/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
*/
package jalview.gui;
-import jalview.datamodel.*;
-import jalview.io.FormatAdapter;
+import java.util.*;
import java.awt.*;
-import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.*;
import java.awt.event.*;
import java.awt.image.*;
-import java.util.Vector;
-
import javax.swing.*;
+import jalview.datamodel.*;
+import jalview.io.*;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class AnnotationLabels extends JPanel implements MouseListener,
+public class AnnotationLabels
+ extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
- 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";
- static String OUTPUT_TEXT = "Export Annotation";
- static String COPYCONS_SEQ = "Copy Consensus Sequence";
- boolean resizePanel = false;
- Image image;
- AlignmentPanel ap;
- AlignViewport av;
- boolean resizing = false;
- MouseEvent dragEvent;
- int oldY;
- int selectedRow;
- int scrollOffset = 0;
- Font font = new Font("Arial", Font.PLAIN, 11);
-
-
- /**
- * Creates a new AnnotationLabels object.
- *
- * @param ap DOCUMENT ME!
- */
- public AnnotationLabels(AlignmentPanel ap)
- {
- this.ap = ap;
- av = ap.av;
-
- 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);
+ static String ADDNEW = "Add New Row";
+ static String EDITNAME = "Edit Label/Description";
+ static String HIDE = "Hide This Row";
+ static String DELETE = "Delete This Row";
+ static String SHOWALL = "Show All Hidden Rows";
+ static String OUTPUT_TEXT = "Export Annotation";
+ static String COPYCONS_SEQ = "Copy Consensus Sequence";
+ boolean resizePanel = false;
+ Image image;
+ AlignmentPanel ap;
+ AlignViewport av;
+ boolean resizing = false;
+ MouseEvent dragEvent;
+ int oldY;
+ int selectedRow;
+ int scrollOffset = 0;
+ Font font = new Font("Arial", Font.PLAIN, 11);
+
+ /**
+ * Creates a new AnnotationLabels object.
+ *
+ * @param ap DOCUMENT ME!
+ */
+ public AnnotationLabels(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ av = ap.av;
+ ToolTipManager.sharedInstance().registerComponent(this);
+
+ java.net.URL url = getClass().getResource("/images/idwidth.gif");
+ Image temp = null;
+
+ if (url != null)
+ {
+ temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
}
- public AnnotationLabels(AlignViewport av)
+ try
{
- this.av = av;
+ MediaTracker mt = new MediaTracker(this);
+ mt.addImage(temp, 0);
+ mt.waitForID(0);
}
-
- /**
- * DOCUMENT ME!
- *
- * @param y DOCUMENT ME!
- */
- public void setScrollOffset(int y)
+ catch (Exception ex)
{
- scrollOffset = y;
- repaint();
}
- void getSelectedRow(int y)
+ 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 AnnotationLabels(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param y DOCUMENT ME!
+ */
+ public void setScrollOffset(int y)
+ {
+ scrollOffset = y;
+ repaint();
+ }
+
+ void getSelectedRow(int y)
+ {
+ int height = 0;
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+ if (aa != null)
{
- int height = 0;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
- if(aa!=null)
+ for (int i = 0; i < aa.length; i++)
{
- for (int i = 0; i < aa.length; i++)
+ if (!aa[i].visible)
{
- if (!aa[i].visible)
- {
- continue;
- }
+ continue;
+ }
- height += aa[i].height;
+ height += aa[i].height;
- if (y < height)
- {
- selectedRow = i;
+ if (y < height)
+ {
+ selectedRow = i;
- break;
- }
+ break;
}
}
}
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void actionPerformed(ActionEvent evt)
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent evt)
+ {
+ int dif = 0;
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+ if (evt.getActionCommand().equals(ADDNEW))
{
- int dif = 0;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
- if (evt.getActionCommand().equals(ADDNEW))
- {
- String label = JOptionPane.showInputDialog(this,
- "Label for annotation");
-
- if (label == null)
- {
- label = "";
- }
-
- AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label,
- "New description",
- new Annotation[ap.av.alignment.getWidth()]);
-
- ap.av.alignment.addAnnotation(newAnnotation);
- ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
- if (aa != null)
- dif = aa[aa.length - 1].height;
- }
- else if (evt.getActionCommand().equals(HIDE))
- {
- aa[selectedRow].visible = false;
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
+ null,
+ new Annotation[ap.av.alignment.getWidth()]);
