X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=c9fa597987f80ad288aec7172c47950d925ae829;hb=0d74306f282be2d15eeb5d8de53a949c0124a0a5;hp=d97c80f78a0c5f0714f119bf97a9f067932ab88a;hpb=893f1fefbcf73ae49776c667b110483ba26ee376;p=jalview.git
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index d97c80f..bd903b3 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,888 +1,1137 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import jalview.datamodel.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-
-import java.util.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class AnnotationPanel extends JPanel implements MouseListener,
- MouseMotionListener, ActionListener, AdjustmentListener
-{
- static String HELIX = "Helix";
- static String SHEET = "Sheet";
- static String LABEL = "Label";
- static String REMOVE = "Remove Annotation";
- static String COLOUR = "Colour";
- static Color HELIX_COLOUR = Color.red.darker();
- static Color SHEET_COLOUR = Color.green.darker().darker();
-
- /** DOCUMENT ME!! */
- public static int GRAPH_HEIGHT = 40;
- AlignViewport av;
- AlignmentPanel ap;
- int activeRow = -1;
- Vector activeRes;
- BufferedImage image;
- Graphics2D gg;
- FontMetrics fm;
- int imgWidth = 0;
- boolean fastPaint = false;
-
- /**
- * Creates a new AnnotationPanel object.
- *
- * @param ap DOCUMENT ME!
- */
- public AnnotationPanel(AlignmentPanel ap)
- {
- ToolTipManager.sharedInstance().registerComponent(this);
- ToolTipManager.sharedInstance().setInitialDelay(0);
- ToolTipManager.sharedInstance().setDismissDelay(10000);
- this.ap = ap;
- av = ap.av;
- this.setLayout(null);
- addMouseListener(this);
- addMouseMotionListener(this);
- ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
- }
-
- public AnnotationPanel(AlignViewport av)
- {
- this.av = av;
- }
-
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- ap.alabels.setScrollOffset(-evt.getValue());
- }
-
- /**
- * DOCUMENT ME!
- */
- public int adjustPanelHeight()
- {
- // setHeight of panels
- image = null;
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- int height = 0;
-
- if (aa != null)
- {
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- continue;
- }
-
- aa[i].height = 0;
-
- if (aa[i].hasText)
- {
- aa[i].height += av.charHeight;
- }
-
- if (aa[i].hasIcons)
- {
- aa[i].height += 16;
- }
-
- if (aa[i].isGraph)
- {
- aa[i].height += GRAPH_HEIGHT;
- }
-
- if (aa[i].height == 0)
- {
- aa[i].height = 20;
- }
-
- height += aa[i].height;
- }
- }
- else
- {
- height = 20;
- }
-
- this.setPreferredSize(new Dimension(1, height));
-
- return height;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param col DOCUMENT ME!
- */
- public void removeEditableColumn(int col)
- {
- if (activeRow == -1)
- {
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- if(aa==null)
- return;
-
- for (int j = 0; j < aa.length; j++)
- {
- if (aa[j].editable)
- {
- activeRow = j;
-
- break;
- }
- }
- }
-
- if ((activeRes != null) && activeRes.contains(String.valueOf(col)))
- {
- activeRes.removeElement(String.valueOf(col));
- }
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param col DOCUMENT ME!
