X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=10fc3cf8358d2f53d5f69867b267badd53d42821;hb=e0556caa4fb141cfce47d03a0750fd5364582ce7;hp=919356f28f3064e6cc57031a3c2fb8cb37068dd9;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 919356f..10fc3cf 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -21,6 +21,7 @@ package jalview.gui; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; @@ -30,6 +31,9 @@ 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; @@ -50,6 +54,7 @@ import java.awt.event.MouseMotionListener; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import java.awt.image.BufferedImage; +import java.beans.PropertyChangeEvent; import java.util.ArrayList; import java.util.Collections; import java.util.List; @@ -70,8 +75,13 @@ import javax.swing.ToolTipManager; */ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, MouseListener, MouseWheelListener, MouseMotionListener, - ActionListener, AdjustmentListener, Scrollable + ActionListener, AdjustmentListener, Scrollable, ViewportListenerI { + enum DragMode + { + Select, Resize, Undefined + }; + String HELIX = MessageManager.getString("label.helix"); String SHEET = MessageManager.getString("label.sheet"); @@ -115,11 +125,11 @@ 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; @@ -156,6 +166,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // and then set our own listener to consume all mousewheel events ap.annotationScroller.addMouseWheelListener(this); renderer = new AnnotationRenderer(); + + av.getRanges().addPropertyChangeListener(this); } public AnnotationPanel(AlignViewport av) @@ -170,13 +182,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (e.isShiftDown()) { e.consume(); - if (e.getWheelRotation() > 0) + double wheelRotation = e.getPreciseWheelRotation(); + if (wheelRotation > 0) { - ap.scrollRight(true); + av.getRanges().scrollRight(true); } - else + else if (wheelRotation < 0) { - ap.scrollRight(false); + av.getRanges().scrollRight(false); } } else @@ -200,7 +213,8 @@ 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 @@ -280,7 +294,8 @@ 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; @@ -408,8 +423,8 @@ 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; } @@ -447,7 +462,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * the selection list (read-only view) is in selection order, not * column order; make a copy so we can sort it */ - List selected = new ArrayList(viscols.getSelected()); + List selected = new ArrayList<>(viscols.getSelected()); Collections.sort(selected); for (int index : selected) { @@ -490,10 +505,11 @@ 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) @@ -504,7 +520,13 @@ 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; @@ -524,11 +546,11 @@ 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; } } @@ -594,17 +616,24 @@ 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; + if (dragMode == DragMode.Resize) + { + ap.adjustAnnotationHeight(); + } + dragMode = DragMode.Undefined; ap.getScalePanel().mouseReleased(evt); /* @@ -643,29 +672,90 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } /** - * DOCUMENT ME! + * Action on starting or continuing a mouse drag. There are two possible + * actions: + *
    + *
  • drag up or down on a graphed annotation increases or decreases the + * height of the graph
    • + *
  • dragging left or right selects the columns dragged across
    • + *
+ * A drag on a graph annotation is treated as column selection if it starts + * with more horizontal than vertical movement, and as resize if it starts + * with more vertical than horizontal movement. Once started, the drag does + * not change mode. * * @param evt - * DOCUMENT ME! */ @Override public void mouseDragged(MouseEvent evt) { - if (graphStretch > -1) + /* + * 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) { - ap.getScalePanel().mouseDragged(evt); + /* + * 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 + { + mouseDragLastX = x; + mouseDragLastY = y; } } @@ -678,30 +768,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void mouseMoved(MouseEvent evt) { + int yPos = evt.getY(); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); - if (aa == null) - { - this.setToolTipText(null); - return; - } - - int row = -1; - int height = 0; - - for (int i = 0; i < aa.length; i++) - { - if (aa[i].visible) - { - height += aa[i].height; - } - - if (evt.getY() < height) - { - row = i; - break; - } - } + int row = getRowIndex(yPos, aa); if (row == -1) { @@ -711,37 +781,75 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, int column = (evt.getX() / av.getCharWidth()) + av.getRanges().getStartRes(); + column = Math.min(column, av.getRanges().getEndRes()); if (av.hasHiddenColumns()) { column = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(column); + .visibleToAbsoluteColumn(column); } AlignmentAnnotation ann = aa[row]; if (row > -1 && ann.annotations != null && column < ann.annotations.length) { - buildToolTip(ann, column, aa); - setStatusMessage(column, ann); + setToolTipText(buildToolTip(ann, column, aa)); + String msg = getStatusMessage(av.getAlignment(), column, ann); + ap.alignFrame.setStatus(msg); } else { this.setToolTipText(null); - ap.alignFrame.statusBar.setText(" "); + ap.alignFrame.setStatus(" "); } } /** - * Builds a tooltip for the annotation at the current mouse position. + * Answers the index in the annotations array of the visible annotation at the + * given y position. This is done by adding the heights of visible annotations + * until the y position has been exceeded. Answers -1 if no annotations are + * visible, or the y position is below all annotations. + * + * @param yPos + * @param aa + * @return + */ + static int getRowIndex(int yPos, AlignmentAnnotation[] aa) + { + if (aa == null) + { + return -1; + } + int row = -1; + int height = 0; + + for (int i = 0; i < aa.length; i++) + { + if (aa[i].visible) + { + height += aa[i].height; + } + + if (height > yPos) + { + row = i; + break; + } + } + return row; + } + + /** + * Answers a tooltip for the annotation at the current mouse position * * @param ann * @param column * @param anns */ - void buildToolTip(AlignmentAnnotation ann, int column, + static String buildToolTip(AlignmentAnnotation ann, int column, AlignmentAnnotation[] anns) { + String tooltip = null; if (ann.graphGroup > -1) { StringBuilder tip = new StringBuilder(32); @@ -763,31 +871,39 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (tip.length() != 6) { tip.setLength(tip.length() - 4); - this.setToolTipText(tip.toString() + ""); + tooltip = tip.toString() + ""; } } - else if (ann.annotations[column] != null) + else if (column < ann.annotations.length + && ann.annotations[column] != null) { String description = ann.annotations[column].description; if (description != null && description.length() > 0) { - this.setToolTipText(JvSwingUtils.wrapTooltip(true, description)); + tooltip = JvSwingUtils.wrapTooltip(true, description); + } + else + { + tooltip = null; // no tooltip if null or empty description } } else { // clear the tooltip. - this.setToolTipText(null); + tooltip = null; } + return tooltip; } /** - * Constructs and displays the status bar message + * Constructs and returns the status bar message * + * @param al * @param column * @param ann */ - void setStatusMessage(int column, AlignmentAnnotation ann) + static String getStatusMessage(AlignmentI al, int column, + AlignmentAnnotation ann) { /* * show alignment column and annotation description if any @@ -796,7 +912,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, text.append(MessageManager.getString("label.column")).append(" ") .append(column + 1); - if (ann.annotations[column] != null) + if (column < ann.annotations.length && ann.annotations[column] != null) { String description = ann.annotations[column].description; if (description != null && description.trim().length() > 0) @@ -812,29 +928,29 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, SequenceI seqref = ann.sequenceRef; if (seqref != null) { - int seqIndex = av.getAlignment().findIndex(seqref); + int seqIndex = al.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)) { text.append(" "); String name; - if (av.getAlignment().isNucleotide()) + if (al.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); @@ -843,7 +959,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } - ap.alignFrame.statusBar.setText(text.toString()); + return text.toString(); } /** @@ -895,6 +1011,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void paintComponent(Graphics g) { + super.paintComponent(g); + g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); @@ -908,8 +1026,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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; @@ -919,8 +1037,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { 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 @@ -949,9 +1068,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, gg.fillRect(0, 0, imgWidth, image.getHeight()); imageFresh = true; } - - drawComponent(gg, av.getRanges().getStartRes(), av.getRanges() - .getEndRes() + 1); + + drawComponent(gg, av.getRanges().getStartRes(), + av.getRanges().getEndRes() + 1); imageFresh = false; g.drawImage(image, 0, 0, this); } @@ -977,14 +1096,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, repaint(); return; } - long stime = System.currentTimeMillis(); - gg.copyArea(0, 0, imgWidth, getHeight(), - -horizontal * av.getCharWidth(), 0); - long mtime = System.currentTimeMillis(); + int sr = av.getRanges().getStartRes(); int er = av.getRanges().getEndRes() + 1; int transX = 0; + gg.copyArea(0, 0, imgWidth, getHeight(), + -horizontal * av.getCharWidth(), 0); + if (horizontal > 0) // scrollbar pulled right, image to the left { transX = (er - sr - horizontal) * av.getCharWidth(); @@ -1000,17 +1119,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, drawComponent(gg, sr, er); gg.translate(-transX, 0); - long dtime = System.currentTimeMillis(); + 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; @@ -1039,8 +1154,8 @@ 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+")"); @@ -1052,8 +1167,8 @@ 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); } @@ -1094,8 +1209,8 @@ 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; @@ -1159,4 +1274,73 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, renderer.dispose(); } } + + @Override + public void propertyChange(PropertyChangeEvent evt) + { + // Respond to viewport range changes (e.g. alignment panel was scrolled) + // 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())[0] + - ((int[]) evt.getOldValue())[0]); + } + else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT)) + { + repaint(); + } + } + + /** + * 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 + { + // maintain same window layout whilst updating sliders + annotationHeight = Math.min(ap.annotationScroller.getSize().height, + availableHeight - 2 * rowHeight); + } + return annotationHeight; + } }