat);
+ }
+ // settings.isExportAnnotations();
- if (reply == JOptionPane.YES_OPTION)
- {
- omitHidden = viewport.getViewAsString(false);
- }
- else
- {
- alignmentToExport = viewport.getAlignment().getHiddenSequences()
- .getFullAlignment();
- }
+ if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
+ {
+ omitHidden = viewport.getViewAsString(false);
+ }
+
+ if (hasHiddenSeqs && settings.isExportHiddenSequences())
+ {
+ alignmentToExport = hiddenSeqs.getFullAlignment();
}
- if (alignmentToExport == null)
+ else
{
alignmentToExport = viewport.getAlignment();
+ alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+ .getColumnSelection().getHiddenColumns());
+ }
+ AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
+ omitHidden, alignmentStartEnd, settings);
+ return ed;
+ }
+
+ public static int[] getStartEnd(int[] aligmentStartEnd,
+ List<int[]> hiddenCols)
+ {
+ int startPos = aligmentStartEnd[0];
+ int endPos = aligmentStartEnd[1];
+
+ int[] lowestRange = new int[2];
+ int[] higestRange = new int[2];
+
+ for (int[] hiddenCol : hiddenCols)
+ {
+ // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
+ lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+ higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+ }
+ // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
+ // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
+
+ if (lowestRange[0] == 0 && lowestRange[1] == 0)
+ {
+ startPos = aligmentStartEnd[0];
+ }
+ else
+ {
+ startPos = lowestRange[1] + 1;
}
- return new ExportData(alignmentToExport, omitHidden);
+
+ if (higestRange[0] == 0 && higestRange[1] == 0)
+ {
+ endPos = aligmentStartEnd[1];
+ }
+ else
+ {
+ endPos = higestRange[0];
+ }
+
+ // System.out.println("Export range : " + minPos + " - " + maxPos);
+ return new int[] { startPos, endPos };
+ }
+
+ public static void main(String[] args)
+ {
+ ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
+ hiddenCols.add(new int[] { 0, 4 });
+ hiddenCols.add(new int[] { 6, 9 });
+ hiddenCols.add(new int[] { 11, 12 });
+ hiddenCols.add(new int[] { 33, 33 });
+ hiddenCols.add(new int[] { 45, 50 });
+
+ int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
+ // System.out.println("Export range : " + x[0] + " - " + x[1]);
}
/**
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- // new HTMLOutput(alignPanel,
- // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
- // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
new HtmlSvgOutput(null, alignPanel);
}
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel,
- alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
bjs.exportJalviewAlignmentAsBioJsHtmlFile();
}
+
public void createImageMap(File file, String image)
{
alignPanel.makePNGImageMap(file, image);
{
alignPanel.makeSVG(f);
}
+
@Override
public void pageSetup_actionPerformed(ActionEvent e)
{
if (closeAllTabs)
{
+ /*
+ * this will raise an INTERNAL_FRAME_CLOSED event and this method will
+ * be called recursively, with the frame now in 'closed' state
+ */
this.setClosed(true);
}
} catch (Exception ex)
undoMenuItem.setEnabled(true);
CommandI command = viewport.getHistoryList().peek();
undoMenuItem.setText(MessageManager.formatMessage(
- "label.undo_command", new Object[]
- { command.getDescription() }));
+ "label.undo_command",
+ new Object[] { command.getDescription() }));
}
else
{
CommandI command = viewport.getRedoList().peek();
redoMenuItem.setText(MessageManager.formatMessage(
- "label.redo_command", new Object[]
- { command.getDescription() }));
+ "label.redo_command",
+ new Object[] { command.getDescription() }));
}
else
{
}
if (viewport != null)
{
- return new AlignmentI[]
- { viewport.getAlignment() };
+ return new AlignmentI[] { viewport.getAlignment() };
}
return null;
}
viewport.getSelectionGroup().getEndRes() + groupAdjustment);
}
+ /*
+ * just extend the last slide command if compatible; but not if in
+ * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
+ */
boolean appendHistoryItem = false;
Deque<CommandI> historyList = viewport.getHistoryList();
- if (historyList != null
- && historyList.size() > 0
+ boolean inSplitFrame = getSplitViewContainer() != null;
+ if (!inSplitFrame && historyList != null && historyList.size() > 0
&& historyList.peek() instanceof SlideSequencesCommand)
{
appendHistoryItem = ssc
}
String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden);
+ omitHidden, null);
StringSelection ss = new StringSelection(output);
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
- hiddenColumns.add(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ hiddenColumns.add(new int[] { region[0] - hiddenOffset,
