X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;fp=src%2Fjalview%2Fgui%2FAlignFrame.java;h=be8af7bff60b7331a5670968b597d2cf2e6e6302;hb=ffea8e06f34c1004671749a799722f64a83d8161;hp=9f5b8f0a81db07655d91f430ab27d4e86f231930;hpb=e06cc22092db00e50cc3e4a375f00a8ee2ca5a2a;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 9f5b8f0..be8af7b 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -59,7 +59,7 @@ 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; @@ -382,7 +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()) @@ -400,7 +400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(0, 1); + alignPanel.getSeqPanel().moveCursor(0, 1); } break; @@ -411,7 +411,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(0, -1); + alignPanel.getSeqPanel().moveCursor(0, -1); } break; @@ -419,11 +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; @@ -431,18 +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; @@ -466,7 +466,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } @@ -475,19 +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; @@ -495,20 +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; @@ -519,10 +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: @@ -741,14 +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 */ @@ -899,7 +899,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public FeatureRenderer getFeatureRenderer() { - return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); + return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer(); } @Override @@ -1230,16 +1230,17 @@ 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(alignPanel); } @Override public void bioJSMenuItem_actionPerformed(ActionEvent e) { new BioJsHTMLOutput(alignPanel, - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); } public void createImageMap(File file, String image) { @@ -1305,7 +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); @@ -1631,7 +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 @@ -1681,7 +1682,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(size, 0); + alignPanel.getSeqPanel().moveCursor(size, 0); } else { @@ -1692,7 +1693,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(-size, 0); + alignPanel.getSeqPanel().moveCursor(-size, 0); } else { @@ -2120,9 +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. @@ -2180,9 +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. @@ -2346,14 +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(); @@ -2754,7 +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); } @@ -2762,7 +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); } @@ -2784,7 +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); } } @@ -4880,7 +4881,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, try { featuresFile = new FeaturesFile(file, type).parse(viewport - .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas + .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas .getFeatureRenderer().featureColours, false, jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } catch (Exception ex) @@ -4892,10 +4893,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.showSequenceFeatures = 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) {