/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
{
this(al, null, width, height);
}
+
/**
- * Creates a new AlignFrame object with specific width, height and sequenceSetId
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
* @param al
* @param width
* @param height
* @param sequenceSetId
*/
- public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId)
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId)
{
this(al, null, width, height, sequenceSetId);
}
+
/**
- * Creates a new AlignFrame object with specific width, height and sequenceSetId
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
* @param al
* @param width
* @param height
* @param sequenceSetId
* @param viewId
*/
- public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId, String viewId)
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId, String viewId)
{
this(al, null, width, height, sequenceSetId, viewId);
}
+
/**
* new alignment window with hidden columns
*
* @param al
- * AlignmentI
+ * AlignmentI
* @param hiddenColumns
- * ColumnSelection or null
- * @param width Width of alignment frame
- * @param height height of frame.
+ * ColumnSelection or null
+ * @param width
+ * Width of alignment frame
+ * @param height
+ * height of frame.
*/
public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
int width, int height)
{
this(al, hiddenColumns, width, height, null);
}
+
/**
- * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
* @param al
* @param hiddenColumns
* @param width
* @param height
- * @param sequenceSetId (may be null)
+ * @param sequenceSetId
+ * (may be null)
*/
public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
int width, int height, String sequenceSetId)
}
/**
- * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
* @param al
* @param hiddenColumns
* @param width
* @param height
- * @param sequenceSetId (may be null)
- * @param viewId (may be null)
+ * @param sequenceSetId
+ * (may be null)
+ * @param viewId
+ * (may be null)
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height,
- String sequenceSetId, String viewId)
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height, String sequenceSetId, String viewId)
{
setSize(width, height);
viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
* Make a new AlignFrame from exisiting alignmentPanels
*
* @param ap
- * AlignmentPanel
+ * AlignmentPanel
* @param av
- * AlignViewport
+ * AlignViewport
*/
public AlignFrame(AlignmentPanel ap)
{
addAlignmentPanel(ap, false);
init();
}
+
/**
- * initalise the alignframe from the underlying viewport data and the configurations
+ * initalise the alignframe from the underlying viewport data and the
+ * configurations
*/
void init()
{
* button functionality.
*
* @param file
- * valid filename
+ * valid filename
* @param format
- * format of file
+ * format of file
*/
public void setFileName(String file, String format)
{
{
boolean toggleSeqs = !evt.isControlDown();
boolean toggleCols = !evt.isShiftDown();
-
- boolean hide = false;
-
- SequenceGroup sg = viewport.getSelectionGroup();
- if (toggleSeqs)
- {
- if (sg != null
- && sg.getSize() != viewport.alignment.getHeight())
- {
- hideSelSequences_actionPerformed(null);
- hide = true;
- }
- else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
- {
- showAllSeqs_actionPerformed(null);
- }
- }
-
- if (toggleCols)
- {
- if (viewport.colSel.getSelected().size() > 0)
- {
- hideSelColumns_actionPerformed(null);
- if (!toggleSeqs)
- {
- viewport.selectionGroup = sg;
- }
- }
- else if (!hide)
- {
- showAllColumns_actionPerformed(null);
- }
- }
- break;
+ toggleHiddenRegions(toggleSeqs,toggleCols);
+ break;
}
case KeyEvent.VK_PAGE_UP:
if (viewport.wrapAlignment)
showTranslation.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
-
+ showGroupConservation.setEnabled(!nucleotide);
// Remember AlignFrame always starts as protein
if (!nucleotide)
{
* loading from Jalview2XML.java
*
* @param av
- * AlignViewport
+ * AlignViewport
*/
void setMenusFromViewport(AlignViewport av)
{
annotationPanelMenuItem.setState(av.showAnnotation);
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
-
+ showUnconservedMenuItem.setSelected(av.showUnconserved);
+ showGroupConsensus.setSelected(av.showGroupConsensus);
