2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 import java.awt.event.*;
22 import java.awt.image.*;
23 import java.util.Hashtable;
27 import jalview.analysis.AAFrequency;
28 import jalview.analysis.StructureFrequency;
29 import jalview.datamodel.*;
30 import jalview.renderer.AnnotationRenderer;
31 import jalview.renderer.AwtRenderPanelI;
39 public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
40 MouseListener, MouseMotionListener, ActionListener,
43 final String HELIX = "Helix";
45 final String SHEET = "Sheet";
48 * For RNA secondary structure "stems" aka helices
50 final String STEM = "RNA Helix";
52 final String LABEL = "Label";
54 final String REMOVE = "Remove Annotation";
56 final String COLOUR = "Colour";
58 public final Color HELIX_COLOUR = Color.red.darker();
60 public final Color SHEET_COLOUR = Color.green.darker().darker();
62 public final Color STEM_COLOUR = Color.blue.darker();
65 public AlignViewport av;
69 public int activeRow = -1;
71 public BufferedImage image;
73 public BufferedImage fadedImage;
77 public FontMetrics fm;
79 public int imgWidth = 0;
81 boolean fastPaint = false;
83 // Used For mouse Dragging and resizing graphs
84 int graphStretch = -1;
86 int graphStretchY = -1;
88 int min; // used by mouseDragged to see if user
90 int max; // used by mouseDragged to see if user
92 boolean mouseDragging = false;
101 public final AnnotationRenderer renderer;
104 * Creates a new AnnotationPanel object.
109 public AnnotationPanel(AlignmentPanel ap)
112 MAC = new jalview.util.Platform().isAMac();
114 ToolTipManager.sharedInstance().registerComponent(this);
115 ToolTipManager.sharedInstance().setInitialDelay(0);
116 ToolTipManager.sharedInstance().setDismissDelay(10000);
119 this.setLayout(null);
120 addMouseListener(this);
121 addMouseMotionListener(this);
122 ap.annotationScroller.getVerticalScrollBar()
123 .addAdjustmentListener(this);
124 renderer = new AnnotationRenderer();
127 public AnnotationPanel(AlignViewport av)
130 renderer = new AnnotationRenderer();
139 public void adjustmentValueChanged(AdjustmentEvent evt)
141 ap.alabels.setScrollOffset(-evt.getValue());
145 * Calculates the height of the annotation displayed in the annotation panel.
146 * Callers should normally call the ap.adjustAnnotationHeight method to ensure
147 * all annotation associated components are updated correctly.
150 public int adjustPanelHeight()
152 int height = calcPanelHeight();
153 this.setPreferredSize(new Dimension(1, height));
156 // revalidate only when the alignment panel is fully constructed
164 * calculate the height for visible annotation, revalidating bounds where
165 * necessary ABSTRACT GUI METHOD
167 * @return total height of annotation
169 public int calcPanelHeight()
171 // setHeight of panels
172 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
177 for (int i = 0; i < aa.length; i++)
181 System.err.println("Null annotation row: ignoring.");
193 aa[i].height += av.charHeight;
203 aa[i].height += aa[i].graphHeight;
206 if (aa[i].height == 0)
211 height += aa[i].height;
228 public void actionPerformed(ActionEvent evt)
230 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
235 Annotation[] anot = aa[activeRow].annotations;
237 if (anot.length < av.getColumnSelection().getMax())
239 Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
240 System.arraycopy(anot, 0, temp, 0, anot.length);
242 aa[activeRow].annotations = anot;
245 if (evt.getActionCommand().equals(REMOVE))
247 for (int i = 0; i < av.getColumnSelection().size(); i++)
249 anot[av.getColumnSelection().columnAt(i)] = null;
252 else if (evt.getActionCommand().equals(LABEL))
254 String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
255 String label = JOptionPane.showInputDialog(this, "Enter label",
263 if ((label.length() > 0) && !aa[activeRow].hasText)
265 aa[activeRow].hasText = true;
268 for (int i = 0; i < av.getColumnSelection().size(); i++)
270 int index = av.getColumnSelection().columnAt(i);
272 if (!av.getColumnSelection().isVisible(index))
275 if (anot[index] == null)
277 anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
284 anot[index].displayCharacter = label;
288 else if (evt.getActionCommand().equals(COLOUR))
290 Color col = JColorChooser.showDialog(this,
291 "Choose foreground colour", Color.black);
293 for (int i = 0; i < av.getColumnSelection().size(); i++)
295 int index = av.getColumnSelection().columnAt(i);
297 if (!av.getColumnSelection().isVisible(index))
300 if (anot[index] == null)
302 anot[index] = new Annotation("", "", ' ', 0);
305 anot[index].colour = col;
312 String symbol = "\u03B1";
