-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.image.*;\r
-import javax.swing.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class AnnotationPanel\r
- extends JPanel implements MouseListener,\r
- MouseMotionListener, ActionListener, AdjustmentListener\r
-{\r
- static String HELIX = "Helix";\r
- static String SHEET = "Sheet";\r
- static String LABEL = "Label";\r
- static String REMOVE = "Remove Annotation";\r
- static String COLOUR = "Colour";\r
- static Color HELIX_COLOUR = Color.red.darker();\r
- static Color SHEET_COLOUR = Color.green.darker().darker();\r
-\r
- public static int GRAPH_HEIGHT = 40;\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- int activeRow = -1;\r
- Vector activeRes;\r
- BufferedImage image;\r
- Graphics2D gg;\r
- FontMetrics fm;\r
- int imgWidth = 0;\r
- boolean fastPaint = false;\r
-\r
- public AnnotationPanel(AlignmentPanel ap)\r
- {\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- ToolTipManager.sharedInstance().setInitialDelay(0);\r
- ToolTipManager.sharedInstance().setDismissDelay(10000);\r
- this.ap = ap;\r
- av = ap.av;\r
- this.setLayout(null);\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);\r
- }\r
-\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- ap.alabels.setScrollOffset( -evt.getValue());\r
- }\r
-\r
- public void adjustPanelHeight()\r
- {\r
- // setHeight of panels\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- int height = 0;\r
-\r
- if (aa != null)\r
- {\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if (!aa[i].visible)\r
- {\r
- continue;\r
- }\r
-\r
- aa[i].height = 0;\r
-\r
- if (aa[i].hasText)\r
- {\r
- aa[i].height += av.charHeight;\r
- }\r
-\r
- if (aa[i].hasIcons)\r
- {\r
- aa[i].height += 16;\r
- }\r
-\r
- if (aa[i].isGraph)\r
- {\r
- aa[i].height += GRAPH_HEIGHT;\r
- }\r
-\r
- if (aa[i].height == 0)\r
- {\r
- aa[i].height = 20;\r
- }\r
-\r
- height += aa[i].height;\r
- }\r
- }\r
- else\r
- {\r
- height = 20;\r
- }\r
-\r
- this.setPreferredSize(new Dimension(1, height));\r
- }\r
-\r
-\r
- public void removeEditableColumn(int col)\r
- {\r
- if (activeRow == -1)\r
- {\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-\r
- for (int j = 0; j < aa.length; j++)\r
- {\r
- if (aa[j].editable)\r
- {\r
- activeRow = j;\r
- break;\r
- }\r
- }\r
- }\r
-\r
- if (activeRes != null && activeRes.contains(String.valueOf(col)))\r
- {\r
- activeRes.removeElement(String.valueOf(col));\r
- }\r
- repaint();\r
- }\r
-\r
-\r
- public void addEditableColumn(int col)\r
- {\r
- if (activeRow == -1)\r
- {\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-\r
- for (int j = 0; j < aa.length; j++)\r
- {\r
- if (aa[j].editable)\r
- {\r
- activeRow = j;\r
- break;\r
- }\r
- }\r
- }\r
-\r
- if (activeRes == null)\r
- activeRes = new Vector();\r
-\r
- if (!activeRes.contains(String.valueOf(col)))\r
- activeRes.addElement(String.valueOf(col));\r
-\r
- repaint();\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- Annotation[] anot = aa[activeRow].annotations;\r
-\r
- if (evt.getActionCommand().equals(REMOVE))\r
- {\r
- for (int i = 0; i < activeRes.size(); i++)\r
- {\r
- anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
- anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
- }\r
- }\r
- else if (evt.getActionCommand().equals(LABEL))\r
- {\r
- String label = JOptionPane.showInputDialog(this, "Enter Label ",\r
- "Enter label",\r
- JOptionPane.QUESTION_MESSAGE);\r
-\r
- if (label == null)\r
- return;\r
-\r
- if ( (label.length() > 0) && !aa[activeRow].hasText)\r