- */
- public void addEditableColumn(int col)
- {
- if (activeRow == -1)
- {
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- if(aa==null)
- return;
-
- for (int j = 0; j < aa.length; j++)
- {
- if (aa[j].editable)
- {
- activeRow = j;
-
- break;
- }
- }
- }
-
- if (activeRes == null)
- {
- activeRes = new Vector();
- }
-
- if (!activeRes.contains(String.valueOf(col)))
- {
- activeRes.addElement(String.valueOf(col));
- }
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void actionPerformed(ActionEvent evt)
- {
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- Annotation[] anot = aa[activeRow].annotations;
-
- if (evt.getActionCommand().equals(REMOVE))
- {
- for (int i = 0; i < activeRes.size(); i++)
- {
- anot[Integer.parseInt(activeRes.get(i).toString())] = null;
- anot[Integer.parseInt(activeRes.get(i).toString())] = null;
- }
- }
- else if (evt.getActionCommand().equals(LABEL))
- {
- String label = JOptionPane.showInputDialog(this, "Enter Label ",
- "Enter label", JOptionPane.QUESTION_MESSAGE);
-
- if (label == null)
- {
- return;
- }
-
- if ((label.length() > 0) && !aa[activeRow].hasText)
- {
- aa[activeRow].hasText = true;
- }
-
- for (int i = 0; i < activeRes.size(); i++)
- {
- int index = Integer.parseInt(activeRes.get(i).toString());
-
- if (anot[index] == null)
- {
- anot[index] = new Annotation(label, "", ' ', 0);
- }
-
- anot[index].displayCharacter = label;
- }
- }
- else if (evt.getActionCommand().equals(COLOUR))
- {
- Color col = JColorChooser.showDialog(this,
- "Choose foreground colour", Color.black);
-
- for (int i = 0; i < activeRes.size(); i++)
- {
- int index = Integer.parseInt(activeRes.get(i).toString());
-
- if (anot[index] == null)
- {
- anot[index] = new Annotation("", "", ' ', 0);
- }
-
- anot[index].colour = col;
- }
- }
- else // HELIX OR SHEET
- {
- char type = 0;
- String symbol = "\u03B1";
-
- if (evt.getActionCommand().equals(HELIX))
- {
- type = 'H';
- }
- else if (evt.getActionCommand().equals(SHEET))
- {
- type = 'E';
- symbol = "\u03B2";
- }
-
- if (!aa[activeRow].hasIcons)
- {
- aa[activeRow].hasIcons = true;
- }
-
- String label = JOptionPane.showInputDialog("Enter a label for the structure?",
- symbol);
-
- if (label == null)
- {
- return;
- }
-
- if ((label.length() > 0) && !aa[activeRow].hasText)
- {
- aa[activeRow].hasText = true;
- }
-
- for (int i = 0; i < activeRes.size(); i++)
- {
- int index = Integer.parseInt(activeRes.get(i).toString());
-
- if (anot[index] == null)
- {
- anot[index] = new Annotation(label, "", type, 0);
- }
-
- anot[index].secondaryStructure = type;
- anot[index].displayCharacter = label;
- }
- }
-
- adjustPanelHeight();
- activeRes = null;
- repaint();
-
- return;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mousePressed(MouseEvent evt)
- {
- int height = 0;
- activeRow = -1;
-
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
- for (int i = 0; i < aa.length; i++)
- {
- if (aa[i].visible)
- {
- height += aa[i].height;
- }
-
- if (evt.getY() < height)
- {
- if (aa[i].editable)
- {
- activeRow = i;
- }
- else
- {
- activeRes = null;
- }
-
- break;
- }
- }
-
- if (SwingUtilities.isRightMouseButton(evt))
- {
- if (activeRes == null)
- {
- return;
- }
-
- JPopupMenu pop = new JPopupMenu("Structure type");
- JMenuItem item = new JMenuItem(HELIX);
- item.addActionListener(this);
- pop.add(item);
- item = new JMenuItem(SHEET);
- item.addActionListener(this);
- pop.add(item);
- 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, evt.getX(), evt.getY());
-
- return;
- }
-
- if (aa == null)
- {
- return;
- }
-
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
- if (evt.isControlDown() || evt.isAltDown())
- {
- addEditableColumn(res);
- }
- else if (evt.isShiftDown())
- {
- if (activeRes == null)
- {
- activeRes = new Vector();
- }
- else
- {
- int start = Integer.parseInt(activeRes.get(activeRes.size() -
- 1).toString());
- int end = res;
-
- if (end < start)
- {
- int temp = end;
- end = start;
- start = temp;
- }
-
- for (int n = start; n <= end; n++)
- {
- addEditableColumn(n);
- }
- }
- }
- else
- {
- activeRes = new Vector();
- activeRes.addElement(String.valueOf(res));
- }
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseExited(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseDragged(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseMoved(MouseEvent evt)
- {
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
- if (aa == 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 res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
- if ((row > -1) && (res < aa[row].annotations.length) &&
- (aa[row].annotations[res] != null))
- {
- this.setToolTipText(aa[row].annotations[res].description);
-
- StringBuffer text = new StringBuffer("Sequence position " +
- (res + 1) + " " + aa[row].annotations[res].description);
- ap.alignFrame.statusBar.setText(text.toString());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- */
- public void paintComponent(Graphics g)
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
-
- if (fastPaint && image!=null)
- {
- g.drawImage(image, 0, 0, this);
- fastPaint = false;
- return;
- }
-
- imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
-
- if (image == null || imgWidth != image.getWidth())
- {
- image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
- BufferedImage.TYPE_INT_RGB);
- gg = (Graphics2D) image.getGraphics();
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
-
- gg.setFont(av.getFont());
- fm = gg.getFontMetrics();
- }
-
- drawComponent(gg, av.startRes, av.endRes + 1);
- g.drawImage(image, 0, 0, this);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param horizontal DOCUMENT ME!