+ region[1] - hiddenOffset });
}
}
}
- Desktop.jalviewClipboard = new Object[]
- { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
+ Desktop.jalviewClipboard = new Object[] { seqs,
+ viewport.getAlignment().getDataset(), hiddenColumns };
statusBar.setText(MessageManager.formatMessage(
- "label.copied_sequences_to_clipboard", new Object[]
- { Integer.valueOf(seqs.length).toString() }));
+ "label.copied_sequences_to_clipboard", new Object[] { Integer
+ .valueOf(seqs.length).toString() }));
}
/**
//
addHistoryItem(new EditCommand(
MessageManager.getString("label.add_sequences"),
- Action.PASTE,
- sequences, 0, alignment.getWidth(), alignment));
+ Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
}
// Add any annotations attached to sequences
for (int i = 0; i < sequences.length; i++)
// found!!<<<
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(
- alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
// found!!<<<
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(
- alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+ alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
}
statusBar.setText(MessageManager.formatMessage(
- "label.removed_columns", new String[]
- { Integer.valueOf(trimRegion.getSize()).toString() }));
+ "label.removed_columns",
+ new String[] { Integer.valueOf(trimRegion.getSize())
+ .toString() }));
addHistoryItem(trimRegion);
addHistoryItem(removeGapCols);
statusBar.setText(MessageManager.formatMessage(
- "label.removed_empty_columns", new Object[]
- { Integer.valueOf(removeGapCols.getSize()).toString() }));
+ "label.removed_empty_columns",
+ new Object[] { Integer.valueOf(removeGapCols.getSize())
+ .toString() }));
// This is to maintain viewport position on first residue
// of first sequence
}
/*
- * Views share the same edits, undo and redo stacks, mappings.
+ * Views share the same edits undo and redo stacks
*/
newap.av.setHistoryList(viewport.getHistoryList());
newap.av.setRedoList(viewport.getRedoList());
- newap.av.getAlignment().setCodonFrames(
- viewport.getAlignment().getCodonFrames());
+
+ /*
+ * Views share the same mappings; need to deregister any new mappings
+ * created by copyAlignPanel, and register the new reference to the shared
+ * mappings
+ */
+ newap.av.replaceMappings(viewport.getAlignment());
newap.av.viewName = getNewViewName(viewTitle);
{
viewport.setShowJVSuffix(seqLimits.isSelected());
- alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
- .calculateIdWidth());
+ alignPanel.getIdPanel().getIdCanvas()
+ .setPreferredSize(alignPanel.calculateIdWidth());
alignPanel.paintAlignment(true);
}
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
-// alignPanel.paintAlignment(true);
+ // alignPanel.paintAlignment(true);
}
/**
public FeatureSettings featureSettings;
@Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return featureSettings;
+ }
+
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
.formatAsHtml();
editPane.setText(MessageManager.formatMessage("label.html_content",
- new Object[]
- { contents.toString() }));
+ new Object[] { contents.toString() }));
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
Desktop.addInternalFrame(frame, MessageManager.formatMessage(
- "label.alignment_properties", new Object[]
- { getTitle() }), 500, 400);
+ "label.alignment_properties", new Object[] { getTitle() }),
+ 500, 400);
}
/**
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, MessageManager.formatMessage(
- "label.overview_params", new Object[]
- { this.getTitle() }), frame.getWidth(), frame.getHeight());
+ "label.overview_params", new Object[] { this.getTitle() }),
+ frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
*/
public void changeColour(ColourSchemeI cs)
{
- // TODO: compare with applet and pull up to model method
- int threshold = 0;
+ // TODO: pull up to controller method
if (cs != null)
{
+ // Make sure viewport is up to date w.r.t. any sliders
if (viewport.getAbovePIDThreshold())
{
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+ int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
"Background");
- cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
- }
- else
- {
- cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
+ viewport.setThreshold(threshold);
}
if (viewport.getConservationSelected())
{
-
- Alignment al = (Alignment) viewport.getAlignment();
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.getConsPercGaps());
-
- cs.setConservation(c);
-
cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
}
- else
- {
- cs.setConservation(null);
- }
-
- cs.setConsensus(viewport.getSequenceConsensusHash());
}
viewport.setGlobalColourScheme(cs);
