X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2ca02fdbe6f8571aabd0b4b25ecbda6886a062a3;hb=8a43b8353b89a47002ef17c959ed61281fc4d826;hp=0e9211a9a1299f9686a95476250a8ecbf1d9fbf8;hpb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 0e9211a..2ca02fd 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,6 +20,58 @@ */ package jalview.gui; +import java.awt.BorderLayout; +import java.awt.Color; +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.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +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.io.FileWriter; +import java.io.PrintWriter; +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.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JComponent; +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.JPanel; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; + +import ext.vamsas.ServiceHandle; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.CrossRef; @@ -103,59 +155,6 @@ import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.seqfetcher.DbSourceProxy; -import java.awt.BorderLayout; -import java.awt.Color; -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.FocusAdapter; -import java.awt.event.FocusEvent; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.awt.event.KeyAdapter; -import java.awt.event.KeyEvent; -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.io.FileWriter; -import java.io.PrintWriter; -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.Vector; - -import javax.swing.ButtonGroup; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JComponent; -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.JPanel; -import javax.swing.JScrollPane; -import javax.swing.SwingUtilities; - -import ext.vamsas.ServiceHandle; - /** * DOCUMENT ME! * @@ -415,7 +414,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addKeyListener(); - final List selviews = new ArrayList<>(); + final List selviews = new ArrayList<>(); final List origview = new ArrayList<>(); final String menuLabel = MessageManager .getString("label.copy_format_from"); @@ -424,7 +423,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { @Override - public AlignmentPanel[] getAllAlignmentPanels() + public AlignmentViewPanel[] getAllAlignmentPanels() { origview.clear(); origview.add(alignPanel); @@ -442,7 +441,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (origview.size() > 0) { - final AlignmentPanel ap = origview.get(0); + final AlignmentViewPanel avp = origview.get(0); /* * Copy the ViewStyle of the selected panel to 'this one'. @@ -455,10 +454,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getAlignViewport().getCodingComplement() != null; if (!fromSplitFrame) { - vs.setScaleProteinAsCdna(ap.getAlignViewport() + vs.setScaleProteinAsCdna(avp.getAlignViewport() .getViewStyle().isScaleProteinAsCdna()); } - ap.getAlignViewport().setViewStyle(vs); + avp.getAlignViewport().setViewStyle(vs); /* * Also rescale ViewStyle of SplitFrame complement if there is @@ -466,7 +465,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * the whole ViewStyle (allow cDNA protein to have different * fonts) */ - AlignViewportI complement = ap.getAlignViewport() + AlignViewportI complement = avp.getAlignViewport() .getCodingComplement(); if (complement != null && vs.isScaleProteinAsCdna()) { @@ -476,10 +475,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, af.setMenusForViewport(); } + avp.setSelected(true); + AlignmentPanel ap = (AlignmentPanel) avp; ap.updateLayout(); - ap.setSelected(true); ap.alignFrame.setMenusForViewport(); - } } }); @@ -1490,10 +1489,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.load_jalview_annotations")); - chooser.setToolTipText( - MessageManager.getString("label.load_jalview_annotations")); + String tooltip = MessageManager.getString("label.load_jalview_annotations"); + chooser.setDialogTitle(tooltip); + chooser.setToolTipText(tooltip); chooser.setResponseHandler(0, new Runnable() { @Override @@ -1544,9 +1542,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, closeView(alignPanel); } } - if (closeAllTabs) { + if (featureSettings != null && featureSettings.isOpen()) + { + featureSettings.close(); + featureSettings = null; + } /* * this will raise an INTERNAL_FRAME_CLOSED event and this method will * be called recursively, with the frame now in 'closed' state @@ -3251,9 +3253,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void featureSettings_actionPerformed(ActionEvent e) { + showFeatureSettingsUI(); + } + + @Override + public FeatureSettingsControllerI showFeatureSettingsUI() + { if (featureSettings != null) { - featureSettings.close(); + featureSettings.closeOldSettings(); featureSettings = null; } if (!showSeqFeatures.isSelected()) @@ -3263,6 +3271,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showSeqFeatures_actionPerformed(null); } featureSettings = new FeatureSettings(this); + return featureSettings; } /** @@ -4792,7 +4801,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (parseFeaturesFile(file, sourceType)) { - alignPanel.paintAlignment(true, true); + SplitFrame splitFrame = (SplitFrame) getSplitViewContainer(); + if (splitFrame != null) + { + splitFrame.repaint(); + } + else + { + alignPanel.paintAlignment(true, true); + } } } else @@ -4848,6 +4865,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport = alignPanel.av; avc.setViewportAndAlignmentPanel(viewport, alignPanel); setMenusFromViewport(viewport); + if (featureSettings != null && featureSettings.isOpen() + && featureSettings.fr.getViewport() != viewport) + { + if (viewport.isShowSequenceFeatures()) + { + // refresh the featureSettings to reflect UI change + showFeatureSettingsUI(); + } + else + { + // close feature settings for this view. + featureSettings.close(); + } + } + } /* @@ -5762,6 +5794,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } + private Rectangle lastFeatureSettingsBounds = null; + @Override + public void setFeatureSettingsGeometry(Rectangle bounds) + { + lastFeatureSettingsBounds = bounds; + } + + @Override + public Rectangle getFeatureSettingsGeometry() + { + return lastFeatureSettingsBounds; + } } class PrintThread extends Thread