- */
- public void fastPaint(int horizontal)
- {
- if ((horizontal == 0) ||
- (av.alignment.getAlignmentAnnotation() == null) ||
- (av.alignment.getAlignmentAnnotation().length < 1))
- {
- repaint();
-
- return;
- }
-
- gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
-
- int sr = av.startRes;
- int er = av.endRes + 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;
- }
-
- gg.translate(transX, 0);
-
- drawComponent(gg, sr, er);
-
- gg.translate(-transX, 0);
-
- fastPaint = true;
-
- repaint();
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startRes DOCUMENT ME!
- * @param endRes DOCUMENT ME!
- */
- public void drawComponent(Graphics g, int startRes, int endRes)
- {
- g.setFont(av.getFont());
-
- if (fm == null)
- fm = g.getFontMetrics();
-
-
- g.setColor(Color.white);
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
-
- if ((av.alignment.getAlignmentAnnotation() == null) ||
- (av.alignment.getAlignmentAnnotation().length < 1))
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
- g.setColor(Color.black);
- g.drawString("Alignment has no annotations", 20, 15);
-
- return;
- }
-
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
- int j;
- int x = 0;
- int y = 0;
- char[] lastSS = new char[aa.length];
- int[] lastSSX = new int[aa.length];
- int iconOffset = av.charHeight / 2;
- boolean validRes = false;
-
- //\u03B2 \u03B1
- for (int i = 0; i < aa.length; i++)
- {
- AlignmentAnnotation row = aa[i];
-
- if (!row.visible)
- {
- continue;
- }
-
-
- if (row.isGraph)
- {
- // this is so that we draw the characters below the graph
- y += row.height;
-
- if (row.hasText)
- {
- y -= av.charHeight;
- }
- }
-
- if (row.hasText)
- {
- iconOffset = av.charHeight / 2;
- }
- else
- {
- iconOffset = 0;
- }
-
- for (j = startRes; j < endRes; j++)
- {
- if ((row.annotations.length <= j) ||
- (row.annotations[j] == null))
- {
- validRes = false;
- }
- else
- {
- validRes = true;
- }
-
- x = (j - startRes) * av.charWidth;
-
- if (activeRow == i)
- {
- g.setColor(Color.red);
-
- if (activeRes != null)
- {
- for (int n = 0; n < activeRes.size(); n++)
- {
- int v = Integer.parseInt(activeRes.get(n).toString());
-
- if (v == j)
- {
- g.fillRect((j - startRes) * av.charWidth, y,
- av.charWidth, row.height);
- }
- }
- }
- }
-
- if (validRes &&
- (row.annotations[j].displayCharacter.length() > 0))
- {
-
- int charOffset = (av.charWidth -
- fm.charWidth(row.annotations[j].displayCharacter.charAt(
- 0))) / 2;
- g.setColor(row.annotations[j].colour);
-
- if (j == 0 || row.isGraph)
- {
- g.drawString(row.annotations[j].displayCharacter, x+charOffset,
- y + iconOffset + 3);
- }
- else if (((row.annotations[j - 1] == null) ||
- (row.annotations[j].displayCharacter != row.annotations[j -
- 1].displayCharacter)))
- {
- g.drawString(row.annotations[j].displayCharacter, x+charOffset,
- y + iconOffset + 3);
- }
- }
-
- if (row.hasIcons)
- {
- if (!validRes ||
- (row.annotations[j].secondaryStructure != lastSS[i]))
- {
- switch (lastSS[i])
- {
- case 'H':
- g.setColor(HELIX_COLOUR);
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
- x - lastSSX[i], 7, 8, 8);
-
- break;
-
- case 'E':
- g.setColor(SHEET_COLOUR);