- {\r
- aa[activeRow].hasText = true;\r
- }\r
-\r
- for (int i = 0; i < activeRes.size(); i++)\r
- {\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
-\r
- if (anot[index] == null)\r
- {\r
- anot[index] = new Annotation(label, "", ' ', 0);\r
- }\r
- anot[index].displayCharacter = label;\r
- }\r
- }\r
- else if (evt.getActionCommand().equals(COLOUR))\r
- {\r
- Color col = JColorChooser.showDialog(this,\r
- "Choose foreground colour",\r
- Color.black);\r
-\r
- for (int i = 0; i < activeRes.size(); i++)\r
- {\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
-\r
- if (anot[index] == null)\r
- {\r
- anot[index] = new Annotation("", "", ' ', 0);\r
- }\r
-\r
- anot[index].colour = col;\r
- }\r
- }\r
- else // HELIX OR SHEET\r
- {\r
- char type = 0;\r
- String symbol = "\u03B1";\r
-\r
- if (evt.getActionCommand().equals(HELIX))\r
- {\r
- type = 'H';\r
- }\r
- else if (evt.getActionCommand().equals(SHEET))\r
- {\r
- type = 'E';\r
- symbol = "\u03B2";\r
- }\r
-\r
- if (!aa[activeRow].hasIcons)\r
- {\r
- aa[activeRow].hasIcons = true;\r
- }\r
-\r
- String label = JOptionPane.showInputDialog(\r
- "Enter a label for the structure?",\r
- symbol);\r
-\r
- if (label == null)\r
- return;\r
-\r
- if ( (label.length() > 0) && !aa[activeRow].hasText)\r
- {\r
- aa[activeRow].hasText = true;\r
- }\r
-\r
- for (int i = 0; i < activeRes.size(); i++)\r
- {\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
-\r
- if (anot[index] == null)\r
- {\r
- anot[index] = new Annotation(label, "", type, 0);\r
- }\r
-\r
- anot[index].secondaryStructure = type;\r
- anot[index].displayCharacter = label;\r
- }\r
- }\r
-\r
- adjustPanelHeight();\r
- activeRes = null;\r
- repaint();\r
-\r
- return;\r
- }\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- int height = 0;\r
- activeRow = -1;\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- height += aa[i].height;\r
-\r
- if (evt.getY() < height)\r
- {\r
- if (aa[i].editable)\r
- activeRow = i;\r
- else\r
- activeRes = null;\r
-\r
- break;\r
- }\r
- }\r
-\r
-\r
- if (SwingUtilities.isRightMouseButton(evt))\r
- {\r
- if (activeRes == null)\r
- {\r
- return;\r
- }\r
-\r
-\r
- JPopupMenu pop = new JPopupMenu("Structure type");\r
- JMenuItem item = new JMenuItem(HELIX);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(SHEET);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(LABEL);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(COLOUR);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(REMOVE);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- pop.show(this, evt.getX(), evt.getY());\r
-\r
- return;\r
- }\r
-\r
-\r
- if (aa == null)\r
- {\r
- return;\r
- }\r
-\r
-\r
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
-\r
- if (evt.isControlDown() || evt.isAltDown())\r
- {\r
- addEditableColumn(res);\r
- }\r
- else if (evt.isShiftDown())\r
- {\r
- if (activeRes == null)\r
- {\r
- activeRes = new Vector();\r
- }\r
- else\r
- {\r
- int start = Integer.parseInt(activeRes.get(activeRes.size() -\r
- 1).toString());\r
- int end = res;\r
-\r
- if (end < start)\r
- {\r
- int temp = end;\r
- end = start;\r
- start = temp;\r
- }\r
-\r
- for (int n = start; n <= end; n++)\r
- {\r
- addEditableColumn(n);\r
- }\r
- }\r
- }\r
- else\r
- {\r
- activeRes = new Vector();\r
- activeRes.addElement(String.valueOf(res));\r
- }\r
-\r
- repaint();\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- }\r
-\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- }\r
