X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=1fc5734efbcbd09176b6cf2cc1df651cacc928f4;hb=ad1a1b9167535b1f6e34d84f8d26f4c63f5d394f;hp=e98b79e898f349f6dd6cdbc9e15abd9372ff5314;hpb=68401761687b7d2ebe7d56eb5a607770ae742c9b;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index e98b79e..1fc5734 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -25,12 +25,15 @@ import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; +import jalview.gui.JalviewColourChooser.ColourChooserListener; import jalview.renderer.AnnotationRenderer; import jalview.renderer.AwtRenderPanelI; import jalview.schemes.ResidueProperties; import jalview.util.Comparison; import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; import java.awt.AlphaComposite; import java.awt.Color; @@ -56,7 +59,6 @@ import java.util.ArrayList; import java.util.Collections; import java.util.List; -import javax.swing.JColorChooser; import javax.swing.JMenuItem; import javax.swing.JPanel; import javax.swing.JPopupMenu; @@ -74,6 +76,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, MouseListener, MouseWheelListener, MouseMotionListener, ActionListener, AdjustmentListener, Scrollable, ViewportListenerI { + enum DragMode + { + Select, Resize, Undefined + }; + String HELIX = MessageManager.getString("label.helix"); String SHEET = MessageManager.getString("label.sheet"); @@ -106,7 +113,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public volatile BufferedImage fadedImage; - Graphics2D gg; + // private Graphics2D gg; public FontMetrics fm; @@ -117,11 +124,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // Used For mouse Dragging and resizing graphs int graphStretch = -1; - int graphStretchY = -1; + int mouseDragLastX = -1; - int min; // used by mouseDragged to see if user + int mouseDragLastY = -1; - int max; // used by mouseDragged to see if user + DragMode dragMode = DragMode.Undefined; boolean mouseDragging = false; @@ -174,11 +181,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (e.isShiftDown()) { e.consume(); - if (e.getWheelRotation() > 0) + double wheelRotation = e.getPreciseWheelRotation(); + if (wheelRotation > 0) { av.getRanges().scrollRight(true); } - else + else if (wheelRotation < 0) { av.getRanges().scrollRight(false); } @@ -204,7 +212,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public Dimension getPreferredScrollableViewportSize() { - return getPreferredSize(); + Dimension ps = getPreferredSize(); + return new Dimension(ps.width, adjustForAlignFrame(false, ps.height)); } @Override @@ -284,7 +293,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (anot.length < av.getColumnSelection().getMax()) { - Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2]; + Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + + 2]; System.arraycopy(anot, 0, temp, 0, anot.length); anot = temp; aa[activeRow].annotations = anot; @@ -304,7 +314,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, else if (action.equals(LABEL)) { String exMesg = collectAnnotVals(anot, LABEL); - String label = JvOptionPane.showInputDialog(this, + String label = JvOptionPane.showInputDialog( MessageManager.getString("label.enter_label"), exMesg); if (label == null) @@ -336,24 +346,29 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } else if (action.equals(COLOUR)) { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_foreground_colour"), - Color.black); - - for (int index : av.getColumnSelection().getSelected()) + final Annotation[] fAnot = anot; + String title = MessageManager + .getString("label.select_foreground_colour"); + ColourChooserListener listener = new ColourChooserListener() { - if (!av.getAlignment().getHiddenColumns().isVisible(index)) - { - continue; - } - - if (anot[index] == null) + @Override + public void colourSelected(Color c) { - anot[index] = new Annotation("", "", ' ', 0); - } - - anot[index].colour = col; - } + HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); + for (int index : av.getColumnSelection().getSelected()) + { + if (hiddenColumns.isVisible(index)) + { + if (fAnot[index] == null) + { + fAnot[index] = new Annotation("", "", ' ', 0); + } + fAnot[index].colour = c; + } + }}; + }; + JalviewColourChooser.showColourChooser(this, + title, Color.black, listener); } else // HELIX, SHEET or STEM @@ -412,8 +427,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, anot[index] = new Annotation(label, "", type, 0); } - anot[index].secondaryStructure = type != 'S' ? type : label - .length() == 0 ? ' ' : label.charAt(0); + anot[index].secondaryStructure = type != 'S' ? type + : label.length() == 0 ? ' ' : label.charAt(0); anot[index].displayCharacter = label; } @@ -494,10 +509,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } /** - * DOCUMENT ME! + * Action on right mouse pressed on Mac is to show a pop-up menu for the + * annotation. Action on left mouse pressed is to find which annotation is + * pressed and mark the start of a column selection or graph resize operation. * * @param evt - * DOCUMENT ME! */ @Override public void mousePressed(MouseEvent evt) @@ -508,7 +524,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { return; } + mouseDragLastX = evt.getX(); + mouseDragLastY = evt.getY(); + /* + * add visible annotation heights until we reach the y + * position, to find which annotation it is in + */ int height = 0; activeRow = -1; @@ -528,11 +550,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } else if (aa[i].graph > 0) { - // Stretch Graph + /* + * we have clicked on a resizable graph annotation + */ graphStretch = i; - graphStretchY = y; } - break; } } @@ -598,17 +620,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } /** - * DOCUMENT ME! + * Action on mouse up is to clear mouse drag data and call mouseReleased on + * ScalePanel, to deal with defining the selection group (if any) defined by + * the mouse drag * * @param evt - * DOCUMENT ME! */ @Override public void mouseReleased(MouseEvent evt) { graphStretch = -1; - graphStretchY = -1; + mouseDragLastX = -1; + mouseDragLastY = -1; mouseDragging = false; + dragMode = DragMode.Undefined; ap.getScalePanel().mouseReleased(evt); /* @@ -631,14 +656,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void mouseEntered(MouseEvent evt) { + this.mouseDragging = false; ap.getScalePanel().mouseEntered(evt); } /** - * DOCUMENT ME! + * On leaving the panel, calls ScalePanel.mouseExited to deal with scrolling + * with column selection on a mouse drag * * @param evt - * DOCUMENT ME! */ @Override public void mouseExited(MouseEvent evt) @@ -655,21 +681,73 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void mouseDragged(MouseEvent evt) { - if (graphStretch > -1) + /* + * todo: if dragMode is Undefined: + * - set to Select if dx > dy + * - set to Resize if dy > dx + * - do nothing if dx == dy + */ + final int x = evt.getX(); + final int y = evt.getY(); + if (dragMode == DragMode.Undefined) { - av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - - evt.getY(); - if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0) + int dx = Math.abs(x - mouseDragLastX); + int dy = Math.abs(y - mouseDragLastY); + if (graphStretch == -1 || dx > dy) + { + /* + * mostly horizontal drag, or not a graph annotation + */ + dragMode = DragMode.Select; + } + else if (dy > dx) { - av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0; + /* + * mostly vertical drag + */ + dragMode = DragMode.Resize; } - graphStretchY = evt.getY(); - adjustPanelHeight(); - ap.paintAlignment(true); } - else + + if (dragMode == DragMode.Undefined) + { + /* + * drag is diagonal - defer deciding whether to + * treat as up/down or left/right + */ + return; + } + + try + { + if (dragMode == DragMode.Resize) + { + /* + * resize graph annotation if mouse was dragged up or down + */ + int deltaY = mouseDragLastY - evt.getY(); + if (deltaY != 0) + { + AlignmentAnnotation graphAnnotation = av.getAlignment() + .getAlignmentAnnotation()[graphStretch]; + int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY); + graphAnnotation.graphHeight = newHeight; + adjustPanelHeight(); + ap.paintAlignment(false, false); + } + } + else + { + /* + * for mouse drag left or right, delegate to + * ScalePanel to adjust the column selection + */ + ap.getScalePanel().mouseDragged(evt); + } + } finally { - ap.getScalePanel().mouseDragged(evt); + mouseDragLastX = x; + mouseDragLastY = y; } } @@ -719,7 +797,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (av.hasHiddenColumns()) { column = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(column); + .visibleToAbsoluteColumn(column); } AlignmentAnnotation ann = aa[row]; @@ -732,7 +810,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, else { this.setToolTipText(null); - ap.alignFrame.statusBar.setText(" "); + ap.alignFrame.setStatus(" "); } } @@ -777,6 +855,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { this.setToolTipText(JvSwingUtils.wrapTooltip(true, description)); } + else + { + this.setToolTipText(null); // no tooltip if null or empty description + } } else { @@ -819,8 +901,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, int seqIndex = av.getAlignment().findIndex(seqref); if (seqIndex != -1) { - text.append(", ") - .append(MessageManager.getString("label.sequence")) + text.append(", ").append(MessageManager.getString("label.sequence")) .append(" ").append(seqIndex + 1); char residue = seqref.getCharAt(column); if (!Comparison.isGap(residue)) @@ -829,16 +910,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, String name; if (av.getAlignment().isNucleotide()) { - name = ResidueProperties.nucleotideName.get(String - .valueOf(residue)); - text.append(" Nucleotide: ").append( - name != null ? name : residue); + name = ResidueProperties.nucleotideName + .get(String.valueOf(residue)); + text.append(" Nucleotide: ") + .append(name != null ? name : residue); } else { - name = 'X' == residue ? "X" : ('*' == residue ? "STOP" - : ResidueProperties.aa2Triplet.get(String - .valueOf(residue))); + name = 'X' == residue ? "X" + : ('*' == residue ? "STOP" + : ResidueProperties.aa2Triplet + .get(String.valueOf(residue))); text.append(" Residue: ").append(name != null ? name : residue); } int residuePos = seqref.findPosition(column); @@ -847,7 +929,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } - ap.alignFrame.statusBar.setText(text.toString()); + ap.alignFrame.setStatus(text.toString()); } /** @@ -889,6 +971,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } private volatile boolean imageFresh = false; + private Rectangle visibleRect = new Rectangle(), clipBounds = new Rectangle(); /** * DOCUMENT ME! @@ -899,32 +982,46 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void paintComponent(Graphics g) { + + // BH: note that this method is generally recommended to + // call super.paintComponent(g). Otherwise, the children of this + // component will not be rendered. That is not needed here + // because AnnotationPanel does not have any children. It is + // just a JPanel contained in a JViewPort. + + computeVisibleRect(visibleRect); + g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); + g.fillRect(0, 0, visibleRect.width, visibleRect.height); if (image != null) { - if (fastPaint || (getVisibleRect().width != g.getClipBounds().width) - || (getVisibleRect().height != g.getClipBounds().height)) + // BH 2018 optimizing generation of new Rectangle(). + if (fastPaint || (visibleRect.width != (clipBounds = g.getClipBounds(clipBounds)).width) + || (visibleRect.height != clipBounds.height)) { - g.drawImage(image, 0, 0, this); + + + g.drawImage(image, 0, 0, this); fastPaint = false; return; } } - imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + 1) - * av.getCharWidth(); + imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + + 1) * av.getCharWidth(); if (imgWidth < 1) { return; } + Graphics2D gg; if (image == null || imgWidth != image.getWidth(this) || image.getHeight(this) != getHeight()) { try { - image = new BufferedImage(imgWidth, ap.getAnnotationPanel() - .getHeight(), BufferedImage.TYPE_INT_RGB); + image = new BufferedImage(imgWidth, + ap.getAnnotationPanel().getHeight(), + BufferedImage.TYPE_INT_RGB); } catch (OutOfMemoryError oom) { try @@ -952,10 +1049,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, gg.setColor(Color.white); gg.fillRect(0, 0, imgWidth, image.getHeight()); imageFresh = true; - } + } else { + gg = (Graphics2D) image.getGraphics(); - drawComponent(gg, av.getRanges().getStartRes(), av.getRanges() - .getEndRes() + 1); + } + + drawComponent(gg, av.getRanges().getStartRes(), + av.getRanges().getEndRes() + 1); + gg.dispose(); imageFresh = false; g.drawImage(image, 0, 0, this); } @@ -971,9 +1072,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * @param horizontal * repaint with horizontal shift in alignment */ - public void fastPaint(int horizontal, boolean isresize) + public void fastPaint(int horizontal) { - if ((horizontal == 0) || gg == null + if ((horizontal == 0) || image == null || av.getAlignment().getAlignmentAnnotation() == null || av.getAlignment().getAlignmentAnnotation().length < 1 || av.isCalcInProgress()) @@ -985,42 +1086,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, int sr = av.getRanges().getStartRes(); int er = av.getRanges().getEndRes() + 1; int transX = 0; - long stime; - long mtime; - - if (isresize) - { - imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() - + 1) * av.getCharWidth(); - BufferedImage newimage = new BufferedImage(imgWidth, - ap.getAnnotationPanel().getHeight(), - BufferedImage.TYPE_INT_ARGB); + Graphics2D gg = (Graphics2D) image.getGraphics(); - gg = (Graphics2D) newimage.getGraphics(); - gg.setFont(av.getFont()); - gg.drawImage(image, null, 0, 0); - image = newimage; + gg.copyArea(0, 0, imgWidth, getHeight(), + -horizontal * av.getCharWidth(), 0); - transX = (er - horizontal - sr) * av.getCharWidth(); - sr = er - horizontal - sr; + if (horizontal > 0) // scrollbar pulled right, image to the left + { + transX = (er - sr - horizontal) * av.getCharWidth(); + sr = er - horizontal; } - else + else