/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
AlignViewport viewport;
Vector alignPanels = new Vector();
-
+
/**
* Last format used to load or save alignments in this window
*/
/**
* Creates a new AlignFrame object with specific width and height.
- *
+ *
* @param al
* @param width
* @param height
/**
* Creates a new AlignFrame object with specific width, height and
* sequenceSetId
- *
+ *
* @param al
* @param width
* @param height
/**
* Creates a new AlignFrame object with specific width, height and
* sequenceSetId
- *
+ *
* @param al
* @param width
* @param height
/**
* new alignment window with hidden columns
- *
+ *
* @param al
* AlignmentI
* @param hiddenColumns
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
- *
+ *
* @param al
* @param hiddenColumns
* @param width
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
- *
+ *
* @param al
* @param hiddenColumns
* @param width
/**
* Make a new AlignFrame from exisiting alignmentPanels
- *
+ *
* @param ap
* AlignmentPanel
* @param av
/**
* Change the filename and format for the alignment, and enable the 'reload'
* button functionality.
- *
+ *
* @param file
* valid filename
* @param format
{
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
}
}
+ @Override
public void keyReleased(KeyEvent evt)
{
switch (evt.getKeyCode())
Desktop.instance.addJalviewPropertyChangeListener("services",
thisListener = new java.beans.PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
// // System.out.println("Discoverer property change.");
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
System.err
});
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
// Finally, build the menu once to get current service state
new Thread(new Runnable()
{
+ @Override
public void run()
{
BuildWebServiceMenu();
/**
* Need to call this method when tabs are selected for multiple views, or when
* loading from Jalview2XML.java
- *
+ *
* @param av
* AlignViewport
*/
updateEditMenuBar();
}
-
+ // methods for implementing IProgressIndicator
+ // need to refactor to a reusable stub class
Hashtable progressBars, progressBarHandlers;
/*
* (non-Javadoc)
- *
+ *
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
+ @Override
public void setProgressBar(String message, long id)
{
if (progressBars == null)
validate();
}
+ @Override
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
{
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
}
/**
- *
+ *
* @return true if any progress bars are still active
*/
+ @Override
public boolean operationInProgress()
{
if (progressBars != null && progressBars.size() > 0)
return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
}
+ @Override
public void fetchSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
}
+ @Override
public void addFromFile_actionPerformed(ActionEvent e)
{
Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
}
+ @Override
public void reload_actionPerformed(ActionEvent e)
{
if (fileName != null)
for (int i = 0; i < frames.length; i++)
{
if (frames[i] instanceof AlignFrame && frames[i] != this
- && ((AlignFrame) frames[i]).fileName.equals(fileName))
+ && ((AlignFrame) frames[i]).fileName!=null && ((AlignFrame) frames[i]).fileName.equals(fileName))
{
try
{
final FeatureSettings nfs = newframe.featureSettings;
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
nfs.frame.setBounds(fspos);
}
}
+ @Override
public void addFromText_actionPerformed(ActionEvent e)
{
Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
}
+ @Override
public void addFromURL_actionPerformed(ActionEvent e)
{
Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
}
+ @Override
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void saveAs_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
FormatAdapter f = new FormatAdapter();
String output = f.formatSequences(
format,
- (Alignment) viewport.getAlignment(), // class cast exceptions will
+ viewport.getAlignment(), // class cast exceptions will
// occur in the distant future
omitHidden, f.getCacheSuffixDefault(format),
viewport.getColumnSelection());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void outputText_actionPerformed(ActionEvent e)
{
String[] omitHidden = null;
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
new HTMLOutput(alignPanel,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createPNG(File f)
{
alignPanel.makePNG(f);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createEPS(File f)
{
alignPanel.makeEPS(f);
}
+ @Override
public void pageSetup_actionPerformed(ActionEvent e)
{
PrinterJob printJob = PrinterJob.getPrinterJob();
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void printMenuItem_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
thread.start();
}
+ @Override
public void exportFeatures_actionPerformed(ActionEvent e)
{
new AnnotationExporter().exportFeatures(alignPanel);
}
+ @Override
public void exportAnnotations_actionPerformed(ActionEvent e)
{
new AnnotationExporter().exportAnnotations(alignPanel,
.getAlignment()).alignmentProperties);
}
+ @Override
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
/**
* 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
*/
+ @Override
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
if (alignPanels != null && alignPanels.size() < 2)
/**
* close alignPanel2 and shuffle tabs appropriately.