- if (aa[selectedRow].label.equals("Conservation"))
- {
- ap.av.showConservation = false;
- }
+ if (!editLabelDescription(newAnnotation))
+ {
+ return;
+ }
- if (aa[selectedRow].label.equals("Quality"))
- {
- ap.av.showQuality = false;
- }
+ ap.av.alignment.addAnnotation(newAnnotation);
+ ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+ if (aa != null)
+ {
+ dif = aa[aa.length - 1].height;
+ }
+ }
+ else if (evt.getActionCommand().equals(EDITNAME))
+ {
+ editLabelDescription(aa[selectedRow]);
+ repaint();
+ }
+ else if (evt.getActionCommand().equals(HIDE))
+ {
+ aa[selectedRow].visible = false;
- if (aa[selectedRow].label.equals("Consensus"))
- {
- ap.av.showIdentity = false;
- }
+ if (aa[selectedRow].label.equals("Quality"))
+ {
+ ap.av.quality = null;
+ }
- dif = aa[selectedRow].height * -1;
- }
- else if (evt.getActionCommand().equals(DELETE))
- {
- ap.av.alignment.deleteAnnotation(aa[selectedRow]);
- dif = aa[selectedRow].height * -1;
- }
- else if (evt.getActionCommand().equals(SHOWALL))
- {
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- dif += aa[i].height;
- aa[i].visible = true;
- }
- }
- }
- else if (evt.getActionCommand().equals(OUTPUT_TEXT))
- {
- new AnnotationExporter().exportAnnotations(
- ap,
- new AlignmentAnnotation[]
- {aa[selectedRow]}
- );
- }
- else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+ dif = aa[selectedRow].height * -1;
+ }
+ else if (evt.getActionCommand().equals(DELETE))
+ {
+ ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+ dif = aa[selectedRow].height * -1;
+ }
+ else if (evt.getActionCommand().equals(SHOWALL))
+ {
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (!aa[i].visible && aa[i].annotations!=null)
{
- SequenceI cons=av.getConsensusSeq();
- if (cons!=null)
- copy_annotseqtoclipboard(cons);
-
+ dif += aa[i].height;
+ aa[i].visible = true;
}
-
- ap.annotationPanel.adjustPanelHeight();
- ap.annotationScroller.validate();
- ap.repaint();
+ }
}
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mousePressed(MouseEvent evt)
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
- getSelectedRow(evt.getY() - scrollOffset);
- oldY = evt.getY();
+ new AnnotationExporter().exportAnnotations(
+ ap,
+ new AlignmentAnnotation[]
+ {aa[selectedRow]},
+ null
+ );
}
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent evt)
+ else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
- int start = selectedRow;
- getSelectedRow(evt.getY() - scrollOffset);
- int end = selectedRow;
+ SequenceI cons = av.getConsensusSeq();
+ if (cons != null)
+ {
+ copy_annotseqtoclipboard(cons);
+ }
- if(start!=end)
- {
- //Swap these annotations
- AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start];
- AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+ }
+ ap.annotationPanel.adjustPanelHeight();
+ ap.annotationScroller.validate();
+ ap.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ boolean editLabelDescription(AlignmentAnnotation annotation)
+ {
+ EditNameDialog dialog = new EditNameDialog(annotation.label,
+ annotation.description,
+ " Annotation Name ",
+ "Annotation Description ",
+ "Edit Annotation Name/Description");
+
+ if (!dialog.accept)
+ {
+ return false;
+ }
- ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
- ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
- }
+ annotation.label = dialog.getName();
- resizePanel = false;
- dragEvent = null;
- repaint();
- ap.annotationPanel.repaint();
+ String text = dialog.getDescription();
+ if (text!=null && text.length() == 0)
+ {
+ text = null;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent evt)
+ annotation.description = text;
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mousePressed(MouseEvent evt)
+ {
+ getSelectedRow(evt.getY() - scrollOffset);
+ oldY = evt.getY();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mouseReleased(MouseEvent evt)
+ {
+ int start = selectedRow;
+ getSelectedRow(evt.getY() - scrollOffset);
+ int end = selectedRow;
+
+ if (start != end)
{
- if(evt.getY()<10)
- {
- resizePanel = true;
- repaint();
- }
+ //Swap these annotations
+ AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[
+ start];
+ AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+
+ ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
+ ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseExited(MouseEvent evt)
+ resizePanel = false;
