X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2371be313e5ee2a4797232f93871e108bfcdfca9;hb=6463d6e0b78c66ca70ebe73c9f0f115185d1e681;hp=d87f0f0eb627215c5b21a4e82a74094ed9fa7f92;hpb=1cec732f963ab102c9d8381203df8c8cba2a9ee4;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index d87f0f0..2371be3 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -107,6 +107,7 @@ import jalview.ws.seqfetcher.DbSourceProxy; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; +import java.awt.Dimension; import java.awt.Rectangle; import java.awt.Toolkit; import java.awt.datatransfer.Clipboard; @@ -130,6 +131,7 @@ import java.awt.event.MouseEvent; import java.awt.print.PageFormat; import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; import java.io.File; import java.io.FileWriter; import java.io.PrintWriter; @@ -192,9 +194,9 @@ public class AlignFrame extends GAlignFrame /** * Current filename for this alignment */ - String fileName = null; + private String fileName = null; - File fileObject; + private File fileObject; /** * Creates a new AlignFrame object with specific width and height. @@ -299,9 +301,6 @@ public class AlignFrame extends GAlignFrame viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); - alignPanel = new AlignmentPanel(this, viewport); - - addAlignmentPanel(alignPanel, true); init(); } @@ -321,8 +320,6 @@ public class AlignFrame extends GAlignFrame { viewport.hideSequence(hiddenSeqs); } - alignPanel = new AlignmentPanel(this, viewport); - addAlignmentPanel(alignPanel, true); init(); } @@ -338,7 +335,6 @@ public class AlignFrame extends GAlignFrame { viewport = ap.av; alignPanel = ap; - addAlignmentPanel(ap, false); init(); } @@ -348,7 +344,28 @@ public class AlignFrame extends GAlignFrame */ void init() { -// setBackground(Color.white); // BH 2019 + boolean newPanel = (alignPanel == null); + viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + if (newPanel) + { + if (Platform.isJS()) + { + // need to set this up front if NOANNOTATION is + // used in conjunction with SHOWOVERVIEW. + + // I have not determined if this is appropriate for + // Jalview/Java, as it means we are setting this flag + // for all subsequent AlignFrames. For now, at least, + // I am setting it to be JalviewJS-only. + + boolean showAnnotation = Jalview.getInstance().getShowAnnotation(); + viewport.setShowAnnotation(showAnnotation); + } + alignPanel = new AlignmentPanel(this, viewport); + } + addAlignmentPanel(alignPanel, newPanel); + + // setBackground(Color.white); // BH 2019 if (!Jalview.isHeadlessMode()) { @@ -381,9 +398,6 @@ public class AlignFrame extends GAlignFrame sortPairwiseMenuItem_actionPerformed(null); } - this.alignPanel.av - .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); - setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); calculateTree.addActionListener(new ActionListener() @@ -400,10 +414,24 @@ public class AlignFrame extends GAlignFrame if (Desktop.getDesktopPane() != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); - if (!Platform.isJS()) + PropertyChangeListener serviceListener = (Platform.isJS() ? null + : addServiceListeners()); + addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { - addServiceListeners(); - } + @Override + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + // System.out.println("deregistering discoverer listener"); + if (serviceListener != null) + { + Desktop.getInstance().removeJalviewPropertyChangeListener( + "services", serviceListener); + } + closeMenuItem_actionPerformed(true); + } + }); + setGUINucleotide(); } @@ -556,7 +584,7 @@ public class AlignFrame extends GAlignFrame switch (evt.getKeyCode()) { - case 27: // escape key + case KeyEvent.VK_ESCAPE: // escape key deselectAllSequenceMenuItem_actionPerformed(null); break; @@ -820,45 +848,30 @@ public class AlignFrame extends GAlignFrame } /* Set up intrinsic listeners for dynamically generated GUI bits. */ - private void addServiceListeners() + private PropertyChangeListener addServiceListeners() { - final java.beans.PropertyChangeListener thisListener; - Desktop.getInstance().addJalviewPropertyChangeListener("services", - thisListener = new java.beans.PropertyChangeListener() - { - @Override - public void propertyChange(PropertyChangeEvent evt) - { - // // System.out.println("Discoverer property change."); - // if (evt.getPropertyName().equals("services")) - { - SwingUtilities.invokeLater(new Runnable() - { - - @Override - public void run() - { - System.err.println( - "Rebuild WS Menu for service change"); - BuildWebServiceMenu(); - } - - }); - } - } - }); - addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + PropertyChangeListener serviceListener = new PropertyChangeListener() { @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + public void propertyChange(PropertyChangeEvent evt) { - // System.out.println("deregistering discoverer listener"); - Desktop.getInstance().removeJalviewPropertyChangeListener("services", - thisListener); - closeMenuItem_actionPerformed(true); + { + SwingUtilities.invokeLater(new Runnable() + { + + @Override + public void run() + { + System.err.println("Rebuild WS Menu for service change"); + BuildWebServiceMenu(); + } + }); + } } - }); + }; + + Desktop.getInstance().addJalviewPropertyChangeListener("services", + serviceListener); // Finally, build the menu once to get current service state new Thread(new Runnable() { @@ -868,6 +881,7 @@ public class AlignFrame extends GAlignFrame BuildWebServiceMenu(); } }).start(); + return serviceListener; } /** @@ -1039,83 +1053,86 @@ public class AlignFrame extends GAlignFrame @Override public void reload_actionPerformed(ActionEvent e) { - if (fileName != null) + if (fileName == null) + { + return; + } + // 