- *
+ *
* @param alignPanel2
*/
public void closeView(AlignmentPanel alignPanel2)
}
/**
- *
+ *
* @return alignment objects for all views
*/
AlignmentI[] getViewAlignments()
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.historyList.empty())
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.redoList.size() < 1)
/**
* DOCUMENT ME!
- *
+ *
* @param up
* DOCUMENT ME!
*/
}
SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
-
+
SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
for (int i = 0; i < invertGroup.size(); i++)
seqs2[i] = (SequenceI) invertGroup.elementAt(i);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void copy_actionPerformed(ActionEvent e)
{
System.gc();
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteNew_actionPerformed(ActionEvent e)
{
paste(true);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteThis_actionPerformed(ActionEvent e)
{
paste(false);
/**
* Paste contents of Jalview clipboard
- *
+ *
* @param newAlignment
* true to paste to a new alignment, otherwise add to this.
*/
}
int alwidth = 0;
+ ArrayList<Integer> newGraphGroups=new ArrayList<Integer>();
+ int fgroup=-1;
if (newAlignment)
{
{
newDs.clear(); // tidy up
}
+ if (alignment.getAlignmentAnnotation()!=null)
+ {
+ for (AlignmentAnnotation alan:alignment.getAlignmentAnnotation())
+ {
+ if (alan.graphGroup>fgroup)
+ {
+ fgroup=alan.graphGroup;
+ }
+ }
+ }
if (pastedal.getAlignmentAnnotation() != null)
{
// Add any annotation attached to alignment.
if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
{
AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+ if (newann.graphGroup>-1)
+ {
+ if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+ {
+ for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+ }
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+ }
+
newann.padAnnotation(alwidth);
alignment.addAnnotation(newann);
}
{
if (sequences[i].getAnnotation() != null)
{
+ AlignmentAnnotation newann;
for (int a = 0; a < sequences[i].getAnnotation().length; a++)
{
annotationAdded = true;
- sequences[i].getAnnotation()[a].adjustForAlignment();
- sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+ newann=sequences[i].getAnnotation()[a];
+ newann.adjustForAlignment();
+ newann.padAnnotation(alwidth);
+ if (newann.graphGroup>-1)
+ {
+ if (newann.graphGroup>-1)
+ {
+ if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+ {
+ for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+ }
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+ }
+ }
alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
// was
// duplicated
newann.padAnnotation(avwidth);
alview[avnum].addAnnotation(newann); // annotation was
// duplicated earlier
+ // TODO JAL-1145 graphGroups are not updated for sequence annotation added to several views. This may cause strangeness
alview[avnum].setAnnotationIndex(newann, a);
}
}
}
viewport.firePropertyChange("alignment", null,
alignment.getSequences());
+ if (alignPanels!=null ) {for (AlignmentPanel ap:((Vector<AlignmentPanel>)alignPanels))
+ {
+ ap.validateAnnotationDimensions(false);
+ }} else { alignPanel.validateAnnotationDimensions(false);}
}
else
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void cut_actionPerformed(ActionEvent e)
{
copy_actionPerformed(null);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void delete_actionPerformed(ActionEvent evt)
{
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
viewport.getAlignment().deleteAllGroups();
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = new SequenceGroup();
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.cursorMode)
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
viewport.sendSelection();
}
+ @Override
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(true);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(false);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
int start = 0, end = viewport.getAlignment().getWidth() - 1;
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
int start = 0, end = viewport.getAlignment().getWidth() - 1;
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.setPadGaps(padGapsMenuitem.isSelected());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
new Finder();
}
+ @Override
public void newView_actionPerformed(ActionEvent e)
{
newView(true);
}
/**
- *
+ *
* @param copyAnnotation
* if true then duplicate all annnotation, groups and settings
* @return new alignment panel, already displayed.
