X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=f04744de71836b9d6da29836eaec316fef39d644;hb=09e3cf7d0e936a9b69fc8f6c7315195694c5127e;hp=07ce23c991ba2cc71df70b5fb8577d6b8be70348;hpb=c9df5bd6e95c23c9b560c0a59003d1f4043f8055;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 07ce23c..f04744d 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,14 +20,13 @@ */ package jalview.gui; -import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; -import jalview.analysis.Conservation; import jalview.analysis.CrossRef; import jalview.analysis.Dna; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; +import jalview.api.AlignExportSettingI; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; @@ -37,6 +36,7 @@ import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; import jalview.api.analysis.ScoreModelI; import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.commands.CommandI; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; @@ -48,6 +48,7 @@ import jalview.commands.TrimRegionCommand; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentExportData; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; @@ -334,7 +335,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { - progressBar = new ProgressBar(this.statusPanel, this.statusBar); + if (!Jalview.isHeadlessMode()) + { + progressBar = new ProgressBar(this.statusPanel, this.statusBar); + } avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); @@ -790,7 +794,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { - System.out.println("deregistering discoverer listener"); + // System.out.println("deregistering discoverer listener"); Desktop.instance.removeJalviewPropertyChangeListener("services", thisListener); closeMenuItem_actionPerformed(true); @@ -1025,7 +1029,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void addFromText_actionPerformed(ActionEvent e) { - Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport); + Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport + .getAlignPanel()); } @Override @@ -1134,13 +1139,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { warningMessage("Cannot save file " + fileName + " using format " + format, "Alignment output format not supported"); - saveAs_actionPerformed(null); - // JBPNote need to have a raise_gui flag here + if (!Jalview.isHeadlessMode()) + { + saveAs_actionPerformed(null); + } return false; } - ExportData exportData = getAlignmentForExport(format); - FormatAdapter f = new FormatAdapter(alignPanel); + AlignmentExportData exportData = getAlignmentForExport(format, + viewport, null); + if (exportData.getSettings().isCancelled()) + { + return false; + } + FormatAdapter f = new FormatAdapter(alignPanel, + exportData.getSettings()); String output = f.formatSequences(format, exportData.getAlignment(), // class cast exceptions will // occur in the distant future @@ -1212,7 +1225,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void outputText_actionPerformed(ActionEvent e) { - ExportData exportData = getAlignmentForExport(e.getActionCommand()); + AlignmentExportData exportData = getAlignmentForExport( + e.getActionCommand(), viewport, null); if (exportData.getSettings().isCancelled()) { return; @@ -1238,9 +1252,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } - public ExportData getAlignmentForExport(String exportFomat) + public static AlignmentExportData getAlignmentForExport(String exportFormat, + AlignViewportI viewport, + AlignExportSettingI exportSettings) { AlignmentI alignmentToExport = null; + AlignExportSettingI settings = exportSettings; String[] omitHidden = null; int[] alignmentStartEnd = new int[2]; @@ -1253,9 +1270,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 0, alignmentToExport.getWidth() - 1 }; boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0; - AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs, - viewport.hasHiddenColumns(), exportFomat); - settings.isExportAnnotations(); + if (settings == null) + { + settings = new AlignExportSettings(hasHiddenSeqs, + viewport.hasHiddenColumns(), exportFormat); + } + // settings.isExportAnnotations(); if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns()) { @@ -1272,11 +1292,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport .getColumnSelection().getHiddenColumns()); } - return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd, + AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd, settings); + return ed; } - private static int[] getStartEnd(int[] aligmentStartEnd, + public static int[] getStartEnd(int[] aligmentStartEnd, List hiddenCols) { int startPos = aligmentStartEnd[0]; @@ -1288,7 +1309,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, for (int[] hiddenCol : hiddenCols) { // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]); - lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange; higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange; } @@ -1483,6 +1503,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (closeAllTabs) { + /* + * this will raise an INTERNAL_FRAME_CLOSED event and this method will + * be called recursively, with the frame now in 'closed' state + */ this.setClosed(true); } } catch (Exception ex) @@ -1813,9 +1837,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getSelectionGroup().getEndRes() + groupAdjustment); } + /* + * just extend the last slide command if compatible; but not if in + * SplitFrame mode (to ensure all edits are broadcast - JAL-1802) + */ boolean appendHistoryItem = false; Deque historyList = viewport.getHistoryList(); - if (historyList != null + boolean inSplitFrame = getSplitViewContainer() != null; + if (!inSplitFrame && historyList != null && historyList.size() > 0 && historyList.peek() instanceof SlideSequencesCommand) { @@ -2730,12 +2759,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /* - * Views share the same edits, undo and redo stacks, mappings. + * Views share the same edits undo and redo stacks */ newap.av.setHistoryList(viewport.getHistoryList()); newap.av.setRedoList(viewport.getRedoList()); - newap.av.getAlignment().setCodonFrames( - viewport.getAlignment().getCodonFrames()); + + /* + * Views