- if (viewport.getColourAppliesToAllGroups())
- {
-
- for (SequenceGroup sg : viewport.getAlignment().getGroups())
- {
- if (cs == null)
- {
- sg.cs = null;
- continue;
- }
-
- if (cs instanceof ClustalxColourScheme)
- {
- sg.cs = new ClustalxColourScheme(sg,
- viewport.getHiddenRepSequences());
- }
- else if (cs instanceof UserColourScheme)
- {
- sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
- }
- else
- {
- try
- {
- sg.cs = cs.getClass().newInstance();
- } catch (Exception ex)
- {
- }
- }
-
- if (viewport.getAbovePIDThreshold()
- || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
- {
- sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
-
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(viewport.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1));
- }
- else
- {
- sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
- }
-
- if (viewport.getConservationSelected())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(viewport
- .getHiddenRepSequences()), sg.getStartRes(),
- sg.getEndRes() + 1);
- c.calculate();
- c.verdict(false, viewport.getConsPercGaps());
- sg.cs.setConservation(c);
- }
- else
- {
- sg.cs.setConservation(null);
- }
- }
- }
-
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
-
alignPanel.paintAlignment(true);
}
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
{
- final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
+ final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
+ "action.by_title_param", new Object[] { title }));
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
calculateTree.removeAll();
// build the calculate menu
- for (final String type : new String[]
- { "NJ", "AV" })
+ for (final String type : new String[] { "NJ", "AV" })
{
String treecalcnm = MessageManager.getString("label.tree_calc_"
+ type.toLowerCase());
// selection may well be aligned - we preserve 2.0.8 behaviour for moment.
if (!viewport.getAlignment().isAligned(false))
{
- seqs.setSequences(new SeqCigar[]
- { seqs.getSequences()[0] });
+ seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
// TODO: if seqs.getSequences().length>1 then should really have warned
// user!
final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
try
{
- System.err.println("Building ws menu again "
- + Thread.currentThread());
+ // System.err.println("Building ws menu again "
+ // + Thread.currentThread());
// TODO: add support for context dependent disabling of services based
// on
// alignment and current selection
{
final long sttime = System.currentTimeMillis();
AlignFrame.this.setProgressBar(MessageManager.formatMessage(
- "status.searching_for_sequences_from", new Object[]
- { source }), sttime);
+ "status.searching_for_sequences_from",
+ new Object[] { source }), sttime);
try
{
// update our local dataset reference
// temporary flag until SplitFrame is released
boolean asSplitFrame = Cache.getDefault(
- Preferences.ENABLE_SPLIT_FRAME, false);
+ Preferences.ENABLE_SPLIT_FRAME, true);
if (asSplitFrame)
{
/*
al.getCodonFrames().addAll(cf);
final StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
- ssm.addMappings(cf);
+ ssm.registerMappings(cf);
}
else
{
}
AlignFrame.this.setProgressBar(MessageManager.formatMessage(
"status.finished_searching_for_sequences_from",
- new Object[]
- { source }),
- sttime);
+ new Object[] { source }), sttime);
}
};
"Exception during translation. Please report this !", ex);
final String msg = MessageManager
.getString("label.error_when_translating_sequences_submit_bug_report");
- final String title = MessageManager
+ final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.ERROR_MESSAGE);
return;
}
{
final String msg = MessageManager
.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
- final String title = MessageManager
+ final String errorTitle = MessageManager
.getString("label.translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.WARNING_MESSAGE);
}
else
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
af.setFileFormat(this.currentFileFormat);
final String newTitle = MessageManager.formatMessage(
- "label.translation_of_params", new Object[]
- { this.getTitle() });
+ "label.translation_of_params",
+ new Object[] { this.getTitle() });
af.setTitle(newTitle);
- if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
+ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
- viewport.openSplitFrame(af, new Alignment(seqs),
- al.getCodonFrames());
+ viewport.openSplitFrame(af, new Alignment(seqs));
}
else
{
* contents or path to retrieve file
* @param type
* access mode of file (see jalview.io.AlignFile)
- * @return true if features file was parsed corectly.