- g.fillRect(lastSSX[i], y + 4 + iconOffset,
- x - lastSSX[i] - 4, 7);
- g.fillPolygon(new int[] { x - 4, x - 4, x },
- new int[]
- {
- y + iconOffset, y + 14 + iconOffset,
- y + 8 + iconOffset
- }, 3);
-
- break;
-
- case 'C':
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX[i], y + 6 + iconOffset,
- x - lastSSX[i], 2);
-
- break;
- }
-
- if (validRes)
- {
- lastSS[i] = row.annotations[j].secondaryStructure;
- }
- else
- {
- lastSS[i] = ' ';
- }
-
- lastSSX[i] = x;
- }
- }
-
- if (validRes && row.isGraph)
- {
- g.setColor(new Color(0, 0, 180));
-
- int height = (int) ((row.annotations[j].value / row.graphMax) * GRAPH_HEIGHT);
-
- if (row.windowLength > 1)
- {
- int total = 0;
-
- for (int i2 = j - (row.windowLength / 2);
- i2 < (j + (row.windowLength / 2)); i2++)
- {
- if ((i2 < 0) || (i2 >= av.alignment.getWidth()))
- {
- continue;
- }
-
- total += row.annotations[i2].value;
- }
-
- total /= row.windowLength;
- height = (int) ((total / row.graphMax) * GRAPH_HEIGHT);
- }
-
- g.setColor(row.annotations[j].colour);
- g.fillRect(x, y - height, av.charWidth, height);
- }
- }
-
- x += av.charWidth;
-
- if (row.hasIcons)
- {
- switch (lastSS[i])
- {
- case 'H':
- g.setColor(HELIX_COLOUR);
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
- x - lastSSX[i], 7, 8, 8);
-
- break;
-
- case 'E':
- g.setColor(SHEET_COLOUR);
- g.fillRect(lastSSX[i], y + 4 + iconOffset,
- x - lastSSX[i] - 4, 7);
- g.fillPolygon(new int[] { x - 4, x - 4, x },
- new int[]
- {
- y + iconOffset, y + 14 + iconOffset,
- y + 7 + iconOffset
- }, 3);
-
- break;
-
- case 'C':
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
-
- break;
- }
- }
-
- if (row.isGraph && row.hasText)
- {
- y += av.charHeight;
- }
-
- if (!row.isGraph)
- {
- y += aa[i].height;
- }
- }
- }
-
- // used by overview window
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, width, y);
- g.setColor(new Color(0, 0, 180));
-
-
- int x = 0, height;
-
- for (int j = sRes; j < eRes; j++)
- {
- g.setColor(new Color(0, 0, 180));
-
- height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
- if(height>y)
- height = y;
-
- g.fillRect(x, y - height, av.charWidth, height);
- x += av.charWidth;
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+
+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.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;
+
+/**
+ * AnnotationPanel displays visible portion of annotation rows below unwrapped
+ * alignment
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
+ MouseListener, MouseWheelListener, MouseMotionListener,
+ ActionListener, AdjustmentListener, Scrollable
+{
+ String HELIX = MessageManager.getString("label.helix");
+
+ String SHEET = MessageManager.getString("label.sheet");
+
+ /**
+ * For RNA secondary structure "stems" aka helices
+ */
+ String STEM = MessageManager.getString("label.rna_helix");
+
+ String LABEL = MessageManager.getString("label.label");
+
+ String REMOVE = MessageManager.getString("label.remove_annotation");
+
+ String COLOUR = MessageManager.getString("action.colour");
+
+ public final Color HELIX_COLOUR = Color.red.darker();
+
+ public final Color SHEET_COLOUR = Color.green.darker().darker();
+
+ public final Color STEM_COLOUR = Color.blue.darker();
