X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=015b95bfca2d7f2e126826dbe95e87e2d74ba3a2;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=00b204e86a2fa09f61009688f70de32fff90a552;hpb=cbd3d4ab55c9b20ae136151149386cde6f4546a5;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 00b204e..015b95b 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -30,10 +30,12 @@ import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; +import jalview.api.AlignmentViewPanel; import jalview.api.analysis.ScoreModelI; import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; import jalview.commands.OrderCommand; import jalview.commands.RemoveGapColCommand; import jalview.commands.RemoveGapsCommand; @@ -53,10 +55,11 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; +import jalview.io.BioJsHTMLOutput; import jalview.io.FeaturesFile; import jalview.io.FileLoader; import jalview.io.FormatAdapter; -import jalview.io.HTMLOutput; +import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; @@ -114,6 +117,7 @@ import java.beans.PropertyChangeEvent; import java.io.File; import java.net.URL; import java.util.ArrayList; +import java.util.Arrays; import java.util.Enumeration; import java.util.Hashtable; import java.util.List; @@ -378,7 +382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) { - alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + alignPanel.getSeqPanel().numberPressed(evt.getKeyChar()); } switch (evt.getKeyCode()) @@ -396,7 +400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(0, 1); + alignPanel.getSeqPanel().moveCursor(0, 1); } break; @@ -407,7 +411,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(0, -1); + alignPanel.getSeqPanel().moveCursor(0, -1); } break; @@ -415,11 +419,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) { - slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1()); } else { - alignPanel.seqPanel.moveCursor(-1, 0); + alignPanel.getSeqPanel().moveCursor(-1, 0); } break; @@ -427,18 +431,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) { - slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1()); } else { - alignPanel.seqPanel.moveCursor(1, 0); + alignPanel.getSeqPanel().moveCursor(1, 0); } break; case KeyEvent.VK_SPACE: if (viewport.cursorMode) { - alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() + alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } break; @@ -462,7 +466,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } @@ -471,19 +475,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_S: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorRow(); + alignPanel.getSeqPanel().setCursorRow(); } break; case KeyEvent.VK_C: if (viewport.cursorMode && !evt.isControlDown()) { - alignPanel.seqPanel.setCursorColumn(); + alignPanel.getSeqPanel().setCursorColumn(); } break; case KeyEvent.VK_P: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorPosition(); + alignPanel.getSeqPanel().setCursorPosition(); } break; @@ -491,20 +495,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_COMMA: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorRowAndColumn(); + alignPanel.getSeqPanel().setCursorRowAndColumn(); } break; case KeyEvent.VK_Q: if (viewport.cursorMode) { - alignPanel.seqPanel.setSelectionAreaAtCursor(true); + alignPanel.getSeqPanel().setSelectionAreaAtCursor(true); } break; case KeyEvent.VK_M: if (viewport.cursorMode) { - alignPanel.seqPanel.setSelectionAreaAtCursor(false); + alignPanel.getSeqPanel().setSelectionAreaAtCursor(false); } break; @@ -515,10 +519,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; + alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq; } - alignPanel.seqPanel.seqCanvas.repaint(); + alignPanel.getSeqPanel().seqCanvas.repaint(); break; case KeyEvent.VK_F1: @@ -737,14 +741,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); conservationMenuItem.setSelected(av.getConservationSelected()); seqLimits.setSelected(av.getShowJVSuffix()); - idRightAlign.setSelected(av.rightAlignIds); + idRightAlign.setSelected(av.isRightAlignIds()); centreColumnLabelsMenuItem.setState(av.centreColumnLabels); renderGapsMenuItem.setSelected(av.renderGaps); wrapMenuItem.setSelected(av.wrapAlignment); scaleAbove.setVisible(av.wrapAlignment); scaleLeft.setVisible(av.wrapAlignment); scaleRight.setVisible(av.wrapAlignment); - annotationPanelMenuItem.setState(av.showAnnotation); + annotationPanelMenuItem.setState(av.isShowAnnotation()); /* * Show/hide annotations only enabled if annotation panel is shown */ @@ -764,7 +768,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, setColourSelected(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); - showSeqFeatures.setSelected(av.showSequenceFeatures); + showSeqFeatures.setSelected(av.isShowSequenceFeatures()); hiddenMarkers.setState(av.showHiddenMarkers); applyToAllGroups.setState(av.getColourAppliesToAllGroups()); showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); @@ -895,7 +899,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public FeatureRenderer getFeatureRenderer() { - return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); + return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer(); } @Override @@ -1226,11 +1230,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { - new HTMLOutput(alignPanel, - alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + // new HTMLOutput(alignPanel, + // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(), + // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); + new HtmlSvgOutput(null, alignPanel); } + @Override + public void bioJSMenuItem_actionPerformed(ActionEvent e) + { + new BioJsHTMLOutput(alignPanel, + alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); + } public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1260,6 +1271,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.makeEPS(f); } + public void createSVG(File f) + { + alignPanel.makeSVG(f); + } @Override public void pageSetup_actionPerformed(ActionEvent e) { @@ -1291,7 +1306,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void exportAnnotations_actionPerformed(ActionEvent e) { new AnnotationExporter().exportAnnotations(alignPanel, - viewport.showAnnotation ? viewport.getAlignment() + viewport.isShowAnnotation() ? viewport.getAlignment() .getAlignmentAnnotation() : null, viewport .getAlignment().getGroups(), ((Alignment) viewport .getAlignment()).alignmentProperties); @@ -1406,7 +1421,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.historyList.size() > 0) { undoMenuItem.setEnabled(true); - CommandI command = (CommandI) viewport.historyList.peek(); + CommandI