X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=e9ef19c03eee53a7f83cdfd88541c743b1c7627c;hp=403634782abaeabe5144cb4d62766e87f9011bd2;hb=71a3cc0202bd8b731f01e5706372e9bae047d592;hpb=58afea88095280d807e5c2ac8b9155de5ba3503c diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 4036347..e9ef19c 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,16 +20,51 @@ */ package jalview.gui; -import java.awt.*; -import java.awt.event.*; -import java.awt.image.*; - -import javax.swing.*; - -import jalview.datamodel.*; +import java.awt.AlphaComposite; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.Image; +import java.awt.Rectangle; +import java.awt.RenderingHints; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +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; + +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.Scrollable; +import javax.swing.ToolTipManager; + +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +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; /** * AnnotationPanel displays visible portion of annotation rows below unwrapped @@ -40,8 +75,13 @@ import jalview.util.MessageManager; */ 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"); @@ -74,7 +114,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public volatile BufferedImage fadedImage; - Graphics2D gg; + // private Graphics2D gg; public FontMetrics fm; @@ -85,16 +125,14 @@ 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; - boolean MAC = false; - // for editing cursor int cursorX = 0; @@ -112,9 +150,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ public AnnotationPanel(AlignmentPanel ap) { - - MAC = new jalview.util.Platform().isAMac(); - ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -131,6 +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) @@ -145,13 +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 @@ -175,7 +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 @@ -215,7 +254,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public void adjustmentValueChanged(AdjustmentEvent evt) { // update annotation label display - ap.alabels.setScrollOffset(-evt.getValue()); + ap.getAlabels().setScrollOffset(-evt.getValue()); } /** @@ -255,23 +294,28 @@ 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; } - if (evt.getActionCommand().equals(REMOVE)) + String action = evt.getActionCommand(); + if (action.equals(REMOVE)) { - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - anot[av.getColumnSelection().columnAt(i)] = null; + if (av.getAlignment().getHiddenColumns().isVisible(index)) + { + anot[index] = null; + } } } - else if (evt.getActionCommand().equals(LABEL)) + else if (action.equals(LABEL)) { - String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL); - String label = JOptionPane.showInputDialog(this, + String exMesg = collectAnnotVals(anot, LABEL); + String label = JvOptionPane.showInputDialog( MessageManager.getString("label.enter_label"), exMesg); if (label == null) @@ -284,19 +328,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, aa[activeRow].hasText = true; } - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - int index = av.getColumnSelection().columnAt(i); - - if (!av.getColumnSelection().isVisible(index)) + if (!av.getAlignment().getHiddenColumns().isVisible(index)) + { continue; + } if (anot[index] == null) { - anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that - // null exceptions - // aren't raised - // elsewhere. + anot[index] = new Annotation(label, "", ' ', 0); } else { @@ -304,47 +345,56 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } } - else if (evt.getActionCommand().equals(COLOUR)) + else if (action.equals(COLOUR)) { - Color col = JColorChooser.showDialog(this, - "Choose foreground colour", Color.black); - - for (int i = 0; i < av.getColumnSelection().size(); i++) + final Annotation[] fAnot = anot; + String title = MessageManager + .getString("label.select_foreground_colour"); + ColourChooserListener listener = new ColourChooserListener() { - int index = av.getColumnSelection().columnAt(i); - - if (!av.getColumnSelection().