-\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- }\r
-\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-\r
- if (aa == null)\r
- {\r
- return;\r
- }\r
-\r
- int row = -1;\r
- int height = 0;\r
-\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if (aa[i].visible)\r
- {\r
- height += aa[i].height;\r
- }\r
-\r
- if (evt.getY() < height)\r
- {\r
- row = i;\r
-\r
- break;\r
- }\r
- }\r
-\r
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
-\r
- if ( (row > -1) && (res < aa[row].annotations.length) &&\r
- (aa[row].annotations[res] != null))\r
- {\r
- this.setToolTipText(aa[row].annotations[res].description);\r
-\r
- StringBuffer text = new StringBuffer("Sequence position " +\r
- (res + 1) + " " +\r
- aa[row].annotations[res].description);\r
- ap.alignFrame.statusBar.setText(text.toString());\r
- }\r
- }\r
-\r
- public void mouseClicked(MouseEvent evt)\r
- {\r
- }\r
-\r
- public void paintComponent(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getWidth(), getHeight());\r
-\r
- if (fastPaint)\r
- {\r
- g.drawImage(image, 0, 0, this);\r
- fastPaint = false;\r
-\r
- return;\r
- }\r
-\r
- imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
-\r
- image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
- BufferedImage.TYPE_INT_RGB);\r
- gg = (Graphics2D) image.getGraphics();\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
-\r
- gg.setFont(av.getFont());\r
- fm = gg.getFontMetrics();\r
-\r
- drawComponent(gg, av.startRes, av.endRes + 1);\r
- g.drawImage(image, 0, 0, this);\r
- }\r
-\r
- public void fastPaint(int horizontal)\r
- {\r
- if ( (horizontal == 0) ||\r
- (av.alignment.getAlignmentAnnotation() == null) ||\r
- (av.alignment.getAlignmentAnnotation().length < 1))\r
- {\r
- repaint();\r
-\r
- return;\r
- }\r
-\r
- gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);\r
-\r
- int sr = av.startRes;\r
- int er = av.endRes + 1;\r
- int transX = 0;\r
-\r
- if (horizontal > 0) // scrollbar pulled right, image to the left\r
- {\r
- transX = (er - sr - horizontal) * av.charWidth;\r
- sr = er - horizontal;\r
- }\r
- else if (horizontal < 0)\r
- {\r
- er = sr - horizontal;\r
- }\r
-\r
- gg.translate(transX, 0);\r
-\r
- drawComponent(gg, sr, er);\r
-\r
- gg.translate( -transX, 0);\r
-\r
- fastPaint = true;\r
- repaint();\r
- }\r
-\r
- public void drawComponent(Graphics2D g, int startRes, int endRes)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
-\r
- if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
- (av.alignment.getAlignmentAnnotation().length < 1))\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getWidth(), getHeight());\r
- g.setColor(Color.black);\r
- g.drawString("Alignment has no annotations", 20, 15);\r
-\r
- return;\r
- }\r
-\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-\r
- int j;\r
- int x = 0;\r
- int y = 0;\r
- char[] lastSS = new char[aa.length];\r
- int[] lastSSX = new int[aa.length];\r
- int iconOffset = av.charHeight / 2;\r
- boolean validRes = false;\r
-\r
- //\u03B2 \u03B1\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- AlignmentAnnotation row = aa[i];\r
-\r
- if (!row.visible)\r
- {\r
- continue;\r
- }\r
-\r
- if (row.isGraph)\r
- {\r
- // this is so that we draw the characters below the graph\r
- y += row.height;\r
-\r
- if (row.hasText)\r
- {\r
- y -= av.charHeight;\r
- }\r
- }\r
-\r
- if (row.hasText)\r
- {\r
- iconOffset = av.charHeight / 2;\r
- }\r
- else\r
- {\r
- iconOffset = 0;\r
- }\r
-\r
- for (j = startRes; j < endRes; j++)\r
- {\r