share the same mappings; need to deregister any new mappings + * created by copyAlignPanel, and register the new reference to the shared + * mappings + */ + newap.av.replaceMappings(viewport.getAlignment()); newap.av.viewName = getNewViewName(viewTitle); @@ -3463,115 +3497,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void changeColour(ColourSchemeI cs) { - // TODO: compare with applet and pull up to model method - int threshold = 0; + // TODO: pull up to controller method if (cs != null) { + // Make sure viewport is up to date w.r.t. any sliders if (viewport.getAbovePIDThreshold()) { - threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, + int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); - cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus()); - } - else - { - cs.setThreshold(0, viewport.isIgnoreGapsConsensus()); + viewport.setThreshold(threshold); } if (viewport.getConservationSelected()) { - - Alignment al = (Alignment) viewport.getAlignment(); - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, - al.getWidth() - 1); - - c.calculate(); - c.verdict(false, viewport.getConsPercGaps()); - - cs.setConservation(c); - cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, "Background")); } - else - { - cs.setConservation(null); - } - - cs.setConsensus(viewport.getSequenceConsensusHash()); } viewport.setGlobalColourScheme(cs); - if (viewport.getColourAppliesToAllGroups()) - { - - for (SequenceGroup sg : viewport.getAlignment().getGroups()) - { - if (cs == null) - { - sg.cs = null; - continue; - } - - if (cs instanceof ClustalxColourScheme) - { - sg.cs = new ClustalxColourScheme(sg, - viewport.getHiddenRepSequences()); - } - else if (cs instanceof UserColourScheme) - { - sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours()); - } - else - { - try - { - sg.cs = cs.getClass().newInstance(); - } catch (Exception ex) - { - } - } - - if (viewport.getAbovePIDThreshold() - || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) - { - sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus()); - - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1)); - } - else - { - sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus()); - } - - if (viewport.getConservationSelected()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(viewport - .getHiddenRepSequences()), sg.getStartRes(), - sg.getEndRes() + 1); - c.calculate(); - c.verdict(false, viewport.getConsPercGaps()); - sg.cs.setConservation(c); - } - else - { - sg.cs.setConservation(null); - } - } - } - - if (alignPanel.getOverviewPanel() != null) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } - alignPanel.paintAlignment(true); } @@ -4506,8 +4452,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final List legacyItems = new ArrayList(); try { - System.err.println("Building ws menu again " - + Thread.currentThread()); + // System.err.println("Building ws menu again " + // + Thread.currentThread()); // TODO: add support for context dependent disabling of services based // on // alignment and current selection @@ -4859,7 +4805,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, al.getCodonFrames().addAll(cf); final StructureSelectionManager ssm = StructureSelectionManager .getStructureSelectionManager(Desktop.instance); - ssm.addMappings(cf); + ssm.registerMappings(cf); } else { @@ -4949,10 +4895,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "Exception during translation. Please report this !", ex); final String msg = MessageManager .getString("label.error_when_translating_sequences_submit_bug_report"); - final String title = MessageManager + final String errorTitle = MessageManager .getString("label.implementation_error") + MessageManager.getString("translation_failed"); - JOptionPane.showMessageDialog(Desktop.desktop, msg, title, + JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, JOptionPane.ERROR_MESSAGE); return; } @@ -4960,9 +4906,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { final String msg = MessageManager .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); - final String title = MessageManager + final String errorTitle = MessageManager .getString("label.translation_failed"); - JOptionPane.showMessageDialog(Desktop.desktop, msg, title, + JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, JOptionPane.WARNING_MESSAGE); } else @@ -4976,8 +4922,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); - viewport.openSplitFrame(af, new Alignment(seqs), - al.getCodonFrames()); + viewport.openSplitFrame(af, new Alignment(seqs)); } else { @@ -5982,7 +5927,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, aa.visible = visible; } } - alignPanel.validateAnnotationDimensions(false); + alignPanel.validateAnnotationDimensions(true); alignPanel.alignmentChanged(); } @@ -6069,67 +6014,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sf.setComplementVisible(this, show); } } - - public class ExportData - { - private AlignmentI alignment; - - private String[] omitHidden; - - private int[] startEnd; - - private AlignExportSettings settings; - - public ExportData(AlignmentI align, String[] ommit, int[] startEnd, - AlignExportSettings settings) - { - this.alignment = align; - this.omitHidden = ommit; - this.startEnd = startEnd; - this.settings = settings; - } - - public AlignmentI getAlignment() - { - return alignment; - } - - public void setAlignment(AlignmentI alignment) - { - this.alignment = alignment; - } - - public String[] getOmitHidden() - { - return omitHidden; - } - - public void setOmitHidden(String[] omitHidden) - { - this.omitHidden = omitHidden; - } - - public int[] getStartEndPostions() - { - return startEnd; - } - - public void setStartEndPostions(int[] startEnd) - { - this.startEnd = startEnd; - } - - public AlignExportSettings getSettings() - { - return settings; - } - - public void setSettings(AlignExportSettings settings) - { - this.settings = settings; - } - } - } class PrintThread extends Thread