314 if (evt.getActionCommand().equals(HELIX))
318 else if (evt.getActionCommand().equals(SHEET))
324 // Added by LML to color stems
325 else if (evt.getActionCommand().equals(STEM))
331 if (!aa[activeRow].hasIcons)
333 aa[activeRow].hasIcons = true;
336 String label = JOptionPane.showInputDialog(
337 "Enter a label for the structure?", symbol);
344 if ((label.length() > 0) && !aa[activeRow].hasText)
346 aa[activeRow].hasText = true;
349 for (int i = 0; i < av.getColumnSelection().size(); i++)
351 int index = av.getColumnSelection().columnAt(i);
353 if (!av.getColumnSelection().isVisible(index))
356 if (anot[index] == null)
358 anot[index] = new Annotation(label, "", type, 0);
361 anot[index].secondaryStructure = type;
362 anot[index].displayCharacter = label;
372 private String collectAnnotVals(Annotation[] anot,
373 ColumnSelection columnSelection, String label2)
375 String collatedInput = "";
377 // TODO: refactor and save av.getColumnSelection for efficiency
378 for (int i = 0; i < columnSelection.size(); i++)
380 int index = columnSelection.columnAt(i);
381 // always check for current display state - just in case
382 if (!av.getColumnSelection().isVisible(index))
384 String tlabel = null;
385 if (anot[index] != null)
386 { // LML added stem code
387 if (label2.equals(HELIX) || label2.equals(SHEET)
388 || label2.equals(STEM) || label2.equals(LABEL))
390 tlabel = anot[index].description;
391 if (tlabel == null || tlabel.length() < 1)
393 if (label2.equals(HELIX) || label2.equals(SHEET)
394 || label2.equals(STEM))
396 tlabel = "" + anot[index].secondaryStructure;
400 tlabel = "" + anot[index].displayCharacter;
404 if (tlabel != null && !tlabel.equals(last))
406 if (last.length() > 0)
408 collatedInput += " ";
410 collatedInput += tlabel;
414 return collatedInput;
423 public void mousePressed(MouseEvent evt)
426 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
435 for (int i = 0; i < aa.length; i++)
439 height += aa[i].height;
442 if (evt.getY() < height)
448 else if (aa[i].graph > 0)
452 graphStretchY = evt.getY();
459 if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1)
461 if (av.getColumnSelection() == null)
466 JPopupMenu pop = new JPopupMenu("Structure type");
469 * Just display the needed structure options
471 if (av.getAlignment().isNucleotide() == true)
473 item = new JMenuItem(STEM);
474 item.addActionListener(this);
479 item = new JMenuItem(HELIX);
480 item.addActionListener(this);
482 item = new JMenuItem(SHEET);
483 item.addActionListener(this);
486 item = new JMenuItem(LABEL);
487 item.addActionListener(this);
489 item = new JMenuItem(COLOUR);
490 item.addActionListener(this);
492 item = new JMenuItem(REMOVE);
493 item.addActionListener(this);
495 pop.show(this, evt.getX(), evt.getY());
505 ap.scalePanel.mousePressed(evt);
515 public void mouseReleased(MouseEvent evt)
519 mouseDragging = false;
520 ap.scalePanel.mouseReleased(evt);
529 public void mouseEntered(MouseEvent evt)
531 ap.scalePanel.mouseEntered(evt);
540 public void mouseExited(MouseEvent evt)
542 ap.scalePanel.mouseExited(evt);
551 public void mouseDragged(MouseEvent evt)
553 if (graphStretch > -1)
555 av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
557 if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
559 av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
561 graphStretchY = evt.getY();
563 ap.paintAlignment(true);
567 ap.scalePanel.mouseDragged(evt);
577 public void mouseMoved(MouseEvent evt)
579 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
583 this.setToolTipText(null);
590 for (int i = 0; i < aa.length; i++)
594 height += aa[i].height;
597 if (evt.getY() < height)
607 this.setToolTipText(null);
611 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
613 if (av.hasHiddenColumns())
615 res = av.getColumnSelection().adjustForHiddenColumns(res);
618 if (row > -1 && aa[row].annotations != null
619 && res < (int) aa[row].annotations.length)
621 if (aa[row].graphGroup > -1)
623 StringBuffer tip = new StringBuffer("<html>");
624 for (int gg = 0; gg < aa.length; gg++)
626 if (aa[gg].graphGroup == aa[row].graphGroup
627 && aa[gg].annotations[res] != null)
629 tip.append(aa[gg].label + " "
630 + aa[gg].annotations[res].description + "<br>");
633 if (tip.length() != 6)
635 tip.setLength(tip.length() - 4);
636 this.setToolTipText(tip.toString() + "</html>");
639 else if (aa[row].annotations[res] != null
640 && aa[row].annotations[res].description != null
641 && aa[row].annotations[res].description.length() > 0)
643 this.setToolTipText(aa[row].annotations[res].description);
647 // clear the tooltip.
648 this.setToolTipText(null);
651 if (aa[row].annotations[res] != null)
653 StringBuffer text = new StringBuffer("Sequence position "
656 if (aa[row].annotations[res].description != null)
658 text.append(" " + aa[row].annotations[res].description);
661 ap.alignFrame.statusBar.setText(text.toString());
666 this.setToolTipText(null);
676 public void mouseClicked(MouseEvent evt)
680 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
681 AlignmentAnnotation anot = aa[activeRow];
683 if (anot.description.equals("secondary structure"))
685 // System.out.println(anot.description+" "+anot.getRNAStruc());
690 // TODO mouseClicked-content and drawCursor are quite experimental!
691 public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
694 int pady = av.charHeight / 5;
696 graphics.setColor(Color.black);
697 graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
699 if (av.validCharWidth)
701 graphics.setColor(Color.white);
703 char s = seq.getCharAt(res);
705 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
706 graphics.drawString(String.valueOf(s), charOffset + x1,
707 (y1 + av.charHeight) - pady);
718 public void paintComponent(Graphics g)
720 g.setColor(Color.white);
721 g.fillRect(0, 0, getWidth(), getHeight());
725 if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
726 || (getVisibleRect().height != g.getClipBounds().height))
728 g.drawImage(image, 0, 0, this);
733 imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
736 if (image == null || imgWidth != image.getWidth()
737 || image.getHeight(this) != getHeight())
739 image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
740 BufferedImage.TYPE_INT_RGB);
741 gg = (Graphics2D) image.getGraphics();
745 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
746 RenderingHints.VALUE_ANTIALIAS_ON);
749 gg.setFont(av.getFont());
750 fm = gg.getFontMetrics();
751 gg.setColor(Color.white);
752 gg.fillRect(0, 0, imgWidth, image.getHeight());
755 drawComponent(gg, av.startRes, av.endRes + 1);
756 g.drawImage(image, 0, 0, this);
760 * non-Thread safe repaint
763 * repaint with horizontal shift in alignment
765 public void fastPaint(int horizontal)
768 if ((horizontal == 0) || gg == null
769 || av.getAlignment().getAlignmentAnnotation() == null
770 || av.getAlignment().getAlignmentAnnotation().length < 1
771 || av.isCalcInProgress())
776 gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
778 int sr = av.startRes;
779 int er = av.endRes + 1;
782 if (horizontal > 0) // scrollbar pulled right, image to the left
784 transX = (er - sr - horizontal) * av.charWidth;
785 sr = er - horizontal;
787 else if (horizontal < 0)
789 er = sr - horizontal;
792 gg.translate(transX, 0);
794 drawComponent(gg, sr, er);
796 gg.translate(-transX, 0);
813 public void drawComponent(Graphics g, int startRes, int endRes)
815 if (av.isCalcInProgress())
821 // We'll keep a record of the old image,
822 // and draw a faded image until the calculation
824 if (fadedImage == null || fadedImage.getWidth() != imgWidth
825 || fadedImage.getHeight() != image.getHeight())
827 fadedImage = new BufferedImage(imgWidth, image.getHeight(),
828 BufferedImage.TYPE_INT_RGB);
830 Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
832 fadedG.setColor(Color.white);
833 fadedG.fillRect(0, 0, imgWidth, image.getHeight());
835 fadedG.setComposite(AlphaComposite.getInstance(
836 AlphaComposite.SRC_OVER, .3f));
837 fadedG.drawImage(image, 0, 0, this);
847 g.setColor(Color.white);
848 g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
850 g.setFont(av.getFont());
853 fm = g.getFontMetrics();
856 if ((av.getAlignment().getAlignmentAnnotation() == null)
857 || (av.getAlignment().getAlignmentAnnotation().length < 1))
859 g.setColor(Color.white);
860 g.fillRect(0, 0, getWidth(), getHeight());
861 g.setColor(Color.black);
862 if (av.validCharWidth)
864 g.drawString("Alignment has no annotations", 20, 15);
869 renderer.drawComponent(this, av, g, activeRow, startRes, endRes);
873 public FontMetrics getFontMetrics()
879 public Image getFadedImage()
885 public int getFadedImageWidth()