}
/**
- *
+ *
* @param viewTitle
* title of newly created view
* @return new alignment panel, already displayed.
}
/**
- *
+ *
* @param viewTitle
* title of newly created view
* @param copyAnnotation
return newap;
}
+ @Override
public void expandViews_actionPerformed(ActionEvent e)
{
Desktop.instance.explodeViews(this);
}
+ @Override
public void gatherViews_actionPerformed(ActionEvent e)
{
Desktop.instance.gatherViews(this);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
new FontChooser(alignPanel);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void seqLimit_actionPerformed(ActionEvent e)
{
viewport.setShowJVSuffix(seqLimits.isSelected());
alignPanel.paintAlignment(true);
}
+ @Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
viewport.rightAlignIds = idRightAlign.isSelected();
alignPanel.paintAlignment(true);
}
+ @Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
/*
* (non-Javadoc)
- *
+ *
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
+ @Override
protected void followHighlight_actionPerformed()
{
if (viewport.followHighlight = this.followHighlightMenuItem.getState())
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
scaleAbove.setVisible(wrapMenuItem.isSelected());
alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
}
+ @Override
public void showAllSeqs_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenSeqs();
}
+ @Override
public void showAllColumns_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
repaint();
}
+ @Override
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
/**
* called by key handler and the hide all/show all menu items
- *
+ *
* @param toggleSeqs
* @param toggleCols
*/
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
* event.ActionEvent)
*/
+ @Override
public void hideAllButSelection_actionPerformed(ActionEvent e)
{
toggleHiddenRegions(false, false);
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
* .ActionEvent)
*/
+ @Override
public void hideAllSelection_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
* ActionEvent)
*/
+ @Override
public void showAllhidden_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
alignPanel.paintAlignment(true);
}
+ @Override
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
}
+ @Override
public void hiddenMarkers_actionPerformed(ActionEvent e)
{
viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
public FeatureSettings featureSettings;
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
/**
* Set or clear 'Show Sequence Features'
- *
+ *
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
/**
* Set or clear 'Show Sequence Features'
- *
+ *
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
}
+ @Override
public void alignmentProperties()
{
JEditorPane editPane = new JEditorPane("text/html", "");
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
if (alignPanel.overviewPanel != null)
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
alignPanel.setOverviewPanel(overview);
}
+ @Override
public void textColour_actionPerformed(ActionEvent e)
{
new TextColourChooser().chooseColour(alignPanel, null);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
changeColour(null);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void clustalColour_actionPerformed(ActionEvent e)
{
changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void zappoColour_actionPerformed(ActionEvent e)
{
changeColour(new ZappoColourScheme());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void taylorColour_actionPerformed(ActionEvent e)
{
changeColour(new TaylorColourScheme());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void hydrophobicityColour_actionPerformed(ActionEvent e)
{
changeColour(new HydrophobicColourScheme());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void helixColour_actionPerformed(ActionEvent e)
{
changeColour(new HelixColourScheme());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void strandColour_actionPerformed(ActionEvent e)
{
changeColour(new StrandColourScheme());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void turnColour_actionPerformed(ActionEvent e)
{
changeColour(new TurnColourScheme());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void buriedColour_actionPerformed(ActionEvent e)
{
changeColour(new BuriedColourScheme());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void nucleotideColour_actionPerformed(ActionEvent e)
{
changeColour(new NucleotideColourScheme());
}
+ @Override
public void purinePyrimidineColour_actionPerformed(ActionEvent e)
{
changeColour(new PurinePyrimidineColourScheme());
* CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
* ()[0])); }
*/
+ @Override
public void annotationColour_actionPerformed(ActionEvent e)
{
new AnnotationColourChooser(viewport, alignPanel);
}
+ @Override
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
new RNAHelicesColourChooser(viewport, alignPanel);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
/**
* DOCUMENT ME!
- *
+ *
* @param cs
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void modifyPID_actionPerformed(ActionEvent e)
{
if (viewport.getAbovePIDThreshold()
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void modifyConservation_actionPerformed(ActionEvent e)
{
if (viewport.getConservationSelected()
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
viewport.setConservationSelected(conservationMenuItem.isSelected());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void abovePIDThreshold_actionPerformed(ActionEvent e)
{
viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void userDefinedColour_actionPerformed(ActionEvent e)
{
if (e.getActionCommand().equals("User Defined..."))