- if ( (row.annotations.length <= j) ||\r
- (row.annotations[j] == null))\r
- {\r
- validRes = false;\r
- }\r
- else\r
- {\r
- validRes = true;\r
- }\r
-\r
- x = (j - startRes) * av.charWidth;\r
-\r
- if (activeRow == i)\r
- {\r
- g.setColor(Color.red);\r
-\r
- if (activeRes != null)\r
- {\r
- for (int n = 0; n < activeRes.size(); n++)\r
- {\r
- int v = Integer.parseInt(activeRes.get(n).toString());\r
-\r
- if (v == j)\r
- {\r
- g.fillRect( (j - startRes) * av.charWidth, y,\r
- av.charWidth, row.height);\r
- }\r
- }\r
- }\r
- }\r
-\r
- if (validRes &&\r
- (row.annotations[j].displayCharacter.length() > 0))\r
- {\r
- int charOffset = (av.charWidth -\r
- fm.charWidth(row.annotations[j].displayCharacter.\r
- charAt(\r
- 0))) / 2;\r
- g.setColor(row.annotations[j].colour);\r
-\r
- if (j == 0)\r
- {\r
- g.drawString(row.annotations[j].displayCharacter,\r
- x, y + iconOffset + 2);\r
- }\r
- else if (\r
- ( (row.annotations[j - 1] == null) ||\r
- (row.annotations[j].displayCharacter != row.annotations[j -\r
- 1].displayCharacter)))\r
- {\r
- g.drawString(row.annotations[j].displayCharacter, x,\r
- y + iconOffset + 2);\r
- }\r
-\r
- }\r
-\r
- if (row.hasIcons)\r
- {\r
- if (!validRes ||\r
- (row.annotations[j].secondaryStructure != lastSS[i]))\r
- {\r
- switch (lastSS[i])\r
- {\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7, 8, 8);\r
-\r
- break;\r
-\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i] - 4, 7);\r
- g.fillPolygon(new int[]\r
- {x - 4, x - 4, x},\r
- new int[]\r
- {\r
- y + iconOffset, y + 14 + iconOffset,\r
- y + 8 + iconOffset\r
- }, 3);\r
-\r
- break;\r
-\r
- case 'C':\r
- break;\r
-\r
- default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y + 6 + iconOffset,\r
- x - lastSSX[i], 2);\r
-\r
- break;\r
- }\r
-\r
- if (validRes)\r
- {\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
- }\r
- else\r
- {\r
- lastSS[i] = ' ';\r
- }\r
-\r
- lastSSX[i] = x;\r
- }\r
- }\r
-\r
- if (validRes && row.isGraph)\r
- {\r
- g.setColor(new Color(0, 0, 180));\r
-\r
- int height = (int) ( (row.annotations[j].value / row.graphMax) *\r
- GRAPH_HEIGHT);\r
-\r
- if (row.windowLength > 1)\r
- {\r
- int total = 0;\r
-\r
- for (int i2 = j - (row.windowLength / 2);\r
- i2 < (j + (row.windowLength / 2)); i2++)\r
- {\r
- if ( (i2 < 0) || (i2 >= av.alignment.getWidth()))\r
- {\r
- continue;\r
- }\r
-\r
- total += row.annotations[i2].value;\r
- }\r
-\r
- total /= row.windowLength;\r
- height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);\r
- }\r
-\r
- g.setColor(row.annotations[j].colour);\r
- g.fillRect(x, y - height, av.charWidth, height);\r
- }\r
- }\r
-\r
- x += av.charWidth;\r
-\r
- if (row.hasIcons)\r
- {\r
- switch (lastSS[i])\r
- {\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7, 8, 8);\r
-\r
- break;\r
-\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i] - 4, 7);\r
- g.fillPolygon(new int[]\r
- {x - 4, x - 4, x},\r
- new int[]\r
- {\r
- y + iconOffset, y + 14 + iconOffset,\r
- y + 7 + iconOffset\r
- }, 3);\r
-\r
- break;\r
-\r
- case 'C':\r
- break;\r
-\r
- default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
-\r
- break;\r
- }\r
- }\r
-\r
- if (row.isGraph && row.hasText)\r
- {\r
- y += av.charHeight;\r
- }\r
-\r
- if (!row.isGraph)\r
- {\r
- y += aa[i].height;\r
- }\r
- }\r
- }\r
-\r
- // used by overview window\r
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, width, y);\r
- g.setColor(new Color(0, 0, 180));\r
-\r
- int x = 0;\r
-\r
- for (int j = 0; j < aa.annotations.length; j++)\r