+
+ /** DOCUMENT ME!! */
+ public AlignViewport av;
+
+ AlignmentPanel ap;
+
+ public int activeRow = -1;
+
+ public BufferedImage image;
+
+ public volatile BufferedImage fadedImage;
+
+ Graphics2D gg;
+
+ public FontMetrics fm;
+
+ public int imgWidth = 0;
+
+ boolean fastPaint = false;
+
+ // Used For mouse Dragging and resizing graphs
+ int graphStretch = -1;
+
+ int graphStretchY = -1;
+
+ int min; // used by mouseDragged to see if user
+
+ int max; // used by mouseDragged to see if user
+
+ boolean mouseDragging = false;
+
+ boolean MAC = false;
+
+ // for editing cursor
+ int cursorX = 0;
+
+ int cursorY = 0;
+
+ public final AnnotationRenderer renderer;
+
+ private MouseWheelListener[] _mwl;
+
+ /**
+ * Creates a new AnnotationPanel object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ */
+ public AnnotationPanel(AlignmentPanel ap)
+ {
+
+ MAC = jalview.util.Platform.isAMac();
+
+ ToolTipManager.sharedInstance().registerComponent(this);
+ ToolTipManager.sharedInstance().setInitialDelay(0);
+ ToolTipManager.sharedInstance().setDismissDelay(10000);
+ this.ap = ap;
+ av = ap.av;
+ this.setLayout(null);
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ ap.annotationScroller.getVerticalScrollBar()
+ .addAdjustmentListener(this);
+ // save any wheel listeners on the scroller, so we can propagate scroll
+ // events to them.
+ _mwl = ap.annotationScroller.getMouseWheelListeners();
+ // and then set our own listener to consume all mousewheel events
+ ap.annotationScroller.addMouseWheelListener(this);
+ renderer = new AnnotationRenderer();
+ }
+
+ public AnnotationPanel(AlignViewport av)
+ {
+ this.av = av;
+ renderer = new AnnotationRenderer();
+ }
+
+ @Override
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ if (e.isShiftDown())
+ {
+ e.consume();
+ if (e.getWheelRotation() > 0)
+ {
+ ap.scrollRight(true);
+ }
+ else
+ {
+ ap.scrollRight(false);
+ }
+ }
+ else
+ {
+ // TODO: find the correct way to let the event bubble up to
+ // ap.annotationScroller
+ for (MouseWheelListener mwl : _mwl)
+ {
+ if (mwl != null)
+ {
+ mwl.mouseWheelMoved(e);
+ }
+ if (e.isConsumed())
+ {
+ break;
+ }
+ }
+ }
+ }
+
+ @Override
+ public Dimension getPreferredScrollableViewportSize()
+ {
+ return getPreferredSize();
+ }
+
+ @Override
+ public int getScrollableBlockIncrement(Rectangle visibleRect,
+ int orientation, int direction)
+ {
+ return 30;
+ }
+
+ @Override
+ public boolean getScrollableTracksViewportHeight()
+ {
+ return false;
+ }
+
+ @Override
+ public boolean getScrollableTracksViewportWidth()
+ {
+ return true;
+ }
+
+ @Override
+ public int getScrollableUnitIncrement(Rectangle visibleRect,
+ int orientation, int direction)
+ {
+ return 30;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event
+ * .AdjustmentEvent)
+ */
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ // update annotation label display
+ ap.getAlabels().setScrollOffset(-evt.getValue());
+ }
+
+ /**
+ * Calculates the height of the annotation displayed in the annotation panel.
+ * Callers should normally call the ap.adjustAnnotationHeight method to ensure
+ * all annotation associated components are updated correctly.