+ showGroupConservation.setSelected(av.showGroupConservation);
+ showConsensusHistogram.setSelected(av.showConsensusHistogram);
+ showSequenceLogo.setSelected(av.showSequenceLogo);
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
updateEditMenuBar();
}
- Hashtable progressBars;
+ Hashtable progressBars, progressBarHandlers;
/*
* (non-Javadoc)
if (progressBars == null)
{
progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
}
JPanel progressPanel;
+ Long lId=new Long(id);
GridLayout layout = (GridLayout) statusPanel.getLayout();
- if (progressBars.get(new Long(id)) != null)
+ if (progressBars.get(lId) != null)
{
progressPanel = (JPanel) progressBars.get(new Long(id));
statusPanel.remove(progressPanel);
- progressBars.remove(progressPanel);
+ progressBars.remove(lId);
progressPanel = null;
if (message != null)
{
statusBar.setText(message);
}
-
+ if (progressBarHandlers.contains(lId))
+ {
+ progressBarHandlers.remove(lId);
+ }
layout.setRows(layout.getRows() - 1);
}
else
layout.setRows(layout.getRows() + 1);
statusPanel.add(progressPanel);
- progressBars.put(new Long(id), progressPanel);
+ progressBars.put(lId, progressPanel);
}
// update GUI
setMenusForViewport();
validate();
}
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ {
+ throw new Error(
+ "call setProgressBar before registering the progress bar's handler.");
+ }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton("Cancel");
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar("Cancelled "
+ + ((JLabel) progressPanel.getComponent(0)).getText(), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
+
/**
*
* @return true if any progress bars are still active
{
if (fileName != null)
{
+ // TODO: work out how to recover feature settings for correct view(s) when file is reloaded.
if (currentFileFormat.equals("Jalview"))
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
protocol, currentFileFormat);
newframe.setBounds(bounds);
-
+ if (featureSettings!=null && featureSettings.isShowing()) {
+ final Rectangle fspos = featureSettings.frame.getBounds();
+ // TODO: need a 'show feature settings' function that takes bounds - need to refactor Desktop.addFrame
+ newframe.featureSettings_actionPerformed(null);
+ final FeatureSettings nfs = newframe.featureSettings;
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run()
+ {
+ nfs.frame.setBounds(fspos);
+ }
+ });
+ this.featureSettings.close();
+ this.featureSettings=null;
+ }
this.closeMenuItem_actionPerformed(true);
}
}
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null
- || (currentFileFormat == null
- || !jalview.io.FormatAdapter.isValidIOFormat(currentFileFormat, true))
+ || (currentFileFormat == null || !jalview.io.FormatAdapter
+ .isValidIOFormat(currentFileFormat, true))
|| fileName.startsWith("http"))
{
saveAs_actionPerformed(null);
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void saveAs_actionPerformed(ActionEvent e)
{
{
if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
{
- // JBPNote need to have a raise_gui flag here
- JOptionPane.showInternalMessageDialog(this, "Cannot save file "
- + fileName + " using format " + format,
- "Alignment output format not supported",
- JOptionPane.WARNING_MESSAGE);
+ 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
return false;
}
return success;
}
+ private void warningMessage(String warning, String title)
+ {
+ if (new jalview.util.Platform().isHeadless())
+ {
+ System.err.println("Warning: " + title + "\nWarning: " + warning);
+
+ }
+ else
+ {
+ JOptionPane.showInternalMessageDialog(this, warning, title,
+ JOptionPane.WARNING_MESSAGE);
+ }
+ return;
+ }
+
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void outputText_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void createPNG(File f)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void createEPS(File f)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void printMenuItem_actionPerformed(ActionEvent e)
{
}
/**
- * Close the current view or all views in the alignment frame.
- * If the frame only contains one view then the alignment will be removed from memory.
+ * Close the current view or all views in the alignment frame. If the frame
+ * only contains one view then the alignment will be removed from memory.
