/*
* 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;
import jalview.io.JalviewFileView;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
+import jalview.io.TCoffeeScoreFile;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import jalview.ws.WSMenuEntryProviderI;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
import javax.swing.JButton;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
/**
* 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
*/
showSeqFeatures.setSelected(av.showSequenceFeatures);
hiddenMarkers.setState(av.showHiddenMarkers);
- applyToAllGroups.setState(av.colourAppliesToAllGroups);
+ applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
showDbRefsMenuitem.setSelected(av.isShowDbRefs());
autoCalculate.setSelected(av.autoCalculateConsensus);
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)
{
+ // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+ // originating file's format
// TODO: work out how to recover feature settings for correct view(s) when
// file is reloaded.
if (currentFileFormat.equals("Jalview"))
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!
*/
{
return;
}
-
- if (up)
- {
- for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
- {
- SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
-
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.getAlignment().getSequences().setElementAt(temp, i);
- viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
- }
- }
- else
- {
- for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
- {
- SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
-
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.getAlignment().getSequences().setElementAt(temp, i);
- viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
- }
- }
-
+ viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true);
}
synchronized void slideSequences(boolean right, int size)
{
- Vector sg = new Vector();
+ List<SequenceI> sg = new Vector();
if (viewport.cursorMode)
{
- sg.addElement(viewport.getAlignment().getSequenceAt(
+ sg.add(viewport.getAlignment().getSequenceAt(
alignPanel.seqPanel.seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
invertGroup.add(viewport.getAlignment().getSequenceAt(i));
}
- SequenceI[] seqs1 = new SequenceI[sg.size()];
- for (int i = 0; i < sg.size(); i++)
- seqs1[i] = (SequenceI) sg.elementAt(i);
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
for (int i = 0; i < invertGroup.size(); 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);
addHistoryItem(trimRegion);
- Vector groups = viewport.getAlignment().getGroups();
-
- for (int i = 0; i < groups.size(); i++)
+ for (SequenceGroup sg :viewport.getAlignment().getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.get(i);
-
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
/**
* 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()
- .getSequences(), viewport.getAlignment().getWidth()));
+ 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!
*/
public void changeColour(ColourSchemeI cs)
{
+ // TODO: compare with applet and pull up to model method
int threshold = 0;
if (cs != null)
if (viewport.getColourAppliesToAllGroups())
{
- Vector groups = viewport.getAlignment().getGroups();
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ for (SequenceGroup sg:viewport.getAlignment().getGroups())
+ {
if (cs == null)
{
sg.cs = null;
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(sg.getSequences(viewport
- .getHiddenRepSequences()), sg.getWidth());
+ sg.cs = new ClustalxColourScheme(sg, viewport
+ .getHiddenRepSequences());
}
else if (cs instanceof UserColourScheme)
{
{
try
{
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+ sg.cs = cs.getClass().newInstance();
} catch (Exception ex)
{
}
/**
* 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
return;
}
- int s = 0;
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- while (s < sg.getSize())
+ for (SequenceI _s:sg.getSequences())
{
- if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
+ if (_s.getLength() < sg
.getEndRes())
{
JOptionPane
/**
* 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)
// almost certainly a quicker way to do this - but we keep it simple
Hashtable scoreSorts = new Hashtable();
AlignmentAnnotation aann[];
- Enumeration sq = viewport.getAlignment().getSequences().elements();
- while (sq.hasMoreElements())
+ for (SequenceI sqa:viewport.getAlignment().getSequences())
{
- aann = ((SequenceI) sq.nextElement()).getAnnotation();
+ aann = sqa.getAnnotation();
for (int i = 0; aann != null && i < aann.length; i++)
{
if (aann[i].hasScore() && aann[i].sequenceRef != 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
}
}
+ @Override
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ }
+
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
return ShowNewickTree(nf, title, 600, 500, 4, 5);
/**
* 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)
wsmenu.add(secstrmenu);
wsmenu.add(dismenu);
wsmenu.add(analymenu);
-// final ArrayList<JMenu> submens=new ArrayList<JMenu>();
-// submens.add(msawsmenu);
- // submens.add(secstrmenu);
- // submens.add(dismenu);
- // submens.add(analymenu);
-
+ // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
+ // submens.add(msawsmenu);
+ // submens.add(secstrmenu);
+ // submens.add(dismenu);
+ // submens.add(analymenu);
+
// No search services yet
// wsmenu.add(seqsrchmenu);
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 (!isAnnotation)
{
- // try to see if its a JNet 'concise' style annotation file *before* we
- // try to parse it as a features file
- if (format == null)
+ // first see if its a T-COFFEE score file
+ TCoffeeScoreFile tcf = null;
+ try
{
- format = new IdentifyFile().Identify(file, protocol);
- }
- if (format.equalsIgnoreCase("JnetFile"))
+ tcf = new TCoffeeScoreFile(file, protocol);
+ if (tcf.isValid())
+ {
+ if (tcf.annotateAlignment(viewport.getAlignment(), true))
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
+ isAnnotation = true;
+ statusBar
+ .setText("Successfully pasted T-Coffee scores to alignment.");
+ }
+ else
+ {
+ // some problem - if no warning its probable that the ID matching process didn't work
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
+ "Problem reading T-COFFEE score file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ else
+ {
+ tcf = null;
+ }
+ } catch (Exception x)
{
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
- protocol);
- new JnetAnnotationMaker().add_annotation(predictions,
- viewport.getAlignment(), 0, false);
- isAnnotation = true;
+ Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
+ tcf = null;
}
- else
+ if (tcf == null)
{
- /*
- * 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 ==
- * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
- * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null)
- * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
- * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { //
- * attempt to find a match in the alignment SequenceI mtch =
- * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
- * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l)
- * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch =
- * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate
- * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
- * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) {
- * System.err.println("Associated file : " + file + " with " +
- * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
- * TODO: maybe need to load as normal otherwise return; } }
- */
+ // try to see if its a JNet 'concise' style annotation file *before*
+ // we
// try to parse it as a features file
- boolean isGroupsFile = parseFeaturesFile(file, protocol);
- // if it wasn't a features file then we just treat it as a general
- // alignment file to load into the current view.
- if (!isGroupsFile)
+ if (format == null)
+ {
+ format = new IdentifyFile().Identify(file, protocol);
+ }
+ if (format.equalsIgnoreCase("JnetFile"))
{
- new FileLoader().LoadFile(viewport, file, protocol, format);
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ file, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ viewport.getAlignment(), 0, false);
+ isAnnotation = true;
}
else
{
- alignPanel.paintAlignment(true);
+ /*
+ * 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 ==
+ * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
+ * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
+ * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+ * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
+ * // attempt to find a match in the alignment SequenceI mtch =
+ * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
+ * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
+ * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
+ * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
+ * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
+ * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
+ * { System.err.println("Associated file : " + file + " with " +
+ * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
+ * TODO: maybe need to load as normal otherwise return; } }
+ */
+ // try to parse it as a features file
+ boolean isGroupsFile = parseFeaturesFile(file, protocol);
+ // if it wasn't a features file then we just treat it as a general
+ // alignment file to load into the current view.
+ if (!isGroupsFile)
+ {
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
+ else
+ {
+ alignPanel.paintAlignment(true);
+ }
}
}
}
}
}
+ @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);
- final String[] otherdb = sf.getOrderedSupportedSources();
- // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- // jalview.util.QuickSort.sort(otherdb, otherdb);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
-
+ String[] dbclasses = sf.getOrderedSupportedSources();
+ // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ // jalview.util.QuickSort.sort(otherdb, otherdb);
+ List<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
- JMenuItem fetchr;
- rfetch.add(dfetch);
- int comp = 0, mcomp = 15;
+ JMenu ifetch = new JMenu();
+ JMenuItem fetchr = null;
+ int comp = 0, icomp = 0, mcomp = 15;
String mname = null;
- if (otherdb != null && otherdb.length > 0)
+ int dbi = 0;
+ for (String dbclass : dbclasses)
{
- for (int i = 0; i < otherdb.length; i++)
+ otherdb = sf.getSourceProxy(dbclass);
+ // add a single entry for this class, or submenu allowing 'fetch
+ // all' or pick one
+ if (otherdb == null || otherdb.size() < 1)
{
- String dbname = sf.getSourceProxy(otherdb[i]).get(0).getDbName();
- if (mname == null)
- {
- mname = "from '" + dbname + "'";
- }
- fetchr = new JMenuItem(otherdb[i]);
- final String[] dassource = new String[]
- { otherdb[i] };
+ continue;
+ }
+ // List<DbSourceProxy> dbs=otherdb;
+ // otherdb=new ArrayList<DbSourceProxy>();
+ // for (DbSourceProxy db:dbs)
+ // {
+ // if (!db.isA(DBRefSource.ALIGNMENTDB)
+ // }
+ if (mname == null)
+ {
+ mname = "From " + dbclass;
+ }
+ if (otherdb.size() == 1)
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem(src.getDbSource());
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.setToolTipText("Retrieve from " + dbname);
+ fetchr.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("Retrieve from "
+ + src.getDbName()) + "<html>");
+ dfetch.add(fetchr);
+ comp++;
+ }
+ else
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ // fetch all entry
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
+ + "'");
+ fetchr.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassource)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+ });
+
+ fetchr.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("Retrieve from all "
+ + otherdb.size() + " sources in "
+ + src.getDbSource() + "<br>First is :"
+ + src.getDbName()) + "<html>");
dfetch.add(fetchr);
- if (comp++ == mcomp || i == (otherdb.length - 1))
+ comp++;
+ // and then build the rest of the individual menus
+ ifetch = new JMenu("Sources from " + src.getDbSource());
+ icomp = 0;
+ String imname = null;
+ int i = 0;
+ for (DbSourceProxy sproxy : otherdb)
{
- dfetch.setText(mname + " to '" + dbname + "'");
- rfetch.add(dfetch);
- dfetch = new JMenu();
- mname = null;
- comp = 0;
+ String dbname = sproxy.getDbName();
+ String sname = dbname.length() > 5 ? dbname.substring(0,
+ 5) + "..." : dbname;
+ String msname = dbname.length() > 10 ? dbname.substring(
+ 0, 10) + "..." : dbname;
+ if (imname == null)
+ {
+ imname = "from '" + sname + "'";
+ }
+ fetchr = new JMenuItem(msname);
+ final DbSourceProxy[] dassrc =
+ { sproxy };
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassrc)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("Retrieve from "
+ + dbname) + "</html>");
+ ifetch.add(fetchr);
+ ++i;
+ if (++icomp >= mcomp || i == (otherdb.size()))
+ {
+ ifetch.setText(imname + " to '" + sname + "'");
+ dfetch.add(ifetch);
+ ifetch = new JMenu();
+ imname = null;
+ icomp = 0;
+ comp++;
+ }
}
}
+ ++dbi;
+ if (comp >= mcomp || dbi >= (dbclasses.length))
+ {
+ dfetch.setText(mname + " to '" + dbclass + "'");
+ rfetch.add(dfetch);
+ dfetch = new JMenu();
+ mname = null;
+ comp = 0;
+ }
}
}
});
/**
* 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)
{
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)
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))
+ for (SequenceI s:gps[g].getSequences())
+ viewport.setSequenceColour(
+ s, col)
;
}
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
/**
* 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