*/
package jalview.gui;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-import jalview.renderer.AwtRenderPanelI;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-
import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.Dimension;
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.JColorChooser;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
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
* alignment
*/
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");
public volatile BufferedImage fadedImage;
- Graphics2D gg;
+ // private Graphics2D gg;
public FontMetrics fm;
// 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;
*/
public AnnotationPanel(AlignmentPanel ap)
{
-
- MAC = jalview.util.Platform.isAMac();
-
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
// 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)
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
@Override
public Dimension getPreferredScrollableViewportSize()
{
- return getPreferredSize();
+ Dimension ps = getPreferredSize();
+ return new Dimension(ps.width, adjustForAlignFrame(false, ps.height));
}
@Override
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;
String action = evt.getActionCommand();
if (action.equals(REMOVE))
{
- for (int sel : av.getColumnSelection().getSelected())
+ for (int index : av.getColumnSelection().getSelected())
{
- anot[sel] = null;
+ if (av.getAlignment().getHiddenColumns().isVisible(index))
+ {
+ anot[index] = null;
+ }
}
}
else if (action.equals(LABEL))
{
String exMesg = collectAnnotVals(anot, LABEL);
- String label = JOptionPane.showInputDialog(this,
+ String label = JvOptionPane.showInputDialog(
MessageManager.getString("label.enter_label"), exMesg);
if (label == null)
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
}
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.getColumnSelection().isVisible(index))
+ @Override
+ public void colourSelected(Color c)
{
- continue;
- }
-
- if (anot[index] == null)
- {
- 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
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)
}
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
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;
}
return;
}
- private String collectAnnotVals(Annotation[] anot, 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 index : viscols.getSelected())
+ 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<Integer> selected = new ArrayList<>(viscols.getSelected());
+ Collections.sort(selected);
+ for (int index : selected)
{
// 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;
}
}
}
{
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)
{
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)
height += aa[i].height;
}
- if (evt.getY() < height)
+ if (y < height)
{
if (aa[i].editable)
{
}
else if (aa[i].graph > 0)
{
- // Stretch Graph
+ /*
+ * we have clicked on a resizable graph annotation
+ */
graphStretch = i;
- graphStretchY = evt.getY();
}
-
break;
}
}
+ /*
+ * isPopupTrigger fires in mousePressed on Mac,
+ * not until mouseRelease on Windows
+ */
if (evt.isPopupTrigger() && activeRow != -1)
{
- if (av.getColumnSelection() == null
- || av.getColumnSelection().isEmpty())
- {
- 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())
- {
- 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;
}
-
- ap.getScalePanel().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;
+ 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());
+ }
+
}
/**
@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)
}
/**
- * DOCUMENT ME!
+ * Action on starting or continuing a mouse drag. There are two possible
+ * actions:
+ * <ul>
+ * <li>drag up or down on a graphed annotation increases or decreases the
+ * height of the graph</li>
+ * <li>dragging left or right selects the columns dragged across</li>
+ * </ul>
+ * 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.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;
}
}
@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)
{
return;
}
- int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+ int column = (evt.getX() / av.getCharWidth())
+ + av.getRanges().getStartRes();
+ column = Math.min(column, av.getRanges().getEndRes());
if (av.hasHiddenColumns())
{
- column = av.getColumnSelection().adjustForHiddenColumns(column);
+ column = av.getAlignment().getHiddenColumns()
+ .visibleToAbsoluteColumn(column);
}
AlignmentAnnotation ann = aa[row];
if (row > -1 && ann.annotations != null
&& column < ann.annotations.length)
{
- buildToolTip(ann, column, aa);
- setStatusMessage(column, ann);
+ 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.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, not
+ * wrapped in <html> tags (apply if wanted). Answers null if there is no
+ * tooltip to show.
*
* @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);
- tip.append("<html>");
+ boolean first = true;
for (int i = 0; i < anns.length; i++)
{
if (anns[i].graphGroup == ann.graphGroup
&& anns[i].annotations[column] != null)
{
+ if (!first)
+ {
+ tip.append("<br>");
+ }
+ first = false;
tip.append(anns[i].label);
String description = anns[i].annotations[column].description;
if (description != null && description.length() > 0)
{
tip.append(" ").append(description);
}
- tip.append("<br>");
}
}
- if (tip.length() != 6)
- {
- tip.setLength(tip.length() - 4);
- this.setToolTipText(tip.toString() + "</html>");
- }
+ tooltip = first ? null : 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));
- }
- }
- else
- {
- // clear the tooltip.
- this.setToolTipText(null);
+ tooltip = ann.annotations[column].description;
}
+
+ 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
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)
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"))
- .append(" ")
- .append(seqIndex + 1);
+ 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 (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(residue).append(" (")
- .append(residuePos).append(")");
+ text.append(" (").append(residuePos).append(")");
}
}
}
- ap.alignFrame.statusBar.setText(text.toString());
+ return text.toString();
}
/**
private volatile boolean imageFresh = false;
+ private Rectangle visibleRect = new Rectangle(),
+ clipBounds = new Rectangle();
+
/**
* DOCUMENT ME!
*
@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.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
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);
}
*/
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())
repaint();
return;
}
- long stime = System.currentTimeMillis();
- gg.copyArea(0, 0, imgWidth, getHeight(),
- -horizontal * av.getCharWidth(), 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.getCharWidth();
- 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;
// 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+")");
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);
}
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;
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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff