src/jalview/gui/AnnotationLabels.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import jalview.datamodel.*;
  22 import jalview.io.FormatAdapter;
  23
  24 import java.awt.*;
  25 import java.awt.datatransfer.StringSelection;
  26 import java.awt.event.*;
  27 import java.awt.image.*;
  28 import java.util.Vector;
  29
  30 import javax.swing.*;
  31
  32
  33 /**
  34  * DOCUMENT ME!
  35  *
  36  * @author $author$
  37  * @version $Revision$
  38  */
  39 public class AnnotationLabels extends JPanel implements MouseListener,
  40     MouseMotionListener, ActionListener
  41 {
  42     static String ADDNEW = "Add New Row";
  43     static String EDITNAME="Edit Label/Description";
  44     static String HIDE = "Hide This Row";
  45     static String DELETE = "Delete This Row";
  46     static String SHOWALL = "Show All Hidden Rows";
  47     static String OUTPUT_TEXT = "Export Annotation";
  48     static String COPYCONS_SEQ = "Copy Consensus Sequence";
  49     boolean resizePanel = false;
  50     Image image;
  51     AlignmentPanel ap;
  52     AlignViewport av;
  53     boolean resizing = false;
  54     MouseEvent dragEvent;
  55     int oldY;
  56     int selectedRow;
  57     int scrollOffset = 0;
  58     Font font = new Font("Arial", Font.PLAIN, 11);
  59
  60
  61     /**
  62      * Creates a new AnnotationLabels object.
  63      *
  64      * @param ap DOCUMENT ME!
  65      */
  66     public AnnotationLabels(AlignmentPanel ap)
  67     {
  68         this.ap = ap;
  69         av = ap.av;
  70         ToolTipManager.sharedInstance().registerComponent(this);
  71
  72         java.net.URL url = getClass().getResource("/images/idwidth.gif");
  73         Image temp = null;
  74
  75         if (url != null)
  76         {
  77             temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
  78         }
  79
  80         try
  81         {
  82             MediaTracker mt = new MediaTracker(this);
  83             mt.addImage(temp, 0);
  84             mt.waitForID(0);
  85         }
  86         catch (Exception ex)
  87         {
  88         }
  89
  90         BufferedImage bi = new BufferedImage(temp.getHeight(this),
  91                 temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
  92         Graphics2D g = (Graphics2D) bi.getGraphics();
  93         g.rotate(Math.toRadians(90));
  94         g.drawImage(temp, 0, -bi.getWidth(this), this);
  95         image = (Image) bi;
  96
  97         addMouseListener(this);
  98         addMouseMotionListener(this);
  99     }
 100
 101     public AnnotationLabels(AlignViewport av)
 102     {
 103       this.av = av;
 104     }
 105
 106     /**
 107      * DOCUMENT ME!
 108      *
 109      * @param y DOCUMENT ME!
 110      */
 111     public void setScrollOffset(int y)
 112     {
 113         scrollOffset = y;
 114         repaint();
 115     }
 116
 117     void getSelectedRow(int y)
 118     {
 119       int height = 0;
 120       AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 121
 122       if(aa!=null)
 123       {
 124         for (int i = 0; i < aa.length; i++)
 125         {
 126           if (!aa[i].visible)
 127           {
 128             continue;
 129           }
 130
 131           height += aa[i].height;
 132
 133           if (y < height)
 134           {
 135             selectedRow = i;
 136
 137             break;
 138           }
 139         }
 140       }
 141     }
 142
 143     /**
 144      * DOCUMENT ME!
 145      *
 146      * @param evt DOCUMENT ME!