*
- * @param closeAllTabs
+ * @param closeAllTabs
*/
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
{
if (closeAllTabs)
{
- for (int i = 0; i < alignPanels.size(); i++)
+ if (this.isClosed())
{
- AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
- jalview.structure.StructureSelectionManager ssm =
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager();
- ssm.removeStructureViewerListener(ap.seqPanel, null);
- ssm.removeSelectionListener(ap.seqPanel);
- PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(ap);
- ap.av.alignment = null;
+ // really close all the windows - otherwise wait till
+ // setClosed(true) is called
+ for (int i = 0; i < alignPanels.size(); i++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ ap.closePanel();
+ }
}
}
else
{
closeView(alignPanel);
- viewport = null;
}
}
}
}
+ /**
+ * close alignPanel2 and shuffle tabs appropriately.
+ *
+ * @param alignPanel2
+ */
public void closeView(AlignmentPanel alignPanel2)
{
int index = tabbedPane.getSelectedIndex();
int closedindex = tabbedPane.indexOfComponent(alignPanel2);
alignPanels.removeElement(alignPanel2);
- PaintRefresher.RemoveComponent(alignPanel2.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(alignPanel2.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(alignPanel2);
- alignPanel2.av.alignment = null;
-
- if (viewport == alignPanel2.av)
- {
- viewport = null;
- }
+ // Unnecessary
+ // if (viewport == alignPanel2.av)
+ // {
+ // viewport = null;
+ // }
+ alignPanel2.closePanel();
alignPanel2 = null;
-
+
tabbedPane.removeTabAt(closedindex);
tabbedPane.validate();
index--;
}
- this.tabSelectionChanged(index);
+ this.tabSelectionChanged(index);
}
/**
viewport.historyList.push(command);
viewport.redoList.clear();
updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ viewport.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
}
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
if (originalSource != null)
{
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
originalSource.firePropertyChange("alignment", null,
originalSource.alignment.getSequences());
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
if (originalSource != null)
{
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
originalSource.firePropertyChange("alignment", null,
originalSource.alignment.getSequences());
}
* DOCUMENT ME!
*
* @param up
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void moveSelectedSequences(boolean up)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void copy_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void pasteNew_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void pasteThis_actionPerformed(ActionEvent e)
{
* Paste contents of Jalview clipboard
*
* @param newAlignment
- * true to paste to a new alignment, otherwise add to this.
+ * true to paste to a new alignment, otherwise add to this.
*/
void paste(boolean newAlignment)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void cut_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void delete_actionPerformed(ActionEvent evt)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void deleteGroups_actionPerformed(ActionEvent e)
{
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.padGaps = padGapsMenuitem.isSelected();
-
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
}
+ // else
+ {
+ // if (justifySeqs>0)
+ {
+ // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
+ }
+ }
+
+ // }
+
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void findMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void font_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void seqLimit_actionPerformed(ActionEvent e)
{
viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
alignPanel.paintAlignment(true);
}
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
protected void followHighlight_actionPerformed()
{
if (viewport.followHighlight = this.followHighlightMenuItem.getState())
{
- alignPanel.scrollToPosition(alignPanel.seqPanel.seqCanvas.searchResults, false);
+ alignPanel.scrollToPosition(
+ alignPanel.seqPanel.seqCanvas.searchResults, false);
}
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
alignPanel.paintAlignment(true);
}
+ /**
+ * called by key handler and the hide all/show all menu items
+ * @param toggleSeqs
+ * @param toggleCols
+ */
+ private void toggleHiddenRegions(boolean toggleSeqs,
+ boolean toggleCols)
+ {
+
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (!toggleSeqs && !toggleCols)
+ {
+ // 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.colSel!=null && viewport.colSel.getSelected()!=null && viewport.colSel.getSelected().size()>0) || (sg!=null && sg.getSize()>0 && sg.getStartRes()<=sg.getEndRes()))
+ {
+ // now invert the sequence set, if required - empty selection implies that no hiding is required.