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
if (evt.isControlDown()
{
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
});
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PIDColour_actionPerformed(ActionEvent e)
{
changeColour(new PIDColourScheme());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
changeColour(new Blosum62ColourScheme());
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
new RedundancyPanel(alignPanel, this);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
if ((viewport.getSelectionGroup() == null)
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
if (((viewport.getSelectionGroup() != null)
new PCAPanel(alignPanel);
}
+ @Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
}
}
+ @Override
public void sortByTreeOption_actionPerformed(ActionEvent e)
{
viewport.sortByTree = sortByTree.isSelected();
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("AV", "PID", "Average distance tree using PID");
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
/**
* DOCUMENT ME!
- *
+ *
* @param type
* DOCUMENT ME!
* @param pwType
/**
* DOCUMENT ME!
- *
+ *
* @param title
* DOCUMENT ME!
* @param order
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
/**
* Add a new sort by annotation score menu item
- *
+ *
* @param sort
* the menu to add the option to
* @param scoreLabel
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
* search the alignment and rebuild the sort by annotation score submenu the
* last alignment annotation vector hash is stored to minimize cost of
* rebuilding in subsequence calls.
- *
+ *
*/
+ @Override
public void buildSortByAnnotationScoresMenu()
{
if (viewport.getAlignment().getAlignmentAnnotation() == null)
* call. Listeners are added to remove the menu item when the treePanel is
* closed, and adjust the tree leaf to sequence mapping when the alignment is
* modified.
- *
+ *
* @param treePanel
* Displayed tree window.
* @param title
* SortBy menu item title.
*/
+ @Override
public void buildTreeMenu()
{
sortByTreeMenu.removeAll();
final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
tp.sortByTree_actionPerformed(null);
/**
* Work out whether the whole set of sequences or just the selected set will
* be submitted for multiple alignment.
- *
+ *
*/
public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
{
/*
* SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
* SequenceI[sz = seqs.getSize(false)];
- *
+ *
* for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
* seqs.getSequenceAt(i); }
*/
{
/*
* Vector seqs = viewport.getAlignment().getSequences();
- *
+ *
* if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
- *
+ *
* for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
* seqs.elementAt(i); } }
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
/**
* Add a treeviewer for the tree extracted from a newick file object to the
* current alignment view
- *
+ *
* @param nf
* the tree
* @param title
/**
* Generates menu items and listener event actions for web service clients
- *
+ *
*/
public void BuildWebServiceMenu()
{
buildingMenu = true;
new Thread(new Runnable()
{
+ @Override
public void run()
{
try
"Secondary Structure Prediction");
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
- final JMenu dismenu = new JMenu("Disorder");
+ final JMenu dismenu = new JMenu("Protein Disorder");
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
try
{
for (int i = 0, j = wsmenu.size(); i < j; i++)
{
- webService.add((JMenu) wsmenu.get(i));
+ webService.add(wsmenu.get(i));
}
}
else
}
} catch (Exception e)
{
+ Cache.log.debug("Exception during web service menu building process.",e);
}
;
}
/**
* construct any groupURL type service menu entries.
- *
+ *
* @param webService
*/
private void build_urlServiceMenu(JMenu webService)
/*
* JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
* AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
- *
+ *
* @Override public void actionPerformed(ActionEvent e) {
* jalview.datamodel.AlignmentView
* .testSelectionViews(af.viewport.getAlignment(),
* af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
- *
+ *
* }); webService.add(testAlView);
*/
// TODO: refactor to RestClient discoverer and merge menu entries for
* public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
* chooser = new JalviewFileChooser(jalview.bin.Cache.
* getProperty("LAST_DIRECTORY"));
- *
+ *
* chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
* to Vamsas file"); chooser.setToolTipText("Export");
- *
+ *
* int value = chooser.showSaveDialog(this);
- *
+ *
* if (value == JalviewFileChooser.APPROVE_OPTION) {
* jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
* //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
*/
/**
* prototype of an automatically enabled/disabled analysis function
- *
+ *
*/
protected void setShowProductsEnabled()
{
/**
* search selection for sequence xRef products and build the show products
* menu.