+ *
+ */
+ public int adjustPanelHeight()
+ {
+ int height = av.calcPanelHeight();
+ this.setPreferredSize(new Dimension(1, height));
+ if (ap != null)
+ {
+ // revalidate only when the alignment panel is fully constructed
+ ap.validate();
+ }
+
+ return height;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
+ Annotation[] anot = aa[activeRow].annotations;
+
+ if (anot.length < av.getColumnSelection().getMax())
+ {
+ 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 index : av.getColumnSelection().getSelected())
+ {
+ if (av.getColumnSelection().isVisible(index))
+ {
+ anot[index] = null;
+ }
+ }
+ }
+ else if (action.equals(LABEL))
+ {
+ String exMesg = collectAnnotVals(anot, LABEL);
+ String label = JOptionPane.showInputDialog(this,
+ MessageManager.getString("label.enter_label"), exMesg);
+
+ if (label == null)
+ {
+ return;
+ }
+
+ if ((label.length() > 0) && !aa[activeRow].hasText)
+ {
+ aa[activeRow].hasText = true;
+ }
+
+ for (int index : av.getColumnSelection().getSelected())
+ {
+ if (!av.getColumnSelection().isVisible(index))
+ {
+ continue;
+ }
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation(label, "", ' ', 0);
+ }
+ else
+ {
+ anot[index].displayCharacter = label;
+ }
+ }
+ }
+ else if (action.equals(COLOUR))
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_foreground_colour"),
+ Color.black);
+
+ for (int index : av.getColumnSelection().getSelected())
+ {
+ if (!av.getColumnSelection().isVisible(index))
+ {
+ continue;
+ }
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation("", "", ' ', 0);
+ }
+
+ anot[index].colour = col;
+ }
+ }
+ else
+ // HELIX, SHEET or STEM
+ {
+ char type = 0;
+ String symbol = "\u03B1"; // alpha
+
+ if (action.equals(HELIX))
+ {
+ type = 'H';
+ }
+ else if (action.equals(SHEET))
+ {
+ type = 'E';
+ symbol = "\u03B2"; // beta
+ }
+
+ // Added by LML to color stems
+ else if (action.equals(STEM))
+ {
+ type = 'S';
+ int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+ symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
+ }
+
+ if (!aa[activeRow].hasIcons)
+ {
+ aa[activeRow].hasIcons = true;
+ }
+
+ String label = JOptionPane.showInputDialog(MessageManager
+ .getString("label.enter_label_for_the_structure"), symbol);
+
+ if (label == null)
+ {
+ return;
+ }
+
+ if ((label.length() > 0) && !aa[activeRow].hasText)
+ {
+ aa[activeRow].hasText = true;
+ if (action.equals(STEM))
+ {
+ aa[activeRow].showAllColLabels = true;
+ }
+ }
+ for (int index : av.getColumnSelection().getSelected())
+ {
+ if (!av.getColumnSelection().isVisible(index))
+ {
+ continue;
+ }
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation(label, "", type, 0);
+ }
+
+ 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;
+ }
+
+ /**
+ * 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)
+ {
+ // 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
+ List selected = viscols.getSelected();
+ Collections.sort(selected);
+ for (int index : selected)
+ {
+ // always check for current display state - just in case
+ if (!viscols.isVisible(index))
+ {
+ continue;
+ }
+ String tlabel = null;
+ if (anots[index] != null)
+ { // LML added stem code
+ if (type.equals(HELIX) || type.equals(SHEET)
+ || type.equals(STEM) || type.equals(LABEL))
+ {
+ tlabel = anots[index].description;
+ if (tlabel == null || tlabel.length() < 1)
+ {
+ if (type.equals(HELIX) || type.equals(SHEET)
+ || type.equals(STEM))
+ {
+ tlabel = "" + anots[index].secondaryStructure;
+ }
+ else
+ {
+ tlabel = "" + anots[index].displayCharacter;
+ }
+ }
+ }
+ if (tlabel != null && !tlabel.equals(last))
+ {
+ if (last.length() > 0)
+ {
+ collatedInput.append(" ");
+ }
+ collatedInput.append(tlabel);
+ }
+ }
+ }
+ return collatedInput.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
+
+ 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 (y < height)
+ {