+ if (sg!=null) {
+ invertSequenceMenuItem_actionPerformed(null);
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
+
+ }
+ viewport.expandColSelection(sg,true);
+ // finally invert the column selection and get the new sequence selection.
+ invertColSel_actionPerformed(null);
+ toggleCols = true;
+ }
+ }
+
+ if (toggleSeqs)
+ {
+ if (sg != null
+ && sg.getSize() != viewport.alignment.getHeight())
+ {
+ hideSelSequences_actionPerformed(null);
+ hide = true;
+ }
+ else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ {
+ showAllSeqs_actionPerformed(null);
+ }
+ }
+
+ if (toggleCols)
+ {
+ if (viewport.colSel.getSelected().size() > 0)
+ {
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
+ {
+ viewport.selectionGroup = sg;
+ }
+ }
+ else if (!hide)
+ {
+ showAllColumns_actionPerformed(null);
+ }
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void hideAllButSelection_actionPerformed(ActionEvent e)
+ {
+ toggleHiddenRegions(false, false);
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void hideAllSelection_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ viewport.expandColSelection(sg,false);
+ viewport.hideAllSelectedSeqs();
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.ActionEvent)
+ */
+ public void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenColumns();
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ }
public void hideSelColumns_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void scaleAbove_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void scaleLeft_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void scaleRight_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
featureSettings.close();
featureSettings = null;
}
+ if (!showSeqFeatures.isSelected())
+ {
+ // make sure features are actually displayed
+ showSeqFeatures.setSelected(true);
+ showSeqFeatures_actionPerformed(null);
+ }
featureSettings = new FeatureSettings(this);
}
/**
- * DOCUMENT ME!
+ * Set or clear 'Show Sequence Features'
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
}
/**
+ * Set or clear 'Show Sequence Features'
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
+ {
+ viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
+ .isSelected());
+ if (viewport.getShowSequenceFeaturesHeight())
+ {
+ // ensure we're actually displaying features
+ viewport.setShowSequenceFeatures(true);
+ showSeqFeatures.setSelected(true);
+ }
+ alignPanel.paintAlignment(true);
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+ }
+
+ /**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void clustalColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void zappoColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void taylorColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void hydrophobicityColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void helixColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void strandColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void turnColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void buriedColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void nucleotideColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param cs
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void changeColour(ColourSchemeI cs)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void modifyPID_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void modifyConservation_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void abovePIDThreshold_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void userDefinedColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void PIDColour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
+ */
+ public void sortLengthMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pwType
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param title
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void NewTreePanel(String type, String pwType, String title)
{
}
else
{
- // are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ // are the visible sequences aligned?
+ if (!viewport.alignment.isAligned(false))
{
JOptionPane
.showMessageDialog(
* DOCUMENT ME!
*
* @param title
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param order
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
* Add a new sort by annotation score menu item
*
* @param sort
- * the menu to add the option to
+ * the menu to add the option to
* @param scoreLabel
- * the label used to retrieve scores for each sequence on the
- * alignment
+ * the label used to retrieve scores for each sequence on the
+ * alignment
*/
public void addSortByAnnotScoreMenuItem(JMenu sort,
final String scoreLabel)
* modified.
*
* @param treePanel
- * Displayed tree window.
+ * Displayed tree window.
* @param title
- * SortBy menu item title.
+ * SortBy menu item title.
*/
public void buildTreeMenu()
{
// jobs
// TODO: viewport.alignment.isAligned is a global state - the local
// selection may well be aligned - we preserve 2.0.8 behaviour for moment.
- if (!viewport.alignment.isAligned())
+ if (!viewport.alignment.isAligned(false))
{
seqs.setSequences(new SeqCigar[]
{ seqs.getSequences()[0] });
+ // TODO: if seqs.getSequences().length>1 then should really have warned user!
