X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=39123d5853e8a8d58a50b70387d83a45a95a446f;hb=4ffa5161216adc501b127408f1596f507b9c7b92;hp=4c9360ed739f233c266dd6850566c46e902b2ae8;hpb=9907d58721e88d7546d5f9d441b575573ae00a9a;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 4c9360e..39123d5 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -24,6 +24,7 @@ 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 +33,7 @@ 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; @@ -64,6 +66,7 @@ import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; +import jalview.io.BackupFiles; import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; import jalview.io.FileFormat; @@ -134,6 +137,7 @@ 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; @@ -733,9 +737,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int aSize = alignPanels.size(); - tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null); + tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null); - if (aSize == 1 && ap.av.viewName == null) + if (aSize == 1 && ap.av.getViewName() == null) { this.getContentPane().add(ap, BorderLayout.CENTER); } @@ -748,7 +752,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, expandViews.setEnabled(true); gatherViews.setEnabled(true); - tabbedPane.addTab(ap.av.viewName, ap); + tabbedPane.addTab(ap.av.getViewName(), ap); ap.setVisible(false); } @@ -771,7 +775,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, gatherViews.setEnabled(true); tabbedPane.setVisible(true); AlignmentPanel first = alignPanels.get(0); - tabbedPane.addTab(first.av.viewName, first); + tabbedPane.addTab(first.av.getViewName(), first); this.getContentPane().add(tabbedPane, BorderLayout.CENTER); } @@ -872,7 +876,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param av * AlignViewport */ - void setMenusFromViewport(AlignViewport av) + public void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.isShowColourText()); @@ -963,10 +967,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return progressBar.operationInProgress(); } + /** + * Sets the text of the status bar. Note that setting a null or empty value + * will cause the status bar to be hidden, with possibly undesirable flicker + * of the screen layout. + */ @Override public void setStatus(String text) { - statusBar.setText(text); + statusBar.setText(text == null || text.isEmpty() ? " " : text); } /* @@ -1154,7 +1163,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, shortName.lastIndexOf(java.io.File.separatorChar) + 1); } - success = new Jalview2XML().saveAlignment(this, file, shortName); + success = new jalview.project.Jalview2XML().saveAlignment(this, file, + shortName); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] @@ -1186,9 +1196,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { + // create backupfiles object and get new temp filename destination + BackupFiles backupfiles = new BackupFiles(file); + try { - PrintWriter out = new PrintWriter(new FileWriter(file)); + PrintWriter out = new PrintWriter( + new FileWriter(backupfiles.getTempFilePath())); out.print(output); out.close(); @@ -1201,6 +1215,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, success = false; ex.printStackTrace(); } + + backupfiles.setWriteSuccess(success); + // do the backup file roll and rename the temp file to actual file + success = backupfiles.rollBackupsAndRenameTempFile(); + } } @@ -1828,7 +1847,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void copy_actionPerformed(ActionEvent e) { - System.gc(); if (viewport.getSelectionGroup() == null) { return; @@ -1864,23 +1882,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; if (viewport.hasHiddenColumns()) { - hiddenColumns = new ArrayList<>(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); - ArrayList hiddenRegions = viewport.getAlignment() - .getHiddenColumns().getHiddenColumnsCopy(); - for (int[] region : hiddenRegions) - { - if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) - { - hiddenColumns - .add(new int[] - { region[0] - hiddenOffset, region[1] - hiddenOffset }); - } - } + + // create new HiddenColumns object with copy of hidden regions + // between startRes and endRes, offset by startRes + hiddenColumns = new HiddenColumns( + viewport.getAlignment().getHiddenColumns(), hiddenOffset, + hiddenCutoff, hiddenOffset); } Desktop.jalviewClipboard = new Object[] { seqs, @@ -2081,7 +2093,7 @@ 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(); @@ -2128,7 +2140,7 @@ 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(); @@ -2209,11 +2221,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int[] region : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is @@ -2268,11 +2277,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int region[] : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is @@ -2410,15 +2416,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - SequenceGroup sg = new SequenceGroup(); - - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) - { - sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); - } + SequenceGroup sg = new SequenceGroup( + viewport.getAlignment().getSequences()); sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); + viewport.isSelectionGroupChanged(true); viewport.sendSelection(); // JAL-2034 - should delegate to // alignPanel to decide if overview needs @@ -2714,7 +2717,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * Create a new AlignmentPanel (with its own, new Viewport) */ - AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel); + AlignmentPanel newap = new jalview.project.Jalview2XML() + .copyAlignPanel(alignPanel); if (!copyAnnotation) { /* @@ -2726,10 +2730,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.av.setGatherViewsHere(false); - if (viewport.viewName == null) + if (viewport.getViewName() == null) { - viewport.viewName = MessageManager - .getString("label.view_name_original"); + viewport.setViewName(MessageManager + .getString("label.view_name_original")); } /* @@ -2739,6 +2743,12 @@ 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 @@ -2753,7 +2763,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.refresh(true); // adjust layout of annotations } - newap.av.viewName = getNewViewName(viewTitle); + newap.av.setViewName(getNewViewName(viewTitle)); addAlignmentPanel(newap, true); newap.alignmentChanged(); @@ -2816,9 +2826,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (comp instanceof AlignmentPanel) { AlignmentPanel ap = (AlignmentPanel) comp; - if (!existingNames.contains(ap.av.viewName)) + if (!existingNames.contains(ap.av.getViewName())) { - existingNames.add(ap.av.viewName); + existingNames.add(ap.av.getViewName()); } } } @@ -2901,7 +2911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setFollowHighlight(state); if (state) { - alignPanel.scrollToPosition(viewport.getSearchResults(), false); + alignPanel.scrollToPosition(viewport.getSearchResults()); } } @@ -3048,6 +3058,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.expandColSelection(sg, false); viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3072,6 +3083,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3093,7 +3105,7 @@ 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); } @@ -3107,6 +3119,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } @@ -3120,6 +3133,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } @@ -3273,6 +3287,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.setOverviewPanel(null); }; }); + if (getKeyListeners().length > 0) + { + frame.addKeyListener(getKeyListeners()[0]); + } alignPanel.setOverviewPanel(overview); } @@ -3337,6 +3355,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * otherwise set the chosen colour scheme (or null for 'None') */ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, + viewport, viewport.getAlignment(), viewport.getHiddenRepSequences()); changeColour(cs); } @@ -3606,9 +3625,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, frameTitle += " from "; - if (viewport.viewName != null) + if (viewport.getViewName() != null) { - frameTitle += viewport.viewName + " of "; + frameTitle += viewport.getViewName() + " of "; } frameTitle += this.title; @@ -4269,14 +4288,14 @@ 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( @@ -4305,7 +4324,7 @@ 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)) { @@ -4473,17 +4492,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int assocfiles = 0; if (filesmatched.size() > 0) { - if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) - || JvOptionPane.showConfirmDialog(thisaf, - MessageManager.formatMessage( - "label.automatically_associate_structure_files_with_sequences_same_name", - new Object[] - { Integer.valueOf(filesmatched.size()) - .toString() }), - MessageManager.getString( - "label.automatically_associate_structure_files_by_name"), - JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION) - + boolean autoAssociate = Cache + .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); + if (!autoAssociate) + { + String msg = MessageManager.formatMessage( + "label.automatically_associate_structure_files_with_sequences_same_name", + new Object[] + { Integer.valueOf(filesmatched.size()) + .toString() }); + String ttl = MessageManager.getString( + "label.automatically_associate_structure_files_by_name"); + int choice = JvOptionPane.showConfirmDialog(thisaf, msg, + ttl, JvOptionPane.YES_NO_OPTION); + autoAssociate = choice == JvOptionPane.YES_OPTION; + } + if (autoAssociate) { for (Object[] fm : filesmatched) { @@ -4495,7 +4519,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, PDBEntry pe = new AssociatePdbFileWithSeq() .associatePdbWithSeq((String) fm[0], (DataSourceType) fm[1], toassoc, false, - Desktop.instance); + Desktop.instance, false); if (pe != null) { System.err.println("Associated file : " @@ -4509,6 +4533,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true, false); } } + else + { + /* + * add declined structures as sequences + */ + for (Object[] o : filesmatched) + { + filesnotmatched.add((String) o[0]); + } + } } if (filesnotmatched.size() > 0) { @@ -4641,11 +4675,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); - SequenceI repseq = viewport.getAlignment().getSequenceAt(0); - viewport.getAlignment().setSeqrep(repseq); - HiddenColumns cs = new HiddenColumns(); - cs.hideInsertionsFor(repseq); - viewport.getAlignment().setHiddenColumns(cs); + viewport.getAlignment().setupJPredAlignment(); isAnnotation = true; } // else if (IdentifyFile.FeaturesFile.equals(format)) @@ -4766,7 +4796,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (reply != null) { - viewport.viewName = reply; + viewport.setViewName(reply); // TODO warn if reply is in getExistingViewNames()? tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); } @@ -4867,14 +4897,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, MessageManager.getString("option.trim_retrieved_seqs")); trimrs.setToolTipText( MessageManager.getString("label.trim_retrieved_sequences")); - trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true)); + trimrs.setSelected( + Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trimrs.setSelected(trimrs.isSelected()); - Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", + Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, Boolean.valueOf(trimrs.isSelected()).toString()); }; }); @@ -4905,6 +4936,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void finished() { + + for (FeatureSettingsModelI srcSettings : dbRefFetcher + .getFeatureSettingsModels()) + { + + alignPanel.av.mergeFeaturesStyle(srcSettings); + } AlignFrame.this.setMenusForViewport(); } }); @@ -4990,6 +5028,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void finished() { + FeatureSettingsModelI srcSettings = dassource[0] + .getFeatureColourScheme(); + alignPanel.av.mergeFeaturesStyle( + srcSettings); AlignFrame.this.setMenusForViewport(); } }); @@ -5282,7 +5324,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true, true); + alignPanel.paintAlignment(true, + viewport.needToUpdateStructureViews()); } } @@ -5303,6 +5346,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (avc.createGroup()) { + if (applyAutoAnnotationSettings.isSelected()) + { + alignPanel.updateAnnotation(true, false); + } alignPanel.alignmentChanged(); } } @@ -5393,7 +5440,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public List getAlignPanels() { - return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + // alignPanels is never null + // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + return alignPanels; } /** @@ -5562,15 +5611,16 @@ 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);