 147      */
 148     public void actionPerformed(ActionEvent evt)
 149     {
 150         int dif = 0;
 151         AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 152
 153         if (evt.getActionCommand().equals(ADDNEW))
 154         {
 155             AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
 156                     null,
 157                     new Annotation[ap.av.alignment.getWidth()]);
 158
 159             if(!editLabelDescription(newAnnotation))
 160               return;
 161
 162             ap.av.alignment.addAnnotation(newAnnotation);
 163             ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
 164             if (aa != null)
 165               dif = aa[aa.length - 1].height;
 166         }
 167         else if(evt.getActionCommand().equals(EDITNAME))
 168         {
 169           editLabelDescription(aa[selectedRow]);
 170           repaint();
 171         }
 172         else if (evt.getActionCommand().equals(HIDE))
 173         {
 174             aa[selectedRow].visible = false;
 175
 176             if (aa[selectedRow].label.equals("Quality"))
 177             {
 178                 ap.av.quality = null;
 179             }
 180
 181             dif = aa[selectedRow].height * -1;
 182         }
 183         else if (evt.getActionCommand().equals(DELETE))
 184         {
 185             ap.av.alignment.deleteAnnotation(aa[selectedRow]);
 186             dif = aa[selectedRow].height * -1;
 187         }
 188         else if (evt.getActionCommand().equals(SHOWALL))
 189         {
 190             for (int i = 0; i < aa.length; i++)
 191             {
 192                 if (!aa[i].visible)
 193                 {
 194                     dif += aa[i].height;
 195                     aa[i].visible = true;
 196                 }
 197             }
 198         }
 199         else if (evt.getActionCommand().equals(OUTPUT_TEXT))
 200         {
 201           new AnnotationExporter().exportAnnotations(
 202               ap,
 203               new AlignmentAnnotation[]
 204               {aa[selectedRow]},
 205               null
 206               );
 207         }
 208         else if (evt.getActionCommand().equals(COPYCONS_SEQ))
 209         {
 210           SequenceI cons=av.getConsensusSeq();
 211           if (cons!=null)
 212             copy_annotseqtoclipboard(cons);
 213
 214         }
 215
 216         ap.annotationPanel.adjustPanelHeight();
 217         ap.annotationScroller.validate();
 218         ap.repaint();
 219     }
 220
 221
 222     /**
 223      * DOCUMENT ME!
 224      *
 225      * @param e DOCUMENT ME!
 226      */
 227     boolean editLabelDescription(AlignmentAnnotation annotation)
 228     {
 229       EditNameDialog dialog = new EditNameDialog(annotation.label,
 230                                                  annotation.description,
 231                                                  "       Annotation Name ",
 232                                                  "Annotation Description ",
 233                                                  "Edit Annotation Name/Description");
 234
 235       if (!dialog.accept)
 236       {
 237         return false;
 238       }
 239
 240         annotation.label = dialog.getName();
 241
 242         String text = dialog.getDescription();
 243         if(text.length()==0)
 244           text = null;
 245         annotation.description = text;
 246
 247         return true;
 248     }
 249
 250     /**
 251      * DOCUMENT ME!
 252      *
 253      * @param evt DOCUMENT ME!
 254      */
 255     public void mousePressed(MouseEvent evt)
 256     {
 257         getSelectedRow(evt.getY() - scrollOffset);
 258         oldY = evt.getY();
 259     }
 260
 261     /**
 262      * DOCUMENT ME!
 263      *
 264      * @param evt DOCUMENT ME!
 265      */
 266     public void mouseReleased(MouseEvent evt)
 267     {
 268         int start = selectedRow;
 269         getSelectedRow(evt.getY() - scrollOffset);
 270         int end = selectedRow;
 271
 272         if(start!=end)
 273         {
 274           //Swap these annotations
 275           AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start];
 276           AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
 277
 278
 279           ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
 280           ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
 281         }
 282
 283         resizePanel = false;
 284         dragEvent = null;
 285         repaint();
 286         ap.annotationPanel.repaint();
 287     }
 288
 289     /**
 290      * DOCUMENT ME!
 291      *
 292      * @param evt DOCUMENT ME!
 293      */
 294     public void mouseEntered(MouseEvent evt)
 295     {
 296       if(evt.getY()<10)
 297       {
 298         resizePanel = true;
 299         repaint();
 300       }
 301     }
 302
 303     /**
 304      * DOCUMENT ME!
 305      *
 306      * @param evt DOCUMENT ME!
 307      */
 308     public void mouseExited(MouseEvent evt)
 309     {
 310       if(dragEvent == null)
 311       {
 312         resizePanel = false;
 313         repaint();
 314       }
 315     }
 316
 317     /**
 318      * DOCUMENT ME!
 319      *
 320      * @param evt DOCUMENT ME!
 321      */
 322     public void mouseDragged(MouseEvent evt)
 323     {
 324       dragEvent = evt;
 325
 326       if (resizePanel)
 327       {
 328         Dimension d = ap.annotationScroller.getPreferredSize();
 329         int dif = evt.getY() - oldY;
 330
 331         dif /= ap.av.charHeight;
 332         dif *= ap.av.charHeight;
 333
 334         if ( (d.height - dif) > 20)
 335         {
 336           ap.annotationScroller.setPreferredSize(new Dimension(d.width,
 337               d.height - dif));
 338           d = ap.annotationSpaceFillerHolder.getPreferredSize();
 339           ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
 340               d.width, d.height - dif));
 341           ap.repaint();
 342         }
 343
 344         ap.addNotify();
 345       }
 346       else
 347         repaint();
 348     }
 349
 350     /**
 351      * DOCUMENT ME!