+
}
return seqs;
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
* current alignment view
*
* @param nf
- * the tree
+ * the tree
* @param title
- * tree viewer title
+ * tree viewer title
* @param input
- * Associated alignment input data (or null)
+ * Associated alignment input data (or null)
* @param w
- * width
+ * width
* @param h
- * height
+ * height
* @param x
- * position
+ * position
* @param y
- * position
+ * position
* @return TreePanel handle
*/
public TreePanel ShowNewickTree(NewickFile nf, String title,
.getServiceClient(sh);
impl.attachWSMenuEntry(seqsrchmenu, this);
}
- // finally, add the whole shebang onto the webservices menu
wsmenu.add(seqsrchmenu);
}
+ // finally, add the whole shebang onto the webservices menu
resetWebServiceMenu();
for (int i = 0, j = wsmenu.size(); i < j; i++)
{
private void resetWebServiceMenu()
{
webService.removeAll();
- // Temporary hack - DBRef Fetcher always top level ws entry.
- JMenuItem rfetch = new JMenuItem("Fetch DB References");
- rfetch
- .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
- webService.add(rfetch);
- rfetch.addActionListener(new ActionListener()
- {
-
- public void actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
-
- public void run()
- {
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(), alignPanel.alignFrame)
- .fetchDBRefs(false);
- }
- }).start();
-
- }
+ build_fetchdbmenu(webService);
+ build_urlServiceMenu(webService);
+ }
- });
+ /**
+ * construct any groupURL type service menu entries.
+ * @param webService
+ */
+ private void build_urlServiceMenu(JMenu webService)
+ {
+ jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(webService, this);
}
/*
showProducts.removeAll();
final boolean dna = viewport.getAlignment().isNucleotide();
final Alignment ds = dataset;
- String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection,
- dataset);
+ String[] ptypes = (selection == null || selection.length == 0) ? null
+ : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
// Object[] prods =
// CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
// selection, dataset, true);
* Try to load a features file onto the alignment.
*
* @param file
- * contents or path to retrieve file
+ * contents or path to retrieve file
* @param type
- * access mode of file (see jalview.io.AlignFile)
+ * access mode of file (see jalview.io.AlignFile)
* @return true if features file was parsed corectly.
*/
public boolean parseFeaturesFile(String file, String type)
{
viewport.showSequenceFeatures = true;
showSeqFeatures.setSelected(true);
+ if (alignPanel.seqPanel.seqCanvas.fr != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+ }
+ if (featureSettings!=null)
+ {
+ featureSettings.setTableData();
+ }
alignPanel.paintAlignment(true);
}
}
java.net.URI uri = new java.net.URI(s);
- java.io.File file = new java.io.File(uri);
- files.add(file);
+ // check to see if we can handle this kind of URI
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ files.add(file.toString());
+ }
}
}
} catch (Exception e)
}
/**
- * Attempt to load a "dropped" file: First by testing whether it's and
- * 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
+ * Attempt to load a "dropped" file or URL string: First by testing whether
+ * it's and 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.
*
* @param file
- * either a filename or a URL string.
+ * either a filename or a URL string.
*/
public void loadJalviewDataFile(String file)
{
try
{
- String protocol = "File";
-
- if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+ String protocol = jalview.io.FormatAdapter.FILE;
+ String f = file.toLowerCase();
+ if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
+ || f.indexOf("file:") == 0)
{
- protocol = "URL";
+ protocol = jalview.io.FormatAdapter.URL;
}
boolean isAnnotation = new AnnotationFile().readAnnotationFile(
}
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
+ * )
*/
protected void showDbRefs_actionPerformed(ActionEvent e)
{
viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
+ * ActionEvent)
*/
protected void showNpFeats_actionPerformed(ActionEvent e)
{
}
/**
- * find the viewport amongst the tabs in this alignment frame and close that tab
+ * find the viewport amongst the tabs in this alignment frame and close that
+ * tab
+ *
* @param av
*/
public boolean closeView(AlignViewport av)
return true;
}
Component[] comp = tabbedPane.getComponents();
- for (int i=0;comp!=null && i<comp.length;i++)
+ for (int i = 0; comp != null && i < comp.length; i++)
{
if (comp[i] instanceof AlignmentPanel)
{
}
return false;
}
+
+ protected void build_fetchdbmenu(JMenu webService)
+ {
+ // Temporary hack - DBRef Fetcher always top level ws entry.