if (horizontal < 0) { - stime = System.currentTimeMillis(); - gg.copyArea(0, 0, imgWidth, getHeight(), - -horizontal * av.getCharWidth(), 0); - mtime = System.currentTimeMillis(); - - if (horizontal > 0) // scrollbar pulled right, image to the left - { - transX = (er - sr - horizontal) * av.getCharWidth(); - sr = er - horizontal; - } - else if (horizontal < 0) - { - er = sr - horizontal; - } + er = sr - horizontal; } gg.translate(transX, 0); @@ -1028,17 +1107,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, drawComponent(gg, sr, er); gg.translate(-transX, 0); - long dtime = System.currentTimeMillis(); + + gg.dispose(); + fastPaint = true; - repaint(); - long rtime = System.currentTimeMillis(); - if (debugRedraw) - { - System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t" - + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime) - + "\tRepaint call:\t" + (rtime - dtime)); - } + // Call repaint on alignment panel so that repaints from other alignment + // panel components can be aggregated. Otherwise performance of the overview + // window and others may be adversely affected. + av.getAlignPanel().repaint(); } private volatile boolean lastImageGood = false; @@ -1067,8 +1144,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // and draw a faded image until the calculation // has completed if (lastImageGood - && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage - .getHeight() != image.getHeight())) + && (fadedImage == null || fadedImage.getWidth() != imgWidth + || fadedImage.getHeight() != image.getHeight())) { // System.err.println("redraw faded image ("+(fadedImage==null ? // "null image" : "") + " lastGood="+lastImageGood+")"); @@ -1080,8 +1157,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, fadedG.setColor(Color.white); fadedG.fillRect(0, 0, imgWidth, image.getHeight()); - fadedG.setComposite(AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, .3f)); + fadedG.setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f)); fadedG.drawImage(image, 0, 0, this); } @@ -1122,8 +1199,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } - lastImageGood = renderer.drawComponent(this, av, g, activeRow, - startRes, endRes); + lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes, + endRes); if (!lastImageGood && fadedImage == null) { fadedImage = oldFaded; @@ -1176,7 +1253,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, ap = null; image = null; fadedImage = null; - gg = null; +// gg = null; _mwl = null; /* @@ -1192,14 +1269,68 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public void propertyChange(PropertyChangeEvent evt) { // Respond to viewport range changes (e.g. alignment panel was scrolled) - if (evt.getPropertyName().equals("startres")) + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + if (evt.getPropertyName().equals(ViewportRanges.STARTRES)) + { + fastPaint((int) evt.getNewValue() - (int) evt.getOldValue()); + } + else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)) { - fastPaint((int) evt.getNewValue() - (int) evt.getOldValue(), false); + fastPaint(((int[]) evt.getNewValue())[0] + - ((int[]) evt.getOldValue())[0]); + } + else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT)) + { + repaint(); } - else if (evt.getPropertyName().equals("endres")) + } + + /** + * computes the visible height of the annotation panel + * + * @param adjustPanelHeight + * - when false, just adjust existing height according to other + * windows + * @param annotationHeight + * @return height to use for the ScrollerPreferredVisibleSize + */ + public int adjustForAlignFrame(boolean adjustPanelHeight, + int annotationHeight) + { + /* + * Estimate available height in the AlignFrame for alignment + + * annotations. Deduct an estimate for title bar, menu bar, scale panel, + * hscroll, status bar, insets. + */ + int stuff = (ap.getViewName() != null ? 30 : 0) + + (Platform.isAMac() ? 120 : 140); + int availableHeight = ap.alignFrame.getHeight() - stuff; + int rowHeight = av.getCharHeight(); + + if (adjustPanelHeight) + { + int alignmentHeight = rowHeight * av.getAlignment().getHeight(); + + /* + * If not enough vertical space, maximize annotation height while keeping + * at least two rows of alignment visible + */ + if (annotationHeight + alignmentHeight > availableHeight) + { + annotationHeight = Math.min(annotationHeight, + availableHeight - 2 * rowHeight); + } + } + else { - // resize - fastPaint((int) evt.getNewValue() - (int) evt.getOldValue(), true); + // maintain same window layout whilst updating sliders + annotationHeight = Math.min(ap.annotationScroller.getSize().height, + availableHeight - 2 * rowHeight); } + return annotationHeight; } }