X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=d4c87d8800ed5c63f958341898cddc37e9410b53;hb=5a74603b846dae238eaca8c1a8aa5bab64ab3c2c;hp=2405bbde9774a3772fdee512995cfa91a76d9283;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 2405bbd..d4c87d8 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -67,6 +67,7 @@ import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.HtmlSvgOutput; @@ -85,6 +86,7 @@ import jalview.schemes.ResidueProperties; import jalview.schemes.TCoffeeColourScheme; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.jws1.Discoverer; @@ -118,6 +120,8 @@ 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; @@ -157,6 +161,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; + ViewportRanges vpRanges; + public AlignViewControllerI avc; List alignPanels = new ArrayList(); @@ -328,6 +334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBar = new ProgressBar(this.statusPanel, this.statusBar); } + vpRanges = viewport.getRanges(); avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) @@ -637,8 +644,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; - alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq; + alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges + .getStartRes(); + alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges + .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); break; @@ -676,8 +685,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - - viewport.endSeq + viewport.startSeq); + alignPanel.setScrollValues(vpRanges.getStartRes(), + 2 * vpRanges.getStartSeq() - vpRanges.getEndSeq()); } break; case KeyEvent.VK_PAGE_DOWN: @@ -687,8 +696,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - + viewport.endSeq - viewport.startSeq); + alignPanel.setScrollValues(vpRanges.getStartRes(), + vpRanges.getEndSeq()); } break; } @@ -842,7 +851,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showReverse.setVisible(nucleotide); showReverseComplement.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); - modifyConservation.setEnabled(!nucleotide); + modifyConservation.setEnabled(!nucleotide + && conservationMenuItem.isSelected()); showGroupConservation.setEnabled(!nucleotide); showComplementMenuItem.setText(nucleotide ? MessageManager @@ -873,7 +883,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.isShowColourText()); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); + modifyPID.setEnabled(abovePIDThreshold.isSelected()); conservationMenuItem.setSelected(av.getConservationSelected()); + modifyConservation.setEnabled(conservationMenuItem.isSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.isRightAlignIds()); centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); @@ -1094,7 +1106,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void saveAs_actionPerformed(ActionEvent e) { String format = currentFileFormat == null ? null : currentFileFormat - .toString(); + .getName(); JalviewFileChooser chooser = JalviewFileChooser.forWrite( Cache.getProperty("LAST_DIRECTORY"), format); @@ -1128,8 +1140,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, fileName = chooser.getSelectedFile().getPath(); - Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat.toString()); + Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); Cache.setProperty("LAST_DIRECTORY", fileName); saveAlignment(fileName, currentFileFormat); @@ -1159,17 +1170,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) - // { - // warningMessage("Cannot save file " + fileName + " using format " - // + format, "Alignment output format not supported"); - // if (!Jalview.isHeadlessMode()) - // { - // saveAs_actionPerformed(null); - // } - // return false; - // } - AlignmentExportData exportData = getAlignmentForExport(format, viewport, null); if (exportData.getSettings().isCancelled()) @@ -1194,15 +1194,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(file)); + PrintWriter out = new PrintWriter(new FileWriter(file)); out.print(output); out.close(); this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", - new Object[] { fileName, format })); + new Object[] { fileName, format.getName() })); } catch (Exception ex) { success = false; @@ -1247,8 +1246,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void outputText_actionPerformed(ActionEvent e) { - - FileFormatI fileFormat = FileFormat.forName(e.getActionCommand()); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); AlignmentExportData exportData = getAlignmentForExport(fileFormat, viewport, null); if (exportData.getSettings().isCancelled()) @@ -1261,8 +1260,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { FileFormatI format = fileFormat; cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) - .formatSequences(format, - exportData.getAlignment(), + .formatSequences(format, exportData.getAlignment(), exportData.getOmitHidden(), exportData.getStartEndPostions(), viewport.getColumnSelection())); @@ -1853,8 +1851,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } String output = new FormatAdapter().formatSequences(FileFormat.Fasta, - seqs, - omitHidden, null); + seqs, omitHidden, null); StringSelection ss = new StringSelection(output); @@ -2150,7 +2147,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - viewport.setEndSeq(alignment.getHeight()); + vpRanges.setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2554,7 +2551,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); - viewport.setStartRes(0); + vpRanges.setStartRes(0); } else { @@ -2621,13 +2618,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + int startRes = seq.findPosition(vpRanges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - viewport.setStartRes(seq.findIndex(startRes) - 1); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2660,12 +2657,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + int startRes = seq.findPosition(vpRanges.getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); - viewport.setStartRes(seq.findIndex(startRes) - 1); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2753,6 +2750,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ newap.av.replaceMappings(viewport.getAlignment()); + /* + * start up cDNA consensus (if applicable) now mappings are in place + */ + if (newap.av.initComplementConsensus()) + { + newap.refresh(true); // adjust layout of annotations + } + newap.av.viewName = getNewViewName(viewTitle); addAlignmentPanel(newap, true); @@ -3307,11 +3312,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * colour scheme to all groups. If unchecked, groups may have their own * independent colour schemes. * + * @param selected */ @Override - protected void applyToAllGroups_actionPerformed() + public void applyToAllGroups_actionPerformed(boolean selected) { - viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); + viewport.setColourAppliesToAllGroups(selected); } /** @@ -3329,7 +3335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ if (ResidueColourScheme.USER_DEFINED.equals(name)) { - new UserDefinedColours(alignPanel, null); + new UserDefinedColours(alignPanel); return; } @@ -3350,108 +3356,79 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void changeColour(ColourSchemeI cs) { // TODO: pull up to controller method - if (cs != null) - { - ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName()); - // Make sure viewport is up to date w.r.t. any sliders - // ? not needed as handled by SliderPanel.valueChanged? -// if (viewport.getAbovePIDThreshold()) -// { - // int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, -// "Background"); - //todo is threshold held in viewport style or in colour scheme? -// viewport.setThreshold(threshold); - // } - // - // if (viewport.getConservationSelected()) - // { - // cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, - // cs, "Background")); - // } - } + ColourMenuHelper.setColourSelected(colourMenu, cs); viewport.setGlobalColourScheme(cs); - if (viewport.getConservationSelected()) - { - int conservationInc = SliderPanel.getConservationValue(); - viewport.getViewportColourScheme() - .setConservationInc(conservationInc); - } alignPanel.paintAlignment(true); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Show the PID threshold slider panel */ @Override protected void modifyPID_actionPerformed() { - if (viewport.getAbovePIDThreshold()) - { - SliderPanel.setPIDSliderSource(alignPanel, - viewport.getViewportColourScheme(), "Background"); - SliderPanel.showPIDSlider(); - } + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.showPIDSlider(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Show the Conservation slider panel */ @Override protected void modifyConservation_actionPerformed() { - if (viewport.getConservationSelected() - && viewport.getGlobalColourScheme() != null) - { - SliderPanel.setConservationSlider(alignPanel, - viewport.getViewportColourScheme(), "Background"); - SliderPanel.showConservationSlider(); - } + SliderPanel.setConservationSlider(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.showConservationSlider(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on selecting or deselecting (Colour) By Conservation */ @Override - protected void conservationMenuItem_actionPerformed() + public void conservationMenuItem_actionPerformed(boolean selected) { - viewport.setConservationSelected(conservationMenuItem.isSelected()); - - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setSelected(false); + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); + viewport.getResidueShading().setConservationApplied(selected); changeColour(viewport.getGlobalColourScheme()); - - modifyConservation_actionPerformed(); + if (selected) + { + modifyConservation_actionPerformed(); + } + else + { + SliderPanel.hideConservationSlider(); + } } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on selecting or deselecting (Colour) Above PID Threshold */ @Override - public void abovePIDThreshold_actionPerformed() + public void abovePIDThreshold_actionPerformed(boolean selected) { - viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); - - conservationMenuItem.setSelected(false); - viewport.setConservationSelected(false); + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); + if (!selected) + { + viewport.getResidueShading().setThreshold(0, + viewport.isIgnoreGapsConsensus()); + } changeColour(viewport.getGlobalColourScheme()); - - modifyPID_actionPerformed(); + if (selected) + { + modifyPID_actionPerformed(); + } + else + { + SliderPanel.hidePIDSlider(); + } } /** @@ -4797,8 +4774,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (FileFormat.Jnet.equals(format)) { - JPredFile predictions = new JPredFile( - file, sourceType); + JPredFile predictions = new JPredFile(file, sourceType); new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); @@ -4868,6 +4844,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /* + * 'focus' any colour slider that is open to the selected viewport + */ + if (viewport.getConservationSelected()) + { + SliderPanel.setConservationSlider(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + } + else + { + SliderPanel.hideConservationSlider(); + } + if (viewport.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + } + else + { + SliderPanel.hidePIDSlider(); + } + + /* * If there is a frame linked to this one in a SplitPane, switch it to the * same view tab index. No infinite recursion of calls should happen, since * tabSelectionChanged() should not get invoked on setting the selected @@ -5707,10 +5705,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, colourMenu.add(annotationColour); ColourSchemeI colourScheme = viewport.getGlobalColourScheme(); - String schemeName = colourScheme == null ? null : colourScheme - .getSchemeName(); - - ColourMenuHelper.setColourSelected(colourMenu, schemeName); + ColourMenuHelper.setColourSelected(colourMenu, colourScheme); } }