 352      *
 353      * @param evt DOCUMENT ME!
 354      */
 355     public void mouseMoved(MouseEvent evt)
 356     {
 357       resizePanel = evt.getY()<10;
 358
 359       getSelectedRow(evt.getY() - scrollOffset);
 360
 361       if(selectedRow>-1)
 362       {
 363         String desc = ap.av.alignment.
 364             getAlignmentAnnotation()[selectedRow].description;
 365
 366         if (desc != null && !desc.equals("New Description"))
 367           setToolTipText(ap.av.alignment.
 368                          getAlignmentAnnotation()[selectedRow].description);
 369
 370       }
 371       repaint();
 372     }
 373
 374     /**
 375      * DOCUMENT ME!
 376      *
 377      * @param evt DOCUMENT ME!
 378      */
 379     public void mouseClicked(MouseEvent evt)
 380     {
 381        if(!SwingUtilities.isRightMouseButton(evt))
 382          return;
 383
 384         AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 385
 386         if ((aa == null) || (aa.length == 0))
 387         {
 388             JPopupMenu pop = new JPopupMenu("Annotations");
 389             JMenuItem item = new JMenuItem(ADDNEW);
 390             item.addActionListener(this);
 391             pop.add(item);
 392             pop.show(this, evt.getX(), evt.getY());
 393
 394             return;
 395         }
 396
 397
 398         JPopupMenu pop = new JPopupMenu("Annotations");
 399         JMenuItem item = new JMenuItem(ADDNEW);
 400         item.addActionListener(this);
 401         pop.add(item);
 402         item = new JMenuItem(EDITNAME);
 403         item.addActionListener(this);
 404         pop.add(item);
 405         item = new JMenuItem(HIDE);
 406         item.addActionListener(this);
 407         pop.add(item);
 408         item = new JMenuItem(DELETE);
 409         item.addActionListener(this);
 410         pop.add(item);
 411         item = new JMenuItem(SHOWALL);
 412         item.addActionListener(this);
 413         pop.add(item);
 414         item = new JMenuItem(OUTPUT_TEXT);
 415         item.addActionListener(this);
 416         pop.add(item);
 417         // annotation object should be typed
 418         if (aa[selectedRow]==ap.av.consensus)
 419         {
 420           pop.addSeparator();
 421           final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
 422               "Ignore Gaps In Consensus",
 423               ap.av.getIgnoreGapsConsensus());
 424           cbmi.addActionListener(new ActionListener()
 425               {public void actionPerformed(ActionEvent e)
 426                {
 427                  ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
 428                }
 429               });
 430           pop.add(cbmi);
 431           final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
 432           consclipbrd.addActionListener(this);
 433           pop.add(consclipbrd);
 434         }
 435
 436         pop.show(this, evt.getX(), evt.getY());
 437     }
 438     /**
 439      * do a single sequence copy to jalview and the system clipboard
 440      *
 441      * @param sq sequence to be copied to clipboard
 442      */
 443     protected void copy_annotseqtoclipboard(SequenceI sq)
 444     {
 445       SequenceI [] seqs = new SequenceI[] { sq };
 446       String[] omitHidden = null;
 447       SequenceI [] dseqs=new SequenceI[] { sq.getDatasetSequence()};
 448       if (dseqs[0]==null) {
 449         dseqs[0] = new Sequence(sq);
 450         dseqs[0].setSequence(
 451             jalview.analysis.AlignSeq.extractGaps(
 452                 jalview.util.Comparison.GapChars,
 453                 sq.getSequenceAsString()));
 454
 455         sq.setDatasetSequence(dseqs[0]);
 456       }
 457       Alignment ds=new Alignment(dseqs);
 458       if (av.hasHiddenColumns)
 459       {
 460         omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs);
 461       }
 462
 463       String output = new FormatAdapter().formatSequences(
 464           "Fasta",
 465           seqs,
 466           omitHidden);
 467
 468
 469       Toolkit.getDefaultToolkit().getSystemClipboard()
 470           .setContents(new StringSelection(output), Desktop.instance);
 471
 472       Vector hiddenColumns = null;
 473       if(av.hasHiddenColumns)
 474       {
 475         hiddenColumns =new Vector();
 476         for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)
 477         {
 478           int[] region = (int[])
 479               av.getColumnSelection().getHiddenColumns().elementAt(i);
 480
 481           hiddenColumns.addElement(new int[]{region[0],
 482                             region[1]});
 483         }
 484       }
 485
 486       Desktop.jalviewClipboard = new Object[]{ seqs,
 487           ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
 488           hiddenColumns};
 489     }
 490     /**
 491      * DOCUMENT ME!