+ * @return true if features file was parsed correctly.
*/
public boolean parseFeaturesFile(String file, String type)
{
- boolean featuresFile = false;
- try
- {
- featuresFile = new FeaturesFile(file, type).parse(viewport
- .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer().getFeatureColours(), false,
- jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ return avc.parseFeaturesFile(file, type,
+ jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
- if (featuresFile)
+ }
+
+ @Override
+ public void refreshFeatureUI(boolean enableIfNecessary)
+ {
+ // note - currently this is only still here rather than in the controller
+ // because of the featureSettings hard reference that is yet to be
+ // abstracted
+ if (enableIfNecessary)
{
viewport.setShowSequenceFeatures(true);
showSeqFeatures.setSelected(true);
- if (alignPanel.getSeqPanel().seqCanvas.fr != null)
- {
- // update the min/max ranges where necessary
- alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
- }
- if (featureSettings != null)
- {
- featureSettings.setTableData();
- }
- alignPanel.paintAlignment(true);
}
- return featuresFile;
}
@Override
{
if (type.equalsIgnoreCase("PDB"))
{
- filesmatched.add(new Object[]
- { file, protocol, mtch });
+ filesmatched.add(new Object[] { file, protocol, mtch });
continue;
}
}
MessageManager
.formatMessage(
"label.automatically_associate_pdb_files_with_sequences_same_name",
- new Object[]
- { Integer.valueOf(
- filesmatched
- .size())
+ new Object[] { Integer
+ .valueOf(
+ filesmatched
+ .size())
.toString() }),
MessageManager
.getString("label.automatically_associate_pdb_files_by_name"),
"AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
.showConfirmDialog(
this,
- "<html>"+MessageManager
- .formatMessage(
- "label.ignore_unmatched_dropped_files_info",
- new Object[]
- { Integer.valueOf(
- filesnotmatched
- .size())
- .toString() })+"</html>",
+ "<html>"
+ + MessageManager
+ .formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new Object[] { Integer
+ .valueOf(
+ filesnotmatched
+ .size())
+ .toString() })
+ + "</html>",
MessageManager
.getString("label.ignore_unmatched_dropped_files"),
JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
// try to parse as annotation.