- {\r
- g.setColor(new Color(0, 0, 180));\r
-\r
- int height = (int) ( (aa.annotations[j].value / aa.graphMax) *\r
- GRAPH_HEIGHT);\r
- g.fillRect(x, y - height, av.charWidth, height);\r
- x += av.charWidth;\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
+
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
+import jalview.util.MessageManager;
+
+/**
+ * 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
+{
+ final String HELIX = "Helix";
+
+ final String SHEET = "Sheet";
+
+ /**
+ * For RNA secondary structure "stems" aka helices
+ */
+ final String STEM = "RNA Helix";
+
+ final String LABEL = "Label";
+
+ final String REMOVE = "Remove Annotation";
+
+ final String COLOUR = "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 = new 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.alabels.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;
+ }
+
+ if (evt.getActionCommand().equals(REMOVE))
+ {
+ for (int i = 0; i < av.getColumnSelection().size(); i++)
+ {
+ anot[av.getColumnSelection().columnAt(i)] = null;
+ }
+ }
+ else if (evt.getActionCommand().equals(LABEL))
+ {
+ String exMesg = collectAnnotVals(anot, av.getColumnSelection(), 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 i = 0; i < av.getColumnSelection().size(); i++)
+ {
+ int index = av.getColumnSelection().columnAt(i);
+
+ if (!av.getColumnSelection().isVisible(index))
+ continue;
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
+ // null exceptions
+ // aren't raised
+ // elsewhere.
+ }
+ else
+ {
+ 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 < av.getColumnSelection().size(); i++)
+ {
+ int index = av.getColumnSelection().columnAt(i);
+
+ if (!av.getColumnSelection().isVisible(index))
+ continue;
+
+ 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";
+ }
+
+ // Added by LML to color stems
+ else if (evt.getActionCommand().equals(STEM))
+ {
+ type = 'S';
+ symbol = "\u03C3";
+ }
+
+ 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;
+ }
+
+ for (int i = 0; i < av.getColumnSelection().size(); i++)
+ {
+ int index = av.getColumnSelection().columnAt(i);
+
+ if (!av.getColumnSelection().isVisible(index))
+ continue;
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation(label, "", type, 0);
+ }
+
+ anot[index].secondaryStructure = type;
+ anot[index].displayCharacter = label;
+ }
+ }
+ av.getAlignment().validateAnnotation(aa[activeRow]);
+ ap.alignmentChanged();
+
+ adjustPanelHeight();
+ repaint();
+
+ return;
+ }
+
+ private String collectAnnotVals(Annotation[] anot,
+ ColumnSelection columnSelection, String label2)
+ {
+ String collatedInput = "";
+ String last = "";
+ ColumnSelection viscols = av.getColumnSelection();
+ // TODO: refactor and save av.getColumnSelection for efficiency
+ for (int i = 0; i < columnSelection.size(); i++)
+ {
+ int index = columnSelection.columnAt(i);
+ // always check for current display state - just in case
+ if (!viscols.isVisible(index))
+ continue;
+ String tlabel = null;
+ if (anot[index] != null)
+ { // LML added stem code
+ if (label2.equals(HELIX) || label2.equals(SHEET)
+ || label2.equals(STEM) || label2.equals(LABEL))
+ {
+ tlabel = anot[index].description;
+ if (tlabel == null || tlabel.length() < 1)
+ {
+ if (label2.equals(HELIX) || label2.equals(SHEET)
+ || label2.equals(STEM))
+ {
+ tlabel = "" + anot[index].secondaryStructure;
+ }
+ else
+ {
+ tlabel = "" + anot[index].displayCharacter;
+ }
+ }
+ }
+ if (tlabel != null && !tlabel.equals(last))
+ {