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 OR SHEET + // HELIX, SHEET or STEM { char type = 0; - String symbol = "\u03B1"; + String symbol = "\u03B1"; // alpha - if (evt.getActionCommand().equals(HELIX)) + if (action.equals(HELIX)) { type = 'H'; } - else if (evt.getActionCommand().equals(SHEET)) + else if (action.equals(SHEET)) { type = 'E'; - symbol = "\u03B2"; + symbol = "\u03B2"; // beta } // Added by LML to color stems - else if (evt.getActionCommand().equals(STEM)) + else if (action.equals(STEM)) { type = 'S'; - symbol = "\u03C3"; + int column = av.getColumnSelection().getSelectedRanges().get(0)[0]; + symbol = aa[activeRow].getDefaultRnaHelixSymbol(column); } if (!aa[activeRow].hasIcons) @@ -352,7 +402,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, aa[activeRow].hasIcons = true; } - String label = JOptionPane.showInputDialog(MessageManager + String label = JvOptionPane.showInputDialog(MessageManager .getString("label.enter_label_for_the_structure"), symbol); if (label == null) @@ -363,67 +413,88 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if ((label.length() > 0) && !aa[activeRow].hasText) { aa[activeRow].hasText = true; - if (evt.getActionCommand().equals(STEM)) + if (action.equals(STEM)) { aa[activeRow].showAllColLabels = true; } } - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - int index = av.getColumnSelection().columnAt(i); - - if (!av.getColumnSelection().isVisible(index)) + if (!av.getAlignment().getHiddenColumns().isVisible(index)) + { continue; + } if (anot[index] == null) { anot[index] = new Annotation(label, "", type, 0); } - anot[index].secondaryStructure = type; + anot[index].secondaryStructure = type != 'S' ? type + : label.length() == 0 ? ' ' : label.charAt(0); anot[index].displayCharacter = label; } } + av.getAlignment().validateAnnotation(aa[activeRow]); ap.alignmentChanged(); - + ap.alignFrame.setMenusForViewport(); adjustPanelHeight(); repaint(); return; } - private String collectAnnotVals(Annotation[] anot, - ColumnSelection columnSelection, String label2) + /** + * Returns any existing annotation concatenated as a string. For each + * annotation, takes the description, if any, else the secondary structure + * character (if type is HELIX, SHEET or STEM), else the display character (if + * type is LABEL). + * + * @param anots + * @param type + * @return + */ + private String collectAnnotVals(Annotation[] anots, String type) { - String collatedInput = ""; + // TODO is this method wanted? why? 'last' is not used + + StringBuilder collatedInput = new StringBuilder(64); String last = ""; ColumnSelection viscols = av.getColumnSelection(); - // TODO: refactor and save av.getColumnSelection for efficiency - for (int i = 0; i < columnSelection.size(); i++) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + + /* + * 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()); + Collections.sort(selected); + for (int index : selected) { - int index = columnSelection.columnAt(i); // always check for current display state - just in case - if (!viscols.isVisible(index)) + if (!hidden.isVisible(index)) + { continue; + } String tlabel = null; - if (anot[index] != null) + if (anots[index] != null) { // LML added stem code - if (label2.equals(HELIX) || label2.equals(SHEET) - || label2.equals(STEM) || label2.equals(LABEL)) + if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM) + || type.equals(LABEL)) { - tlabel = anot[index].description; + tlabel = anots[index].description; if (tlabel == null || tlabel.length() < 1) { - if (label2.equals(HELIX) || label2.equals(SHEET) - || label2.equals(STEM)) + if (type.equals(HELIX) || type.equals(SHEET) + || type.equals(STEM)) { - tlabel = "" + anot[index].secondaryStructure; + tlabel = "" + anots[index].secondaryStructure; } else { - tlabel = "" + anot[index].displayCharacter; + tlabel = "" + anots[index].displayCharacter; } } } @@ -431,20 +502,21 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { if (last.length() > 0) { - collatedInput += " "; + collatedInput.append(" "); } - collatedInput += tlabel; + collatedInput.append(tlabel); } } } - return collatedInput; + return collatedInput.toString(); } /** - * 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) @@ -455,10 +527,17 @@ 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; + final int y = evt.getY(); for (int i = 0; i < aa.length; i++) { if (aa[i].visible) @@ -466,7 +545,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, height += aa[i].height; } - if (evt.getY() < height) + if (y < height) { if (aa[i].editable) { @@ -474,79 +553,105 @@ 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 = evt.getY(); } - break; } } - if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1) + /* + * isPopupTrigger fires in mousePressed on Mac, + * not until mouseRelease on Windows + */ + if (evt.isPopupTrigger() && activeRow != -1) { - if (av.getColumnSelection() == null) - { - return; - } + showPopupMenu(y, evt.getX()); + return; + } - JPopupMenu pop = new JPopupMenu( - MessageManager.getString("label.structure_type")); - JMenuItem item; - /* - * Just display the needed structure options - */ - if (av.getAlignment().isNucleotide() == true) - { - item = new JMenuItem(STEM); - item.addActionListener(this); - pop.add(item); - } - else - { - item = new JMenuItem(HELIX); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(SHEET); - item.addActionListener(this); - pop.add(item); - } - item = new JMenuItem(LABEL); + ap.getScalePanel().mousePressed(evt); + } + + /** + * Construct and display a context menu at the right-click position + * + * @param y + * @param x + */ + void showPopupMenu(final int y, int x) + { + if (av.getColumnSelection() == null + || av.getColumnSelection().isEmpty()) + { + return; + } + + JPopupMenu pop = new JPopupMenu( + MessageManager.getString("label.structure_type")); + JMenuItem item; + /* + * Just display the needed structure options + */ + if (av.getAlignment().isNucleotide()) + { + item = new JMenuItem(STEM); item.addActionListener(this); pop.add(item); - item = new JMenuItem(COLOUR); + } + else + { + item = new JMenuItem(HELIX); item.addActionListener(this); pop.add(item); - item = new JMenuItem(REMOVE); + item = new JMenuItem(SHEET); item.addActionListener(this); pop.add(item); - pop.show(this, evt.getX(), evt.getY()); - - return; } - - if (aa == null) - { - return; - } - - ap.scalePanel.mousePressed(evt); - + item = new JMenuItem(LABEL); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(COLOUR); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(REMOVE); + item.addActionListener(this); + pop.add(item); + pop.show(this, x, y); } /** - * 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; - ap.scalePanel.mouseReleased(evt); + if (dragMode == DragMode.Resize) + { + ap.adjustAnnotationHeight(); + } + dragMode = DragMode.Undefined; + ap.getScalePanel().mouseReleased(evt); + + /* + * isPopupTrigger is set in mouseReleased on Windows + * (in mousePressed on Mac) + */ + if (evt.isPopupTrigger() && activeRow != -1) + { + showPopupMenu(evt.getY(), evt.getX()); + } + } /** @@ -558,65 +663,173 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void mouseEntered(MouseEvent evt) { - ap.scalePanel.mouseEntered(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) { - ap.scalePanel.mouseExited(evt); + ap.getScalePanel().mouseExited(evt); } /** - * DOCUMENT ME! + * Action on starting or continuing a mouse drag. There are two possible + * actions: + * + * 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) { - av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0; + /* + * mostly horizontal drag, or not a graph annotation + */ + dragMode = DragMode.Select; + } + else if (dy > dx) + { + /* + * mostly vertical drag + */ + dragMode = DragMode.Resize; } - graphStretchY = evt.getY(); - adjustPanelHeight(); - ap.paintAlignment(true); } - else + + if (dragMode == DragMode.Undefined) { - ap.scalePanel.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; } } /** - * DOCUMENT ME! + * Constructs the tooltip, and constructs and displays a status message, for + * the current mouse position * * @param evt - * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent evt) { + int yPos = evt.getY(); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); - if (aa == null) + int row = getRowIndex(yPos, aa); + + if (row == -1) { this.setToolTipText(null); return; } + int column = (evt.getX() / av.getCharWidth()) + + av.getRanges().getStartRes(); + column = Math.min(column, av.getRanges().getEndRes()); + + if (av.hasHiddenColumns()) + { + column = av.getAlignment().getHiddenColumns() + .visibleToAbsoluteColumn(column); + } + + AlignmentAnnotation ann = aa[row]; + if (row > -1 && ann.annotations != null + && column < ann.annotations.length) + { + String toolTip = buildToolTip(ann, column, aa); + setToolTipText(toolTip == null ? null + : JvSwingUtils.wrapTooltip(true, toolTip)); + String msg = getStatusMessage(av.getAlignment(), column, ann); + ap.alignFrame.setStatus(msg); + } + else + { + this.setToolTipText(null); + ap.alignFrame.setStatus(" "); + } + } + + /** + * 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; @@ -627,80 +840,126 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, height += aa[i].height; } - if (evt.getY() < height) + if (height > yPos) { row = i; - break; } } + return row; + } - if (row == -1) - { - this.setToolTipText(null); - return; - } - - int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - - if (av.hasHiddenColumns()) - { - res = av.getColumnSelection().adjustForHiddenColumns(res); - } - - if (row > -1 && aa[row].annotations != null - && res < aa[row].annotations.length) + /** + * Answers a tooltip for the annotation at the current mouse position, not + * wrapped in <html> tags (apply if wanted). Answers null if there is no + * tooltip to show. + * + * @param ann + * @param column + * @param anns + */ + static String buildToolTip(AlignmentAnnotation ann, int column, + AlignmentAnnotation[] anns) + { + String tooltip = null; + if (ann.graphGroup > -1) { - if (aa[row].graphGroup > -1) + StringBuilder tip = new StringBuilder(32); + boolean first = true; + for (int i = 0; i < anns.length; i++) { - StringBuffer tip = new StringBuffer(""); - for (int gg = 0; gg < aa.length; gg++) + if (anns[i].graphGroup == ann.graphGroup + && anns[i].annotations[column] != null) { - if (aa[gg].graphGroup == aa[row].graphGroup - && aa[gg].annotations[res] != null) + if (!first) { - tip.append(aa[gg].label + " " - + aa[gg].annotations[res].description + "
"); + tip.append("
"); + } + first = false; + tip.append(anns[i].label); + String description = anns[i].annotations[column].description; + if (description != null && description.length() > 0) + { + tip.append(" ").append(description); } - } - if (tip.length() != 6) - { - tip.setLength(tip.length() - 4); - this.setToolTipText(tip.toString() + ""); } } - else if (aa[row].annotations[res] != null - && aa[row].annotations[res].description != null - && aa[row].annotations[res].description.length() > 0) - { - this.setToolTipText("" - + JvSwingUtils - .wrapTooltip(aa[row].annotations[res].description) - + ""); - } - else + tooltip = first ? null : tip.toString(); + } + else if (column < ann.annotations.length + && ann.annotations[column] != null) + { + tooltip = ann.annotations[column].description; + } + + return tooltip; + } + + /** + * Constructs and returns the status bar message + * + * @param al + * @param column + * @param ann + */ + static String getStatusMessage(AlignmentI al, int column, + AlignmentAnnotation ann) + { + /* + * show alignment column and annotation description if any + */ + StringBuilder text = new StringBuilder(32); + text.append(MessageManager.getString("label.column")).append(" ") + .append(column + 1); + + if (column < ann.annotations.length && ann.annotations[column] != null) + { + String description = ann.annotations[column].description; + if (description != null && description.trim().length() > 0) { - // clear the tooltip. - this.setToolTipText(null); + text.append(" ").append(description); } + } - if (aa[row].annotations[res] != null) + /* + * if the annotation is sequence-specific, show the sequence number + * in the alignment, and (if not a gap) the residue and position + */ + SequenceI seqref = ann.sequenceRef; + if (seqref != null) + { + int seqIndex = al.findIndex(seqref); + if (seqIndex != -1) { - StringBuffer text = new StringBuffer("Sequence position " - + (res + 1)); - - if (aa[row].annotations[res].description != null) + text.append(", ").append(MessageManager.getString("label.sequence")) + .append(" ").append(seqIndex + 1); + char residue = seqref.getCharAt(column); + if (!Comparison.isGap(residue)) { - text.append(" " + aa[row].annotations[res].description); + text.append(" "); + String name; + if (al.isNucleotide()) + { + 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))); + text.append(" Residue: ").append(name != null ? name : residue); + } + int residuePos = seqref.findPosition(column); + text.append(" (").append(residuePos).append(")"); } - - ap.alignFrame.statusBar.setText(text.toString()); } } - else - { - this.setToolTipText(null); - } + + return text.toString(); } /** @@ -723,10 +982,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1, int y1) { - int pady = av.charHeight / 5; + int pady = av.getCharHeight() / 5; int charOffset = 0; graphics.setColor(Color.black); - graphics.fillRect(x1, y1, av.charWidth, av.charHeight); + graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight()); if (av.validCharWidth) { @@ -734,15 +993,18 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, char s = seq.getCharAt(res); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; + charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; graphics.drawString(String.valueOf(s), charOffset + x1, - (y1 + av.charHeight) - pady); + (y1 + av.getCharHeight()) - pady); } } private volatile boolean imageFresh = false; + private Rectangle visibleRect = new Rectangle(), + clipBounds = new Rectangle(); + /** * DOCUMENT ME! * @@ -752,28 +1014,46 @@ 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); fastPaint = false; return; } } - imgWidth = (av.endRes - av.startRes + 1) * av.charWidth; + 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.annotationPanel.getHeight(), + image = new BufferedImage(imgWidth, + ap.getAnnotationPanel().getHeight(), BufferedImage.TYPE_INT_RGB); } catch (OutOfMemoryError oom) { @@ -803,8 +1083,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, gg.fillRect(0, 0, imgWidth, image.getHeight()); imageFresh = true; } + else + { + gg = (Graphics2D) image.getGraphics(); - drawComponent(gg, av.startRes, av.endRes + 1); + } + + drawComponent(gg, av.getRanges().getStartRes(), + av.getRanges().getEndRes() + 1); + gg.dispose(); imageFresh = false; g.drawImage(image, 0, 0, this); } @@ -822,7 +1109,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ 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()) @@ -830,39 +1117,42 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, repaint(); return; } - long stime = System.currentTimeMillis(); - gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0); - long mtime = System.currentTimeMillis(); - int sr = av.startRes; - int er = av.endRes + 1; + + int sr = av.getRanges().getStartRes(); + int er = av.getRanges().getEndRes() + 1; int transX = 0; - if (horizontal > 0) // scrollbar pulled right, image to the left - { - transX = (er - sr - horizontal) * av.charWidth; - sr = er - horizontal; - } - else if (horizontal < 0) - { - er = sr - horizontal; - } + Graphics2D gg = (Graphics2D) image.getGraphics(); + if (imgWidth>Math.abs(horizontal*av.getCharWidth())) { + //scroll is less than imgWidth away so can re-use buffered graphics + 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(); + sr = er - horizontal; + } + else if (horizontal < 0) + { + er = sr - horizontal; + } + } gg.translate(transX, 0); 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; @@ -891,8 +1181,8 @@ 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+")"); @@ -904,8 +1194,8 @@ 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); } @@ -924,7 +1214,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } g.setColor(Color.white); - g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight()); + g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight()); g.setFont(av.getFont()); if (fm == null) @@ -946,8 +1236,8 @@ 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; @@ -977,15 +1267,107 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public int[] getVisibleVRange() { - if (ap != null && ap.alabels != null) + if (ap != null && ap.getAlabels() != null) { - int sOffset = -ap.alabels.scrollOffset; + int sOffset = -ap.getAlabels().getScrollOffset(); int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight(); bounds[0] = sOffset; bounds[1] = visHeight; return bounds; } else + { return null; + } + } + + /** + * Try to ensure any references held are nulled + */ + public void dispose() + { + av = null; + ap = null; + image = null; + fadedImage = null; + // gg = null; + _mwl = null; + + /* + * I created the renderer so I will dispose of it + */ + if (renderer != null) + { + 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.isAMacAndNotJS() ? 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; } }