 492      *
 493      * @param g1 DOCUMENT ME!
 494      */
 495     public void paintComponent(Graphics g)
 496     {
 497
 498         int width = getWidth();
 499         if(width==0)
 500          width = ap.calculateIdWidth().width + 4;
 501
 502        Graphics2D g2 = (Graphics2D) g;
 503        if(av.antiAlias)
 504         g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
 505             RenderingHints.VALUE_ANTIALIAS_ON);
 506
 507        drawComponent(g2, width);
 508
 509     }
 510
 511     /**
 512      * DOCUMENT ME!
 513      *
 514      * @param g DOCUMENT ME!
 515      */
 516     public void drawComponent(Graphics g, int width)
 517     {
 518         if(av.getFont().getSize()<10)
 519           g.setFont(font);
 520         else
 521           g.setFont(av.getFont());
 522
 523         FontMetrics fm = g.getFontMetrics(g.getFont());
 524         g.setColor(Color.white);
 525         g.fillRect(0, 0, getWidth(), getHeight());
 526
 527         g.translate(0, scrollOffset);
 528         g.setColor(Color.black);
 529
 530         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 531         int fontHeight = g.getFont().getSize();
 532         int y = fontHeight;
 533         int x = 0;
 534         int graphExtras = 0;
 535
 536
 537
 538         if (aa != null)
 539         {
 540             for (int i = 0; i < aa.length; i++)
 541             {
 542                 if (!aa[i].visible)
 543                 {
 544                     continue;
 545                 }
 546
 547                 x = width - fm.stringWidth(aa[i].label) - 3;
 548
 549                 if (aa[i].graph>0 && aa[i].graphHeight>0)
 550                 {
 551                     graphExtras = y;
 552
 553                     y += (aa[i].height / 3);
 554
 555                     if(aa[i].graphGroup<0)
 556                         graphExtras = y + fontHeight;
 557                 }
 558
 559                 if(aa[i].graphGroup>-1)
 560                 {
 561                   int groupSize = 0;
 562                   for (int gg = 0; gg < aa.length; gg++)
 563                   {
 564                     if (aa[gg].graphGroup == aa[i].graphGroup)
 565                       groupSize++;
 566                   }
 567
 568                   if(groupSize * (fontHeight+8) < aa[i].height)
 569                     graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2;
 570
 571                  for(int gg=0; gg<aa.length; gg++)
 572                  {
 573                    if(aa[gg].graphGroup==aa[i].graphGroup)
 574                    {
 575                      x = width - fm.stringWidth(aa[gg].label) - 3;
 576                      g.drawString(aa[gg].label, x, graphExtras );
 577                      if(aa[gg].annotations[0]!=null)
 578                        g.setColor(aa[gg].annotations[0].colour);
 579
 580                      g.drawLine( x, graphExtras+3,
 581                                  x+fm.stringWidth(aa[gg].label),
 582                                  graphExtras+3);
 583
 584                      g.setColor(Color.black);
 585                      graphExtras += fontHeight+8;
 586                    }
 587                  }
 588                 }
 589                 else
 590                   g.drawString(aa[i].label, x, y);
 591
 592                 if (aa[i].graph>0)
 593                 {
 594                 /*  if (aa[i].graphLines != null)
 595                   {
 596                     for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
 597                     {
 598                        x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;
 599                       g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);
 600                       g.setColor(aa[i].getGraphLine(gl).colour);
 601                       Graphics2D g2 = (Graphics2D) g;
 602                       g2.setStroke(new BasicStroke(1,
 603                           BasicStroke.CAP_SQUARE,
 604                           BasicStroke.JOIN_ROUND, 3f,
 605                           new float[]
 606                           {5f, 3f}, 0f));
 607
 608                       graphExtras += 3;
 609
 610                       g.drawLine(x, graphExtras,
 611                                  x+fm.stringWidth(aa[i].label),
 612                                  graphExtras);
 613                       g2.setStroke(new BasicStroke());
 614                     }
 615                   }*/
 616                     y += ((2 * aa[i].height) / 3);
 617                 }
 618                 else
 619                 {
 620                     y += aa[i].height;
 621                 }
 622             }
 623         }
 624
 625         if (resizePanel)
 626         {
 627           g.drawImage(image, 2, 0 - scrollOffset, this);
 628         }
 629         else if (dragEvent != null && aa!=null)
 630         {
 631           g.setColor(Color.lightGray);
 632           g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset);
 633         }
 634
 635
 636         if ((aa == null) || (aa.length < 1))
 637         {
 638             g.drawString("Right click", 2, 8);
 639             g.drawString("to add annotation", 2, 18);
 640         }
 641     }
 642 }