X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=4268353fb37e3d585a97f778ac9e8ec8c78f3199;hb=a575ad65d52a25cbaf25a9a3995bdd981aa50611;hp=9c12b894f20c1df6fc2a85cac6dfe8bc586dad0b;hpb=8bce732732fcf8d96f03ff8a916ec2896ff1a4ff;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 9c12b89..4268353 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,217 +1,591 @@ - -package jalview.gui; - -import javax.swing.*; -import java.awt.event.*; -import java.awt.*; -import java.awt.image.*; -import jalview.datamodel.*; - -public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener -{ - boolean active = false; - Image image; - AlignmentPanel ap ; - boolean resizing = false; - int oldY, mouseX; - static String ADDNEW = "Add new row"; - static String HIDE = "Hide this row"; - static String DELETE = "Delete this row"; - static String SHOWALL="Show all hidden rows"; - int selectedRow = 0; - int scrollOffset = 0; - - public AnnotationLabels(AlignmentPanel ap) - { - this.ap = ap; - - java.net.URL url = getClass().getResource("/images/idwidth.gif"); - Image temp = null; - if (url != null) - temp = java.awt.Toolkit.getDefaultToolkit().createImage(url); - - try - { - MediaTracker mt = new MediaTracker(this); - mt.addImage(temp, 0); - mt.waitForID(0); - } - catch (Exception ex) {} - - BufferedImage bi = new BufferedImage(temp.getHeight(this), temp.getWidth(this), - BufferedImage.TYPE_INT_RGB); - Graphics2D g = (Graphics2D) bi.getGraphics(); - g.rotate(Math.toRadians(90)); - g.drawImage(temp, 0, -bi.getWidth(this), this); - image = (Image) bi; - - addMouseListener(this); - addMouseMotionListener(this); - } - - public void setScrollOffset(int y) - { - scrollOffset = y; - repaint(); - } - - public void actionPerformed(ActionEvent evt) - { - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - - if(evt.getActionCommand().equals(ADDNEW)) - { - String label = JOptionPane.showInputDialog(this, "Label for annotation"); - if(label==null) - label = ""; - ap.av.alignment.addAnnotation(new AlignmentAnnotation - (label, - "New description", - new Annotation[ap.av.alignment.getWidth()])); - } - else if(evt.getActionCommand().equals(HIDE)) - { - aa[selectedRow].visible = false; - } - else if(evt.getActionCommand().equals(DELETE)) - { - ap.av.alignment.deleteAnnotation(aa[selectedRow]); - } - else if(evt.getActionCommand().equals(SHOWALL)) - { - for(int i=0; i20) - { - ap.annotationScroller.setPreferredSize(new Dimension(d.width,d.height - dif)); - d = ap.annotationSpaceFillerHolder.getPreferredSize(); - ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,d.height - dif)); - ap.RefreshPanels(); - } - ap.addNotify(); - } - - public void mouseMoved(MouseEvent evt) {} - public void mouseClicked(MouseEvent evt) {} - - public void paintComponent(Graphics g1) - { - Graphics2D g = (Graphics2D)g1; - g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON); - - drawComponent(g); - } - - public void drawComponent(Graphics2D g) - { - FontMetrics fm = g.getFontMetrics(g.getFont()); - g.setColor(Color.white); - g.fillRect(0,0, getWidth(), getHeight()); - - g.translate(0, scrollOffset); - g.setColor(Color.black); - - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - int y = g.getFont().getSize(); - int x = 0; - - if(aa!=null) - for(int i=0; i 20) + { + ap.annotationScroller.setPreferredSize(new Dimension(d.width, + d.height - dif)); + d = ap.annotationSpaceFillerHolder.getPreferredSize(); + ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( + d.width, d.height - dif)); + ap.repaint(); + } + + ap.addNotify(); + } + else + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseMoved(MouseEvent evt) + { + resizePanel = evt.getY()<10; + + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseClicked(MouseEvent evt) + { + if(!SwingUtilities.isRightMouseButton(evt)) + return; + + AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + + if ((aa == null) || (aa.length == 0)) + { + JPopupMenu pop = new JPopupMenu("Annotations"); + JMenuItem item = new JMenuItem(ADDNEW); + item.addActionListener(this); + pop.add(item); + pop.show(this, evt.getX(), evt.getY()); + + return; + } + + + JPopupMenu pop = new JPopupMenu("Annotations"); + JMenuItem item = new JMenuItem(ADDNEW); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(HIDE); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(DELETE); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(SHOWALL); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(OUTPUT_TEXT); + item.addActionListener(this); + pop.add(item); + // annotation object should be typed + if (aa[selectedRow].label.equals("Consensus")) + { + pop.addSeparator(); + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + "Ignore Gaps In Consensus", + ap.av.getIgnoreGapsConsensus()); + cbmi.addActionListener(new ActionListener() + {public void actionPerformed(ActionEvent e) + { + ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); + } + }); + pop.add(cbmi); + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); + } + + pop.show(this, evt.getX(), evt.getY()); + } + /** + * do a single sequence copy to jalview and the system clipboard + * + * @param sq sequence to be copied to clipboard + */ + protected void copy_annotseqtoclipboard(SequenceI sq) + { + SequenceI [] seqs = new SequenceI[] { sq }; + String[] omitHidden = null; + SequenceI [] dseqs=new SequenceI[] { sq.getDatasetSequence()}; + if (dseqs[0]==null) { + dseqs[0] = new Sequence(sq); + dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sq.getSequence())); + sq.setDatasetSequence(dseqs[0]); + } + Alignment ds=new Alignment(dseqs); + if (av.hasHiddenColumns) + { + omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs); + } + + String output = new FormatAdapter().formatSequences( + "Fasta", + seqs, + omitHidden); + + + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(new StringSelection(output), Desktop.instance); + + Vector hiddenColumns = null; + if(av.hasHiddenColumns) + { + hiddenColumns =new Vector(); + for(int i=0; i0 && aa[i].graphHeight>0) + { + graphExtras = y; + + y += (aa[i].height / 3); + + if(aa[i].graphGroup<0) + graphExtras = y + fontHeight; + } + + if(aa[i].graphGroup>-1) + { + int groupSize = 0; + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == aa[i].graphGroup) + groupSize++; + } + + if(groupSize * (fontHeight+8) < aa[i].height) + graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2; + + for(int gg=0; gg0) + { + /* if (aa[i].graphLines != null) + { + for (int gl = 0; gl < aa[i].graphLines.size(); gl++) + { + x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3; + g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras); + g.setColor(aa[i].getGraphLine(gl).colour); + Graphics2D g2 = (Graphics2D) g; + g2.setStroke(new BasicStroke(1, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, 3f, + new float[] + {5f, 3f}, 0f)); + + graphExtras += 3; + + g.drawLine(x, graphExtras, + x+fm.stringWidth(aa[i].label), + graphExtras); + g2.setStroke(new BasicStroke()); + } + }*/ + y += ((2 * aa[i].height) / 3); + } + else + { + y += aa[i].height; + } + } + } + + if (resizePanel) + { + g.drawImage(image, 2, 0 - scrollOffset, this); + } + else if (dragEvent != null && aa!=null) + { + g.setColor(Color.lightGray); + g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset); + } + + + if ((aa == null) || (aa.length < 1)) + { + g.drawString("Right click", 2, 8); + g.drawString("to add annotation", 2, 18); + } + } +}