+ if (aa[i].editable)
+ {
+ activeRow = i;
+ }
+ else if (aa[i].graph > 0)
+ {
+ // Stretch Graph
+ graphStretch = i;
+ graphStretchY = y;
+ }
+
+ break;
+ }
+ }
+
+ /*
+ * isPopupTrigger fires in mousePressed on Mac,
+ * not until mouseRelease on Windows
+ */
+ if (evt.isPopupTrigger() && activeRow != -1)
+ {
+ showPopupMenu(y, evt.getX());
+ return;
+ }
+
+ 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);
+ }
+ 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);
+ 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!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ graphStretch = -1;
+ graphStretchY = -1;
+ mouseDragging = false;
+ 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());
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ ap.getScalePanel().mouseEntered(evt);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ ap.getScalePanel().mouseExited(evt);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (graphStretch > -1)
+ {
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ - evt.getY();
+ if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ {
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ }
+ graphStretchY = evt.getY();
+ adjustPanelHeight();
+ ap.paintAlignment(true);
+ }
+ else
+ {
+ ap.getScalePanel().mouseDragged(evt);
+ }
+ }
+
+ /**
+ * Constructs the tooltip, and constructs and displays a status message, for
+ * the current mouse position
+ *
+ * @param evt
+ */
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ 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;
+ }
+ }
+
+ if (row == -1)
+ {
+ this.setToolTipText(null);
+ return;
+ }
+
+ int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+ if (av.hasHiddenColumns())
+ {
+ column = av.getColumnSelection().adjustForHiddenColumns(column);
+ }
+
+ AlignmentAnnotation ann = aa[row];
+ if (row > -1 && ann.annotations != null
+ && column < ann.annotations.length)
+ {
+ buildToolTip(ann, column, aa);
+ setStatusMessage(column, ann);
+ }
+ else
+ {
+ this.setToolTipText(null);
+ ap.alignFrame.statusBar.setText(" ");
+ }
+ }
+
+ /**
+ * Builds a tooltip for the annotation at the current mouse position.
+ *
+ * @param ann
+ * @param column
+ * @param anns
+ */
+ void buildToolTip(AlignmentAnnotation ann, int column,
+ AlignmentAnnotation[] anns)
+ {
+ if (ann.graphGroup > -1)
+ {
+ StringBuilder tip = new StringBuilder(32);
+ tip.append("");
+ for (int i = 0; i < anns.length; i++)
+ {
+ if (anns[i].graphGroup == ann.graphGroup
+ && anns[i].annotations[column] != null)
+ {
+ tip.append(anns[i].label);
+ String description = anns[i].annotations[column].description;
+ if (description != null && description.length() > 0)
+ {
+ tip.append(" ").append(description);
+ }
+ tip.append("
");
+ }
+ }
+ if (tip.length() != 6)
+ {
+ tip.setLength(tip.length() - 4);
+ this.setToolTipText(tip.toString() + "");
+ }
+ }
+ else if (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);
+ }
+ }
+
+ /**
+ * Constructs and displays the status bar message
+ *
+ * @param column
+ * @param ann
+ */
+ void setStatusMessage(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 (ann.annotations[column] != null)
+ {
+ String description = ann.annotations[column].description;
+ if (description != null && description.trim().length() > 0)
+ {
+ text.append(" ").append(description);
+ }
+ }
+
+ /*
+ * 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 = av.getAlignment().findIndex(seqref);
+ if (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 (av.getAlignment().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());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ // if (activeRow != -1)
+ // {
+ // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ // AlignmentAnnotation anot = aa[activeRow];
+ // }
+ }
+
+ // TODO mouseClicked-content and drawCursor are quite experimental!
+ public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
+ int y1)
+ {
+ int pady = av.getCharHeight() / 5;
+ int charOffset = 0;
+ graphics.setColor(Color.black);
+ graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
+
+ if (av.validCharWidth)
+ {
+ graphics.setColor(Color.white);
+
+ char s = seq.getCharAt(res);
+
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s), charOffset + x1,
+ (y1 + av.getCharHeight()) - pady);
+ }
+
+ }
+
+ private volatile boolean imageFresh = false;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+
+ if (image != null)
+ {
+ if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
+ || (getVisibleRect().height != g.getClipBounds().height))
+ {
+ g.drawImage(image, 0, 0, this);
+ fastPaint = false;
+ return;
+ }
+ }
+ imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
+ if (imgWidth < 1)
+ {
+ return;
+ }
+ if (image == null || imgWidth != image.getWidth(this)
+ || image.getHeight(this) != getHeight())
+ {
+ try
+ {
+ image = new BufferedImage(imgWidth, ap.getAnnotationPanel()
+ .getHeight(), BufferedImage.TYPE_INT_RGB);
+ } catch (OutOfMemoryError oom)
+ {
+ try
+ {
+ System.gc();
+ } catch (Exception x)
+ {
+ }
+ ;
+ new OOMWarning(
+ "Couldn't allocate memory to redraw screen. Please restart Jalview",
+ oom);
+ return;
+ }
+ gg = (Graphics2D) image.getGraphics();
+
+ if (av.antiAlias)
+ {
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+
+ gg.setFont(av.getFont());
+ fm = gg.getFontMetrics();
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, imgWidth, image.getHeight());
+ imageFresh = true;
+ }
+
+ drawComponent(gg, av.startRes, av.endRes + 1);
+ imageFresh = false;
+ g.drawImage(image, 0, 0, this);
+ }
+
+ /**
+ * set true to enable redraw timing debug output on stderr
+ */
+ private final boolean debugRedraw = false;
+
+ /**
+ * non-Thread safe repaint
+ *
+ * @param horizontal
+ * repaint with horizontal shift in alignment
+ */
+ public void fastPaint(int horizontal)
+ {
+ if ((horizontal == 0) || gg == 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 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;
+ }
+
+ gg.translate(transX, 0);
+
+ 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));
+ }
+
+ }
+
+ private volatile boolean lastImageGood = false;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ * @param endRes
+ * DOCUMENT ME!
+ */
+ public void drawComponent(Graphics g, int startRes, int endRes)
+ {
+ BufferedImage oldFaded = fadedImage;
+ if (av.isCalcInProgress())
+ {
+ if (image == null)
+ {
+ lastImageGood = false;
+ return;
+ }
+ // We'll keep a record of the old image,
+ // and draw a faded image until the calculation
+ // has completed
+ if (lastImageGood
+ && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage
+ .getHeight() != image.getHeight()))
+ {
+ // System.err.println("redraw faded image ("+(fadedImage==null ?
+ // "null image" : "") + " lastGood="+lastImageGood+")");
+ fadedImage = new BufferedImage(imgWidth, image.getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+
+ Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
+
+ fadedG.setColor(Color.white);
+ fadedG.fillRect(0, 0, imgWidth, image.getHeight());
+
+ fadedG.setComposite(AlphaComposite.getInstance(
+ AlphaComposite.SRC_OVER, .3f));
+ fadedG.drawImage(image, 0, 0, this);
+
+ }
+ // make sure we don't overwrite the last good faded image until all
+ // calculations have finished
+ lastImageGood = false;
+
+ }
+ else
+ {
+ if (fadedImage != null)
+ {
+ oldFaded = fadedImage;
+ }
+ fadedImage = null;
+ }
+
+ g.setColor(Color.white);
+ g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
+
+ g.setFont(av.getFont());
+ if (fm == null)
+ {
+ fm = g.getFontMetrics();
+ }
+
+ if ((av.getAlignment().getAlignmentAnnotation() == null)
+ || (av.getAlignment().getAlignmentAnnotation().length < 1))
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+ g.setColor(Color.black);
+ if (av.validCharWidth)
+ {
+ g.drawString(MessageManager
+ .getString("label.alignment_has_no_annotations"), 20, 15);
+ }
+
+ return;
+ }
+ lastImageGood = renderer.drawComponent(this, av, g, activeRow,
+ startRes, endRes);
+ if (!lastImageGood && fadedImage == null)
+ {
+ fadedImage = oldFaded;
+ }
+ }
+
+ @Override
+ public FontMetrics getFontMetrics()
+ {
+ return fm;
+ }
+
+ @Override
+ public Image getFadedImage()
+ {
+ return fadedImage;
+ }
+
+ @Override
+ public int getFadedImageWidth()
+ {
+ return imgWidth;
+ }
+
+ private int[] bounds = new int[2];
+
+ @Override
+ public int[] getVisibleVRange()
+ {
+ if (ap != null && ap.getAlabels() != null)
+ {
+ int sOffset = -ap.getAlabels().getScrollOffset();
+ int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
+ bounds[0] = sOffset;
+ bounds[1] = visHeight;
+ return bounds;
+ }
+ else
+ {
+ return null;
+ }
+ }
+}