boolean isAnnotation = (format == null || format
.equalsIgnoreCase("PFAM")) ? new AnnotationFile()
- .annotateAlignmentView(viewport, file, protocol)
- : false;
+ .annotateAlignmentView(viewport, file, protocol) : false;
if (!isAnnotation)
{
}
});
- fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage(
+ "label.fetch_retrieve_from",
+ new Object[] { src.getDbName() })));
dfetch.add(fetchr);
comp++;
}
// fetch all entry
DbSourceProxy src = otherdb.get(0);
fetchr = new JMenuItem(MessageManager.formatMessage(
- "label.fetch_all_param", new Object[]
- { src.getDbSource() }));
+ "label.fetch_all_param",
+ new Object[] { src.getDbSource() }));
fetchr.addActionListener(new ActionListener()
{
@Override
}
});
- fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
+ fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage(
+ "label.fetch_retrieve_from_all_sources",
+ new Object[] {
+ Integer.valueOf(otherdb.size())
+ .toString(), src.getDbSource(),
+ src.getDbName() })));
dfetch.add(fetchr);
comp++;
// and then build the rest of the individual menus
- ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
+ ifetch = new JMenu(MessageManager.formatMessage(
+ "label.source_from_db_source",
+ new Object[] { src.getDbSource() }));
icomp = 0;
String imname = null;
int i = 0;
0, 10) + "..." : dbname;
if (imname == null)
{
- imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
+ imname = MessageManager.formatMessage(
+ "label.from_msname", new Object[] { sname });
}
fetchr = new JMenuItem(msname);
- final DbSourceProxy[] dassrc =
- { sproxy };
+ final DbSourceProxy[] dassrc = { sproxy };
fetchr.addActionListener(new ActionListener()
{
});
fetchr.setToolTipText("<html>"
- + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
+ + MessageManager.formatMessage(
+ "label.fetch_retrieve_from", new Object[]
+ { dbname }));
ifetch.add(fetchr);
++i;
if (++icomp >= mcomp || i == (otherdb.size()))
alignPanel.paintAlignment(true);
}
}
+
public void clearAlignmentSeqRep()
{
// TODO refactor alignmentseqrep to controller
- if (viewport.getAlignment().hasSeqrep()) {
+ if (viewport.getAlignment().hasSeqrep())
+ {
viewport.getAlignment().setSeqrep(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
if (!viewport.getSequenceSetId().equals(
alignmentPanel.av.getSequenceSetId()))
{
- throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_show_view_alignment_frame"));
}
if (tabbedPane != null
&& tabbedPane.getTabCount() > 0
aa.visible = visible;
}
}
- alignPanel.validateAnnotationDimensions(false);
+ alignPanel.validateAnnotationDimensions(true);
alignPanel.alignmentChanged();
}
*/
public List<? extends AlignmentViewPanel> getAlignPanels()
{
- return alignPanels == null ? Arrays.asList(alignPanel)
- : alignPanels;
+ return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
}
/**
return;
}
List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
- for (SequenceI aaSeq : alignment.getSequences()) {
- for (AlignedCodonFrame acf : mappings) {
+ for (SequenceI aaSeq : alignment.getSequences())
+ {
+ for (AlignedCodonFrame acf : mappings)
+ {
SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
if (dnaSeq != null)
{
String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
+ this.title;
Desktop.addInternalFrame(alignFrame, newtitle,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
/**
protected void showComplement_actionPerformed(boolean show)
{
SplitContainerI sf = getSplitViewContainer();
- if (sf != null) {
- sf.setComplementVisible(this, show);
- }
- }
-
- public class ExportData
- {
- private AlignmentI alignment;
-
- private String[] omitHidden;
-
- public ExportData(AlignmentI align, String[] ommit)
- {
- this.alignment = align;
- this.omitHidden = ommit;
- System.out.println();
- }
-
- public AlignmentI getAlignment()
- {
- return alignment;
- }
-
- public void setAlignment(AlignmentI alignment)
- {
- this.alignment = alignment;
- }
-
- public String[] getOmitHidden()
- {
- return omitHidden;
- }
-
- public void setOmitHidden(String[] omitHidden)
+ if (sf != null)
{
- this.omitHidden = omitHidden;
- }
- }
-
- @Override
- public void hideColumns(List<int[]> colsToHide)
- {
- for (int[] colRange : colsToHide)
- {
- viewport.hideColumns(colRange[0], colRange[1]);
+ sf.setComplementVisible(this, show);
}
-
- }
-
- @Override
- public void syncHiddenSequences()
- {
- AlignmentI al = viewport.getAlignment();
- HiddenSequences hiddenSeqs = al.getHiddenSequences();
- for (SequenceI seq : al.getSequencesArray())
- {
- if (seq.isHidden())
- {
- hiddenSeqs.hideSequence(seq);
- }
- }
}
}
git://source.jalview.org / jalview.git / blobdiff