X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=f4845086581325d531b0bee16932cea52068cfd1;hb=54eed9103392453c8dac3aa568fde793c4667f28;hp=b080a25341af9267b3eb8f6b33d889715ee342ac;hpb=985fd5ff517f3eb5221a7aefec88138341514779;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index b080a25..f484508 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,10 +20,58 @@ */ package jalview.gui; +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.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.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; + import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.CrossRef; import jalview.analysis.Dna; +import jalview.analysis.GeneticCodeI; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignExportSettingI; @@ -32,6 +80,7 @@ import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureSettingsControllerI; +import jalview.api.FeatureSettingsModelI; import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; import jalview.api.analysis.SimilarityParamsI; @@ -88,6 +137,7 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; +import jalview.util.HttpUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; @@ -98,52 +148,6 @@ 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.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.JCheckBoxMenuItem; -import javax.swing.JEditorPane; -import javax.swing.JInternalFrame; -import javax.swing.JLayeredPane; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JScrollPane; -import javax.swing.SwingUtilities; - /** * DOCUMENT ME! * @@ -533,7 +537,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, 1); + alignPanel.getSeqPanel().moveCursor(0, 1, + evt.isShiftDown() && !evt.isAltDown()); } break; @@ -544,9 +549,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, -1); + alignPanel.getSeqPanel().moveCursor(0, -1, + evt.isShiftDown() && !evt.isAltDown()); } - break; case KeyEvent.VK_LEFT: @@ -557,7 +562,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(-1, 0); + alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); } break; @@ -569,7 +574,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(1, 0); + alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); } break; @@ -972,7 +977,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void setStatus(String text) { - statusBar.setText(text); + statusBar.setText(text == null || text.isEmpty() ? " " : text); } /* @@ -1031,7 +1036,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance.closeAssociatedWindows(); FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") + DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName) ? DataSourceType.URL : DataSourceType.FILE; loader.LoadFile(viewport, fileName, protocol, currentFileFormat); @@ -1041,7 +1046,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Rectangle bounds = this.getBounds(); FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") + DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName) ? DataSourceType.URL : DataSourceType.FILE; AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, @@ -1088,7 +1093,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void save_actionPerformed(ActionEvent e) { if (fileName == null || (currentFileFormat == null) - || fileName.startsWith("http")) + || HttpUtils.startsWithHttpOrHttps(fileName)) { saveAs_actionPerformed(null); } @@ -1476,9 +1481,13 @@ 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 @@ -1733,19 +1742,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, synchronized void slideSequences(boolean right, int size) { List sg = new ArrayList<>(); - if (viewport.cursorMode) - { - sg.add(viewport.getAlignment() - .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY)); - } - else if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() != viewport - .getAlignment().getHeight()) + if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup() + .getSize() != viewport.getAlignment().getHeight()) { sg = viewport.getSelectionGroup() .getSequences(viewport.getHiddenRepSequences()); } + if (sg.size() == 0 && viewport.cursorMode) + { + sg.add(viewport.getAlignment() + .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY)); + } + if (sg.size() < 1) { return; @@ -2090,7 +2099,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newGraphGroups.add(q, null); } newGraphGroups.set(newann.graphGroup, - new Integer(++fgroup)); + Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2137,7 +2146,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newGraphGroups.add(q, null); } newGraphGroups.set(newann.graphGroup, - new Integer(++fgroup)); + Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2443,7 +2452,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); + viewport.setSearchResults(null); alignPanel.getIdPanel().getIdCanvas().searchResults = null; // JAL-2034 - should delegate to // alignPanel to decide if overview needs @@ -2729,8 +2738,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getViewName() == null) { - viewport.setViewName(MessageManager - .getString("label.view_name_original")); + viewport.setViewName( + MessageManager.getString("label.view_name_original")); } /* @@ -2740,6 +2749,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.av.setRedoList(viewport.getRedoList()); /* + * copy any visualisation settings that are not saved in the project + */ + newap.av.setColourAppliesToAllGroups( + viewport.getColourAppliesToAllGroups()); + + /* * Views share the same mappings; need to deregister any new mappings * created by copyAlignPanel, and register the new reference to the shared * mappings @@ -3096,7 +3111,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); - // TODO: do we actually need to update overview for scale above change ? + alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } @@ -3110,6 +3125,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } @@ -3123,6 +3139,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } @@ -3176,9 +3193,15 @@ 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()) @@ -3188,6 +3211,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showSeqFeatures_actionPerformed(null); } featureSettings = new FeatureSettings(this); + return featureSettings; } /** @@ -3344,7 +3368,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * otherwise set the chosen colour scheme (or null for 'None') */ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, - viewport.getAlignment(), viewport.getHiddenRepSequences()); + viewport, viewport.getAlignment(), + viewport.getHiddenRepSequences()); changeColour(cs); } @@ -4276,14 +4301,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * frame's DNA sequences to their aligned protein (amino acid) equivalents. */ @Override - public void showTranslation_actionPerformed(ActionEvent e) + public void showTranslation_actionPerformed(GeneticCodeI codeTable) { AlignmentI al = null; try { Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); - al = dna.translateCdna(); + al = dna.translateCdna(codeTable); } catch (Exception ex) { jalview.bin.Cache.log.error( @@ -4312,7 +4337,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, af.setFileFormat(this.currentFileFormat); final String newTitle = MessageManager .formatMessage("label.translation_of_params", new Object[] - { this.getTitle() }); + { this.getTitle(), codeTable.getId() }); af.setTitle(newTitle); if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { @@ -4480,7 +4505,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int assocfiles = 0; if (filesmatched.size() > 0) { - boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false); + boolean autoAssociate = Cache + .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); if (!autoAssociate) { String msg = MessageManager.formatMessage( @@ -4670,7 +4696,15 @@ 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 @@ -4726,6 +4760,21 @@ 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(); + } + } + } /* @@ -4923,6 +4972,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void finished() { + + for (FeatureSettingsModelI srcSettings : dbRefFetcher + .getFeatureSettingsModels()) + { + + alignPanel.av.mergeFeaturesStyle(srcSettings); + } AlignFrame.this.setMenusForViewport(); } }); @@ -5008,6 +5064,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void finished() { + FeatureSettingsModelI srcSettings = dassource[0] + .getFeatureColourScheme(); + alignPanel.av.mergeFeaturesStyle( + srcSettings); AlignFrame.this.setMenusForViewport(); } }); @@ -5300,7 +5360,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true, true); + alignPanel.paintAlignment(true, + viewport.needToUpdateStructureViews()); } } @@ -5586,15 +5647,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, colourMenu.add(textColour); colourMenu.addSeparator(); - ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(), - false); + ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, + viewport.getAlignment(), false); + colourMenu.add(annotationColour); + bg.add(annotationColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); colourMenu.add(modifyConservation); colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); - colourMenu.add(annotationColour); ColourSchemeI colourScheme = viewport.getGlobalColourScheme(); ColourMenuHelper.setColourSelected(colourMenu, colourScheme); @@ -5632,6 +5694,20 @@ 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