- *
+ *
* @param selection
* @param dataset
* @return true if showProducts menu should be enabled.
xtype.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: new thread for this call with vis-delay
Runnable foo = new Runnable()
{
+ @Override
public void run()
{
final long sttime = System.currentTimeMillis();
}
}
+ @Override
public void showProducts_actionPerformed(ActionEvent e)
{
// /////////////////////////////
}
}
+ @Override
public void showTranslation_actionPerformed(ActionEvent e)
{
// /////////////////////////////
/**
* Try to load a features file onto the alignment.
- *
+ *
* @param file
* contents or path to retrieve file
* @param type
return featuresFile;
}
+ @Override
public void dragEnter(DropTargetDragEvent evt)
{
}
+ @Override
public void dragExit(DropTargetEvent evt)
{
}
+ @Override
public void dragOver(DropTargetDragEvent evt)
{
}
+ @Override
public void dropActionChanged(DropTargetDragEvent evt)
{
}
+ @Override
public void drop(DropTargetDropEvent evt)
{
Transferable t = evt.getTransferable();
* 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.
*/
{
/*
* if (format.equalsIgnoreCase("PDB")) {
- *
+ *
* String pdbfn = ""; // try to match up filename with sequence id
* try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
* new File(file); pdbfn = fl.getName(); } else if (protocol ==
{
ex.printStackTrace();
}
+ catch (OutOfMemoryError oom)
+ {
+ try {
+ System.gc();
+ } catch (Exception x){};
+ new OOMWarning("loading data "+(protocol!=null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." : "using "+protocol+" from "+file) : ".")+(format!=null ? "(parsing as '"+format+"' file)" :""), oom, Desktop.desktop);
+ }
}
+ @Override
public void tabSelectionChanged(int index)
{
if (index > -1)
}
}
+ @Override
public void tabbedPane_mousePressed(MouseEvent e)
{
if (SwingUtilities.isRightMouseButton(e))
/**
* Open the dialog for regex description parsing.
*/
+ @Override
protected void extractScores_actionPerformed(ActionEvent e)
{
ParseProperties pp = new jalview.analysis.ParseProperties(
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
* )
*/
+ @Override
protected void showDbRefs_actionPerformed(ActionEvent e)
{
viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
/*
* (non-Javadoc)
- *
+ *
* @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
* ActionEvent)
*/
+ @Override
protected void showNpFeats_actionPerformed(ActionEvent e)
{
viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
/**
* find the viewport amongst the tabs in this alignment frame and close that
* tab
- *
+ *
* @param av
*/
public boolean closeView(AlignViewport av)
fetchr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
final AlignFrame me = this;
new Thread(new Runnable()
{
+ @Override
public void run()
{
final jalview.ws.SequenceFetcher sf = SequenceFetcher
.getSequenceFetcherSingleton(me);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
String[] dbclasses = sf.getOrderedSupportedSources();
fetchr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
+ "'");
fetchr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
fetchr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
/**
* Left justify the whole alignment.
*/
+ @Override
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
/**
* Right justify the whole alignment.
*/
+ @Override
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
* awt.event.ActionEvent)
*/
+ @Override
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowUnconserved(showNonconservedMenuItem.getState());
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
* .ActionEvent)
*/
+ @Override
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConsensus(showGroupConsensus.getState());
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConservation(showGroupConservation.getState());
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
viewport.setShowSequenceLogo(showSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+ @Override
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
+ showSequenceLogo.setState(true);
+ viewport.setShowSequenceLogo(true);
viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+ @Override
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
if (viewport.getSelectionGroup() != null)
/**
* make the given alignmentPanel the currently selected tab
- *
+ *
* @param alignmentPanel
*/
public void setDisplayedView(AlignmentPanel alignmentPanel)
static PageFormat pf;
+ @Override
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();
git://source.jalview.org / jalview.git / blobdiff