+ // TODO We probably want to store a sequence database checklist in
+ // preferences and have checkboxes.. rather than individual sources selected
+ // here
+ JMenu rfetch = new JMenu("Fetch DB References");
+ rfetch
+ .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+ webService.add(rfetch);
+
+ JMenuItem fetchr = new JMenuItem("Standard Databases");
+ fetchr
+ .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(), alignPanel.alignFrame)
+ .fetchDBRefs(false);
+ }
+ }).start();
+
+ }
+
+ });
+ rfetch.add(fetchr);
+ JMenu dfetch = new JMenu();
+ rfetch.add(dfetch);
+ jalview.ws.SequenceFetcher sf = SequenceFetcher
+ .getSequenceFetcherSingleton(this);
+ String[] otherdb = sf.getOrderedSupportedSources();
+ // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ // jalview.util.QuickSort.sort(otherdb, otherdb);
+ int comp = 0, mcomp = 15;
+ String mname = null;
+ if (otherdb != null && otherdb.length > 0)
+ {
+ for (int i = 0; i < otherdb.length; i++)
+ {
+ String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
+ if (mname == null)
+ {
+ mname = "from '" + dbname + "'";
+ }
+ fetchr = new JMenuItem(otherdb[i]);
+ final String[] dassource = new String[]
+ { otherdb[i] };
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(), alignPanel.alignFrame,
+ dassource).fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText("Retrieve from " + dbname);
+ dfetch.add(fetchr);
+ if (comp++ == mcomp || i == (otherdb.length - 1))
+ {
+ dfetch.setText(mname + " to '" + dbname + "'");
+ rfetch.add(dfetch);
+ dfetch = new JMenu();
+ mname = null;
+ comp = 0;
+ }
+ }
+ }
+ }
+
+ /**
+ * Left justify the whole alignment.
+ */
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(false);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+
+ /**
+ * Right justify the whole alignment.
+ */
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(true);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+
+ public void setShowSeqFeatures(boolean b)
+ {
+ showSeqFeatures.setSelected(true);
+ viewport.setShowSequenceFeatures(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
+ * awt.event.ActionEvent)
+ */
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowUnconserved(showUnconservedMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowGroupConservation(showGroupConservation.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt.event.ActionEvent)
+ */
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt.event.ActionEvent)
+ */
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+ {
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getSelectionGroup() != null)
+ {
+ SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(), viewport.getAlignmentView(
+ true).getSequenceStrings(viewport.getGapCharacter()),
+ viewport.alignment.getGroups());
+ viewport.alignment.deleteAllGroups();
+ viewport.sequenceColours = null;
+ viewport.setSelectionGroup(null);
+ // set view properties for each group
+ for (int g = 0; g < gps.length; g++)
+ {
+ gps[g].setShowunconserved(viewport.getShowUnconserved());
+ gps[g].setIncludeAllConsSymbols(viewport.isIncludeAllConsensusSymbols());
+ viewport.alignment.addGroup(gps[g]);
+ Color col = new Color((int) (Math.random() * 255), (int) (Math
+ .random() * 255), (int) (Math.random() * 255));
+ col = col.brighter();
+ for (Enumeration sq = gps[g].getSequences(null).elements(); sq
+ .hasMoreElements(); viewport.setSequenceColour(
+ (SequenceI) sq.nextElement(), col))
+ ;
+ }
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff