X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=553ddd2c6b215c19e94004e2fb710a6ae923b424;hb=a576517d22220abb490437a02c9b37a1f4c2839e;hp=fcf43011e1a12ca692ba1cdd2dca1fd56ece1a07;hpb=febd250089c9672b66d2c7a5ed0c06e0763c2233;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index fcf4301..553ddd2 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,57 +20,6 @@ */ package jalview.gui; -import java.awt.BorderLayout; -import java.awt.Component; -import java.awt.GridLayout; -import java.awt.Rectangle; -import java.awt.Toolkit; -import java.awt.datatransfer.Clipboard; -import java.awt.datatransfer.DataFlavor; -import java.awt.datatransfer.StringSelection; -import java.awt.datatransfer.Transferable; -import java.awt.dnd.DnDConstants; -import java.awt.dnd.DropTargetDragEvent; -import java.awt.dnd.DropTargetDropEvent; -import java.awt.dnd.DropTargetEvent; -import java.awt.dnd.DropTargetListener; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.awt.event.KeyAdapter; -import java.awt.event.KeyEvent; -import java.awt.event.MouseAdapter; -import java.awt.event.MouseEvent; -import java.awt.print.PageFormat; -import java.awt.print.PrinterJob; -import java.beans.PropertyChangeEvent; -import java.io.File; -import java.net.URL; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Deque; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.List; -import java.util.Set; -import java.util.Vector; - -import javax.swing.JButton; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JEditorPane; -import javax.swing.JInternalFrame; -import javax.swing.JLabel; -import javax.swing.JLayeredPane; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JPanel; -import javax.swing.JProgressBar; -import javax.swing.JRadioButtonMenuItem; -import javax.swing.JScrollPane; -import javax.swing.SwingUtilities; - import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; @@ -148,6 +97,52 @@ import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.seqfetcher.DbSourceProxy; +import java.awt.BorderLayout; +import java.awt.Component; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.io.File; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Deque; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Set; +import java.util.Vector; + +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; + /** * DOCUMENT ME! * @@ -315,6 +310,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) @@ -364,7 +361,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final List selviews = new ArrayList(); final List origview = new ArrayList(); - ViewSelectionMenu vsel = new ViewSelectionMenu("Transfer colours from", + final String menuLabel = MessageManager + .getString("label.copy_format_from"); + ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel, new ViewSetProvider() { @@ -373,7 +372,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { origview.clear(); origview.add(alignPanel); - return Desktop.getAlignmentPanels(null); + // make an array of all alignment panels except for this one + List aps = new ArrayList( + Arrays.asList(Desktop.getAlignmentPanels(null))); + aps.remove(AlignFrame.this.alignPanel); + return aps.toArray(new AlignmentPanel[aps.size()]); } }, selviews, new ItemListener() { @@ -383,32 +386,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (origview.size() > 0) { + final AlignmentPanel ap = origview.get(0); + + /* + * Copy the ViewStyle of the selected panel to 'this one'. + * Don't change value of 'scaleProteinAsCdna' unless copying + * from a SplitFrame. + */ ViewStyleI vs = selviews.get(0).getAlignViewport() .getViewStyle(); - origview.get(0).getAlignViewport().setViewStyle(vs); - AlignViewportI complement = origview.get(0) - .getAlignViewport().getCodingComplement(); - if (complement != null) + boolean fromSplitFrame = selviews.get(0) + .getAlignViewport().getCodingComplement() != null; + if (!fromSplitFrame) + { + vs.setScaleProteinAsCdna(ap.getAlignViewport() + .getViewStyle().isScaleProteinAsCdna()); + } + ap.getAlignViewport().setViewStyle(vs); + + /* + * Also rescale ViewStyle of SplitFrame complement if there is + * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy + * the whole ViewStyle (allow cDNA protein to have different + * fonts) + */ + AlignViewportI complement = ap.getAlignViewport() + .getCodingComplement(); + if (complement != null && vs.isScaleProteinAsCdna()) { AlignFrame af = Desktop.getAlignFrameFor(complement); - if (complement.isNucleotide()) - { - complement.setViewStyle(vs); - vs.setCharWidth(vs.getCharWidth() / 3); - } - else - { - int rw = vs.getCharWidth(); - vs.setCharWidth(rw * 3); - complement.setViewStyle(vs); - vs.setCharWidth(rw); - } - af.alignPanel.updateLayout(); + ((SplitFrame) af.getSplitViewContainer()) + .adjustLayout(); af.setMenusForViewport(); } - origview.get(0).updateLayout(); - origview.get(0).setSelected(true); - origview.get(0).alignFrame.setMenusForViewport(); + + ap.updateLayout(); + ap.setSelected(true); + ap.alignFrame.setMenusForViewport(); } } @@ -856,9 +870,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, updateEditMenuBar(); } - // methods for implementing IProgressIndicator - // need to refactor to a reusable stub class - Hashtable progressBars, progressBarHandlers; + private IProgressIndicator progressBar; /* * (non-Javadoc) @@ -868,78 +880,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void setProgressBar(String message, long id) { - if (progressBars == null) - { - progressBars = new Hashtable(); - progressBarHandlers = new Hashtable(); - } - - JPanel progressPanel; - Long lId = new Long(id); - GridLayout layout = (GridLayout) statusPanel.getLayout(); - if (progressBars.get(lId) != null) - { - progressPanel = (JPanel) progressBars.get(new Long(id)); - statusPanel.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 - { - progressPanel = new JPanel(new BorderLayout(10, 5)); - - JProgressBar progressBar = new JProgressBar(); - progressBar.setIndeterminate(true); - - progressPanel.add(new JLabel(message), BorderLayout.WEST); - progressPanel.add(progressBar, BorderLayout.CENTER); - - layout.setRows(layout.getRows() + 1); - statusPanel.add(progressPanel); - - progressBars.put(lId, progressPanel); - } - // update GUI - // setMenusForViewport(); - validate(); + progressBar.setProgressBar(message, id); } @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { - if (progressBarHandlers == null || !progressBars.contains(new Long(id))) - { - throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler")); - } - progressBarHandlers.put(new Long(id), handler); - final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); - if (handler.canCancel()) - { - JButton cancel = new JButton( - MessageManager.getString("action.cancel")); - final IProgressIndicator us = this; - cancel.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - handler.cancelActivity(id); - us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new Object[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); - } - }); - progressPanel.add(cancel, BorderLayout.EAST); - } + progressBar.registerHandler(id, handler); } /** @@ -949,18 +897,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public boolean operationInProgress() { - if (progressBars != null && progressBars.size() > 0) - { - return true; - } - return false; + return progressBar.operationInProgress(); } @Override public void setStatus(String text) { statusBar.setText(text); - }; + } /* * Added so Castor Mapping file can obtain Jalview Version @@ -1195,7 +1139,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, omitHidden = viewport.getViewAsString(false); } } - FormatAdapter f = new FormatAdapter(); + FeatureRenderer fr = new FeatureRenderer(this.alignPanel); + viewport.setFeatureRenderer(fr); + FormatAdapter f = new FormatAdapter(viewport); String output = f.formatSequences(format, viewport.getAlignment(), // class cast exceptions will // occur in the distant future @@ -1265,7 +1211,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void outputText_actionPerformed(ActionEvent e) { String[] omitHidden = null; - + FeatureRenderer fr = new FeatureRenderer(this.alignPanel); + viewport.setFeatureRenderer(fr); if (viewport.hasHiddenColumns()) { int reply = JOptionPane @@ -1289,7 +1236,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, try { - cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), + cap.setText(new FormatAdapter(viewport).formatSequences( + e.getActionCommand(), viewport.getAlignment(), omitHidden, viewport.getColumnSelection())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( @@ -1321,8 +1269,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void bioJSMenuItem_actionPerformed(ActionEvent e) { - new BioJsHTMLOutput(alignPanel, + BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); + bjs.exportJalviewAlignmentAsBioJsHtmlFile(); } public void createImageMap(File file, String image) { @@ -5770,8 +5719,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void setShowSeqFeatures(boolean b) { - showSeqFeatures.setSelected(true); - viewport.setShowSequenceFeatures(true); + showSeqFeatures.setSelected(b); + viewport.setShowSequenceFeatures(b); } /* @@ -5943,6 +5892,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, for (AlignmentAnnotation aa : alignPanel.getAlignment() .getAlignmentAnnotation()) { + /* + * don't display non-positional annotations on an alignment + */ + if (aa.annotations == null) + { + continue; + } boolean apply = (aa.sequenceRef == null && forAlignment) || (aa.sequenceRef != null && forSequences); if (apply)