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 (FileFormat.Jalview.equals(currentFileFormat)) { - // 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 (FileFormat.Jalview.equals(currentFileFormat)) + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); + for (int i = 0; i < frames.length; i++) { - JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); - for (int i = 0; i < frames.length; i++) + if (frames[i] instanceof AlignFrame && frames[i] != this + && ((AlignFrame) frames[i]).fileName != null + && ((AlignFrame) frames[i]).fileName.equals(fileName)) { - if (frames[i] instanceof AlignFrame && frames[i] != this - && ((AlignFrame) frames[i]).fileName != null - && ((AlignFrame) frames[i]).fileName.equals(fileName)) + try + { + frames[i].setSelected(true); + Desktop.getInstance().closeAssociatedWindows(); + } catch (java.beans.PropertyVetoException ex) { - try - { - frames[i].setSelected(true); - Desktop.getInstance().closeAssociatedWindows(); - } catch (java.beans.PropertyVetoException ex) - { - } } - } - Desktop.getInstance().closeAssociatedWindows(); - FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE; - loader.loadFile(viewport, fileName, protocol, currentFileFormat); } - else - { - Rectangle bounds = this.getBounds(); + Desktop.getInstance().closeAssociatedWindows(); - FileLoader loader = new FileLoader(); + FileLoader loader = new FileLoader(); + DataSourceType protocol = fileName.startsWith("http:") + ? DataSourceType.URL + : DataSourceType.FILE; + loader.loadFile(viewport, + (fileObject == null ? fileName : fileObject), protocol, + currentFileFormat); + } + else + { + Rectangle bounds = this.getBounds(); - AlignFrame newframe = null; + FileLoader loader = new FileLoader(); - if (fileObject == null) - { + AlignFrame newframe = null; - DataSourceType protocol = (fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE); - newframe = loader.loadFileWaitTillLoaded(fileName, protocol, - currentFileFormat); - } - else - { - newframe = loader.loadFileWaitTillLoaded(fileObject, - DataSourceType.FILE, currentFileFormat); - } + if (fileObject == null) + { - newframe.setBounds(bounds); - if (featureSettings != null && featureSettings.isShowing()) + DataSourceType protocol = (fileName.startsWith("http:") + ? DataSourceType.URL + : DataSourceType.FILE); + newframe = loader.loadFileWaitTillLoaded(fileName, protocol, + currentFileFormat); + } + else + { + newframe = loader.loadFileWaitTillLoaded(fileObject, + DataSourceType.FILE, currentFileFormat); + } + + newframe.setBounds(bounds); + if (featureSettings != null && featureSettings.isShowing()) + { + final Rectangle fspos = featureSettings.frame.getBounds(); + // TODO: need a 'show feature settings' function that takes bounds - + // need to refactor Desktop.addFrame + newframe.featureSettings_actionPerformed(null); + final FeatureSettings nfs = newframe.featureSettings; + SwingUtilities.invokeLater(new Runnable() { - final Rectangle fspos = featureSettings.frame.getBounds(); - // TODO: need a 'show feature settings' function that takes bounds - - // need to refactor Desktop.addFrame - newframe.featureSettings_actionPerformed(null); - final FeatureSettings nfs = newframe.featureSettings; - SwingUtilities.invokeLater(new Runnable() + @Override + public void run() { - @Override - public void run() - { - nfs.frame.setBounds(fspos); - } - }); - this.featureSettings.close(); - this.featureSettings = null; - } - this.closeMenuItem_actionPerformed(true); + nfs.frame.setBounds(fspos); + } + }); + this.featureSettings.close(); + this.featureSettings = null; } + this.closeMenuItem_actionPerformed(true); } } @@ -3374,12 +3391,36 @@ public class AlignFrame extends GAlignFrame } JInternalFrame frame = new JInternalFrame(); - final OverviewPanel overview = new OverviewPanel(alignPanel); + + // BH 2019.07.26 we allow for an embedded + // undecorated overview with defined size + frame.setName(Jalview.getAppID("overview")); + // + Dimension dim = Platform.getDimIfEmbedded(frame, -1, -1); + if (dim != null && dim.width == 0) + { + dim = null; // hidden, not embedded + } + OverviewPanel overview = new OverviewPanel(alignPanel, dim); + frame.setContentPane(overview); + if (dim == null) + { + dim = new Dimension(); + // was frame.getSize(), but that is 0,0 at this point; + } + else + { + // we are imbedding, and so we have an undecorated frame + // and we can set the the frame dimensions accordingly. + } + // allowing for unresizable option using, style="resize:none" + boolean resizable = (Platform.getEmbeddedAttribute(frame, + "resize") != "none"); Desktop.addInternalFrame(frame, MessageManager .formatMessage("label.overview_params", new Object[] - { this.getTitle() }), true, frame.getWidth(), frame.getHeight(), - true, true, "overview"); + { this.getTitle() }), true, dim.width, dim.height, resizable, + true); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener( @@ -3738,7 +3779,8 @@ public class AlignFrame extends GAlignFrame frameTitle += this.title; - Desktop.addInternalFrame(tp, frameTitle, 600, 500); + Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500); + Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height); } /** @@ -4090,15 +4132,24 @@ public class AlignFrame extends GAlignFrame if (nf.getTree() != null) { tp = new TreePanel(alignPanel, nf, treeTitle, input); - - tp.setSize(w, h); + Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1); + if (dim == null) + { + dim = new Dimension(w, h); + } + else + { + // no offset, either + x = 0; + } + tp.setSize(dim.width, dim.height); if (x > 0 && y > 0) { tp.setLocation(x, y); } - Desktop.addInternalFrame(tp, treeTitle, w, h); + Desktop.addInternalFrame(tp, treeTitle, dim.width, dim.height); } } catch (Exception ex) {