command = viewport.historyList.peek(); undoMenuItem.setText(MessageManager.formatMessage( "label.undo_command", new String[] { command.getDescription() })); @@ -1421,7 +1436,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { redoMenuItem.setEnabled(true); - CommandI command = (CommandI) viewport.redoList.peek(); + CommandI command = viewport.redoList.peek(); redoMenuItem.setText(MessageManager.formatMessage( "label.redo_command", new String[] { command.getDescription() })); @@ -1485,7 +1500,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return; } - CommandI command = (CommandI) viewport.historyList.pop(); + CommandI command = viewport.historyList.pop(); viewport.redoList.push(command); command.undoCommand(getViewAlignments()); @@ -1524,7 +1539,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - CommandI command = (CommandI) viewport.redoList.pop(); + CommandI command = viewport.redoList.pop(); viewport.historyList.push(command); command.doCommand(getViewAlignments()); @@ -1617,7 +1632,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.cursorMode) { sg.add(viewport.getAlignment().getSequenceAt( - alignPanel.seqPanel.seqCanvas.cursorY)); + alignPanel.getSeqPanel().seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() != viewport @@ -1667,7 +1682,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(size, 0); + alignPanel.getSeqPanel().moveCursor(size, 0); } else { @@ -1678,7 +1693,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(-size, 0); + alignPanel.getSeqPanel().moveCursor(-size, 0); } else { @@ -1986,7 +2001,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // ///// // ADD HISTORY ITEM // - addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE, + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), + Action.PASTE, sequences, 0, alignment.getWidth(), alignment)); } // Add any annotations attached to sequences @@ -2104,9 +2121,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // >>>This is a fix for the moment, until a better solution is // found!!<<< - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings( - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2164,9 +2181,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // >>>This is a fix for the moment, until a better solution is // found!!<<< - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings( - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2257,8 +2274,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * //ADD HISTORY ITEM */ - addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut, - sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, viewport.getAlignment())); viewport.setSelectionGroup(null); @@ -2329,14 +2347,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (viewport.cursorMode) { - alignPanel.seqPanel.keyboardNo1 = null; - alignPanel.seqPanel.keyboardNo2 = null; + alignPanel.getSeqPanel().keyboardNo1 = null; + alignPanel.getSeqPanel().keyboardNo2 = null; } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); - alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.idPanel.idCanvas.searchResults = null; + alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null); + alignPanel.getIdPanel().getIdCanvas().searchResults = null; alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); @@ -2737,7 +2755,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.setShowJVSuffix(seqLimits.isSelected()); - alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel + alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel .calculateIdWidth()); alignPanel.paintAlignment(true); } @@ -2745,7 +2763,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void idRightAlign_actionPerformed(ActionEvent e) { - viewport.rightAlignIds = idRightAlign.isSelected(); + viewport.setRightAlignIds(idRightAlign.isSelected()); alignPanel.paintAlignment(true); } @@ -2767,7 +2785,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.followHighlight = this.followHighlightMenuItem.getState()) { alignPanel.scrollToPosition( - alignPanel.seqPanel.seqCanvas.searchResults, false); + alignPanel.getSeqPanel().seqCanvas.searchResults, false); } } @@ -3074,7 +3092,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight .isSelected()); - if (viewport.getShowSequenceFeaturesHeight()) + if (viewport.isShowSequenceFeaturesHeight()) { // ensure we're actually displaying features viewport.setShowSequenceFeatures(true); @@ -4176,16 +4194,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ msa = viewport.getAlignmentView(true); } + else if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() == 1) + { + int option = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.oneseq_msainput_selection"), + MessageManager.getString("label.invalid_selection"), + JOptionPane.OK_CANCEL_OPTION); + if (option == JOptionPane.OK_OPTION) + { + msa = viewport.getAlignmentView(false); + } + } else { - /* - * Vector seqs = viewport.getAlignment().getSequences(); - * - * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()]; - * - * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI) - * seqs.elementAt(i); } } - */ msa = viewport.getAlignmentView(false); } return msa; @@ -4859,8 +4881,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, try { featuresFile = new FeaturesFile(file, type).parse(viewport - .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureColours, false, + .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer().getFeatureColours(), false, jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } catch (Exception ex) { @@ -4869,12 +4891,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (featuresFile) { - viewport.showSequenceFeatures = true; + viewport.setShowSequenceFeatures(true); showSeqFeatures.setSelected(true); - if (alignPanel.seqPanel.seqCanvas.fr != null) + if (alignPanel.getSeqPanel().seqCanvas.fr != null) { // update the min/max ranges where necessary - alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); + alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true); } if (featureSettings != null) { @@ -5793,7 +5815,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, aa.visible = visible; } } - this.alignPanel.paintAlignment(true); + alignPanel.validateAnnotationDimensions(false); + alignPanel.alignmentChanged(); } /** @@ -5807,6 +5830,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); alignPanel.paintAlignment(true); } + + /** + * + * @return alignment panels in this alignemnt frame + */ + public List getAlignPanels() + { + return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + } } class PrintThread extends Thread