+ dragEvent = null;
+ repaint();
+ ap.annotationPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent evt)
+ {
+ if (evt.getY() < 10)
+ {
+ resizePanel = true;
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent evt)
+ {
+ if (dragEvent == null)
{
- if(dragEvent == null)
+ resizePanel = false;
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mouseDragged(MouseEvent evt)
+ {
+ dragEvent = evt;
+
+ if (resizePanel)
+ {
+ Dimension d = ap.annotationScroller.getPreferredSize();
+ int dif = evt.getY() - oldY;
+
+ dif /= ap.av.charHeight;
+ dif *= ap.av.charHeight;
+
+ if ( (d.height - dif) > 20)
{
- resizePanel = false;
- repaint();
+ 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.paintAlignment(true);
}
- }
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseDragged(MouseEvent evt)
+ ap.addNotify();
+ }
+ else
{
- dragEvent = evt;
+ repaint();
+ }
+ }
- if (resizePanel)
- {
- Dimension d = ap.annotationScroller.getPreferredSize();
- int dif = evt.getY() - oldY;
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent evt)
+ {
+ resizePanel = evt.getY() < 10;
- dif /= ap.av.charHeight;
- dif *= ap.av.charHeight;
+ getSelectedRow(evt.getY() - scrollOffset);
- if ( (d.height - dif) > 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();
- }
+ if (selectedRow > -1
+ && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
+ {
+ String desc = ap.av.alignment.
+ getAlignmentAnnotation()[selectedRow].description;
- ap.addNotify();
+ if (desc != null && !desc.equals("New description"))
+ {
+ setToolTipText(ap.av.alignment.
+ getAlignmentAnnotation()[selectedRow].description);
}
- 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;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent evt)
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+ if ( (aa == null) || (aa.length == 0))
{
- if(!SwingUtilities.isRightMouseButton(evt))
- return;
+ JPopupMenu pop = new JPopupMenu("Annotations");
+ JMenuItem item = new JMenuItem(ADDNEW);
+ item.addActionListener(this);
+ pop.add(item);
+ pop.show(this, evt.getX(), evt.getY());
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ return;
+ }
- if ((aa == null) || (aa.length == 0))
+ JPopupMenu pop = new JPopupMenu("Annotations");
+ JMenuItem item = new JMenuItem(ADDNEW);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(EDITNAME);
+ 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] == ap.av.consensus)
+ {
+ pop.addSeparator();
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ "Ignore Gaps In Consensus",
+ ap.av.getIgnoreGapsConsensus());
+ cbmi.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
{
- JPopupMenu pop = new JPopupMenu("Annotations");
- JMenuItem item = new JMenuItem(ADDNEW);
- item.addActionListener(this);
- pop.add(item);
- pop.show(this, evt.getX(), evt.getY());
-
- return;
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
+ });
+ pop.add(cbmi);
+ final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+ consclipbrd.addActionListener(this);
+ pop.add(consclipbrd);
+ }
-
- 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.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[]
{
- 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.repaint();
- }
- });
- 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);
- }
+ 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.getSequenceAsString()));
- String output = new FormatAdapter().formatSequences(
- "Fasta",
- seqs,
- omitHidden);
+ 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);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.instance);
- Vector hiddenColumns = null;
- if(av.hasHiddenColumns)
+ Vector hiddenColumns = null;
+ if (av.hasHiddenColumns)
+ {
+ hiddenColumns = new Vector();
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
{
- hiddenColumns =new Vector();
- for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)
- {
- int[] region = (int[])
- av.getColumnSelection().getHiddenColumns().elementAt(i);
+ int[] region = (int[])
+ av.getColumnSelection().getHiddenColumns().elementAt(i);
- hiddenColumns.addElement(new int[]{region[0],
- region[1]});
- }
+ hiddenColumns.addElement(new int[]
+ {region[0],
+ region[1]});
}
-
- Desktop.jalviewClipboard = new Object[]{ seqs,
- ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
- hiddenColumns};
}
- /**
- * DOCUMENT ME!
- *
- * @param g1 DOCUMENT ME!
- */
- public void paintComponent(Graphics g)
+
+ Desktop.jalviewClipboard = new Object[]
+ {
+ seqs,
+ ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
+ hiddenColumns};
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g1 DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g)
+ {
+
+ int width = getWidth();
+ if (width == 0)
{
+ width = ap.calculateIdWidth().width + 4;
+ }
- int width = getWidth();
- if(width==0)
- width = ap.calculateIdWidth().width + 4;
+ Graphics2D g2 = (Graphics2D) g;
+ if (av.antiAlias)
+ {
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
- Graphics2D g2 = (Graphics2D) g;
- if(av.antiAlias)
- g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ drawComponent(g2, width);
- drawComponent(g2, width);
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void drawComponent(Graphics g, int width)
+ {
+ if (av.getFont().getSize() < 10)
+ {
+ g.setFont(font);
}
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- */
- public void drawComponent(Graphics g, int width)
+ else
{
- if(av.getFont().getSize()<10)
- g.setFont(font);
- else
- g.setFont(av.getFont());
+ g.setFont(av.getFont());
+ }
+
+ FontMetrics fm = g.getFontMetrics(g.getFont());
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
- FontMetrics fm = g.getFontMetrics(g.getFont());
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
+ g.translate(0, scrollOffset);
+ g.setColor(Color.black);
- g.translate(0, scrollOffset);
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ int fontHeight = g.getFont().getSize();
+ int y = 0;
+ int x = 0;
+ int graphExtras = 0;
+ int offset =0;
+
+ if (aa != null)
+ {
+ for (int i = 0; i < aa.length; i++)
+ {
g.setColor(Color.black);
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- int fontHeight = g.getFont().getSize();
- int y = fontHeight;
- int x = 0;
- int graphExtras = 0;
+ if (!aa[i].visible)
+ {
+ continue;
+ }
+ y += aa[i].height;
- if (aa != null)
+ offset = -aa[i].height/2;
+
+ if(aa[i].hasText)
{
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- continue;
- }
-
- x = width - fm.stringWidth(aa[i].label) - 3;
-
- if (aa[i].graph>0 && 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; gg<aa.length; gg++)
- {
- if(aa[gg].graphGroup==aa[i].graphGroup)
- {
- x = width - fm.stringWidth(aa[gg].label) - 3;
- g.drawString(aa[gg].label, x, graphExtras );
- if(aa[gg].annotations[0]!=null)
- g.setColor(aa[gg].annotations[0].colour);
-
- g.drawLine( x, graphExtras+3,
- x+fm.stringWidth(aa[gg].label),
- graphExtras+3);
-
- g.setColor(Color.black);
- graphExtras += fontHeight+8;
- }
- }
- }
- else
- g.drawString(aa[i].label, x, y);
-
- if (aa[i].graph>0)
- {
- /* 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;
- }
- }
+ offset += fm.getHeight()/2;
+ offset -= fm.getDescent();
}
+ else
+ offset += fm.getDescent();
+
+ x = width - fm.stringWidth(aa[i].label) - 3;
- if (resizePanel)
+ if (aa[i].graphGroup > -1)
{
- g.drawImage(image, 2, 0 - scrollOffset, this);
+ 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; gg < aa.length; gg++)
+ {
+ if (aa[gg].graphGroup == aa[i].graphGroup)
+ {
+ x = width - fm.stringWidth(aa[gg].label) - 3;
+ g.drawString(aa[gg].label, x,y - graphExtras);
+ if (aa[gg].annotations[0] != null)
+ {
+ g.setColor(aa[gg].annotations[0].colour);
+ }
+
+ g.drawLine(x, y - graphExtras - 3,
+ x + fm.stringWidth(aa[gg].label),
+ y - graphExtras - 3);
+
+ g.setColor(Color.black);
+ graphExtras += fontHeight + 8;
+ }
+ }
}
- else if (dragEvent != null && aa!=null)
+ else
{
- g.setColor(Color.lightGray);
- g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset);
+ g.drawString(aa[i].label, x, y +offset);
}
+ }
+ }
+ 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);
- }
+ if ( (aa == null) || (aa.length < 1))
+ {
+ g.drawString("Right click", 2, 8);
+ g.drawString("to add annotation", 2, 18);
}
+ }
}
git://source.jalview.org / jalview.git / blobdiff