+ if (last.length() > 0)
+ {
+ collatedInput += " ";
+ }
+ collatedInput += tlabel;
+ }
+ }
+ }
+ return collatedInput;
+ }
+
+ /**
+ * 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;
+
+ 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 if (aa[i].graph > 0)
+ {
+ // Stretch Graph
+ graphStretch = i;
+ graphStretchY = evt.getY();
+ }
+
+ break;
+ }
+ }
+
+ if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1)
+ {
+ if (av.getColumnSelection() == null)
+ {
+ 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);
+ 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;
+ }
+
+ ap.scalePanel.mousePressed(evt);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ graphStretch = -1;
+ graphStretchY = -1;
+ mouseDragging = false;
+ ap.scalePanel.mouseReleased(evt);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ ap.scalePanel.mouseEntered(evt);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ ap.scalePanel.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.scalePanel.mouseDragged(evt);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @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 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)
+ {
+ if (aa[row].graphGroup > -1)
+ {
+ StringBuffer tip = new StringBuffer("<html>");
+ for (int gg = 0; gg < aa.length; gg++)
+ {
+ if (aa[gg].graphGroup == aa[row].graphGroup
+ && aa[gg].annotations[res] != null)
+ {
+ tip.append(aa[gg].label + " "
+ + aa[gg].annotations[res].description + "<br>");
+ }
+ }
+ if (tip.length() != 6)
+ {
+ tip.setLength(tip.length() - 4);
+ this.setToolTipText(tip.toString() + "</html>");
+ }
+ }
+ else if (aa[row].annotations[res] != null
+ && aa[row].annotations[res].description != null
+ && aa[row].annotations[res].description.length() > 0)
+ {
+ this.setToolTipText("<html>"+JvSwingUtils.wrapTooltip(aa[row].annotations[res].description)+"</html>");
+ }
+ else
+ {
+ // clear the tooltip.
+ this.setToolTipText(null);
+ }
+
+ if (aa[row].annotations[res] != null)
+ {
+ StringBuffer text = new StringBuffer("Sequence position "
+ + (res + 1));
+
+ if (aa[row].annotations[res].description != null)
+ {
+ text.append(" " + aa[row].annotations[res].description);
+ }
+
+ ap.alignFrame.statusBar.setText(text.toString());
+ }
+ }
+ else
+ {
+ this.setToolTipText(null);
+ }
+ }
+
+ /**
+ * 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.charHeight / 5;
+ int charOffset = 0;
+ graphics.setColor(Color.black);
+ graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+
+ if (av.validCharWidth)
+ {
+ graphics.setColor(Color.white);
+
+ char s = seq.getCharAt(res);
+
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s), charOffset + x1,
+ (y1 + av.charHeight) - 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.charWidth;
+ if (imgWidth < 1)
+ return;
+ if (image == null || imgWidth != image.getWidth(this)
+ || image.getHeight(this) != getHeight())
+ {
+ try
+ {
+ image = new BufferedImage(imgWidth, ap.annotationPanel.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.charWidth, 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.charWidth;
+ 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.charWidth, 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.alabels!=null)
+ {
+ int sOffset=-ap.alabels.scrollOffset;
+ int visHeight = sOffset+ap.annotationSpaceFillerHolder.getHeight();
+ bounds[0] = sOffset; bounds[1]=visHeight;
+ return bounds;
+ } else return null;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff