-/*\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 jalview.datamodel.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.image.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class AnnotationLabels extends JPanel implements MouseListener,\r
- MouseMotionListener, ActionListener\r
-{\r
- static String ADDNEW = "Add New Row";\r
- static String HIDE = "Hide This Row";\r
- static String DELETE = "Delete This Row";\r
- static String SHOWALL = "Show All Hidden Rows";\r
- static String OUTPUT_TEXT = "Show Values In Textbox";\r
- boolean active = false;\r
- Image image;\r
- AlignmentPanel ap;\r
- AlignViewport av;\r
- boolean resizing = false;\r
- int oldY;\r
- int mouseX;\r
- int selectedRow = 0;\r
- int scrollOffset = 0;\r
-\r
-\r
- /**\r
- * Creates a new AnnotationLabels object.\r
- *\r
- * @param ap DOCUMENT ME!\r
- */\r
- public AnnotationLabels(AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- av = ap.av;\r
-\r
- java.net.URL url = getClass().getResource("/images/idwidth.gif");\r
- Image temp = null;\r
-\r
- if (url != null)\r
- {\r
- temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
- }\r
-\r
- try\r
- {\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(temp, 0);\r
- mt.waitForID(0);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- BufferedImage bi = new BufferedImage(temp.getHeight(this),\r
- temp.getWidth(this), BufferedImage.TYPE_INT_RGB);\r
- Graphics2D g = (Graphics2D) bi.getGraphics();\r
- g.rotate(Math.toRadians(90));\r
- g.drawImage(temp, 0, -bi.getWidth(this), this);\r
- image = (Image) bi;\r
-\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- }\r
-\r
- public AnnotationLabels(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param y DOCUMENT ME!\r
- */\r
- public void setScrollOffset(int y)\r
- {\r
- scrollOffset = y;\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- int dif = 0;\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
-\r
- if (evt.getActionCommand().equals(ADDNEW))\r
- {\r
- String label = JOptionPane.showInputDialog(this,\r
- "Label for annotation");\r
-\r
- if (label == null)\r
- {\r
- label = "";\r
- }\r
-\r
- ap.av.alignment.addAnnotation(new AlignmentAnnotation(label,\r
- "New description",\r
- new Annotation[ap.av.alignment.getWidth()]));\r
-\r
- dif = aa[aa.length - 1].height;\r
- }\r
- else if (evt.getActionCommand().equals(HIDE))\r
- {\r
- aa[selectedRow].visible = false;\r
-\r
- if (aa[selectedRow].label.equals("Conservation"))\r
- {\r
- ap.av.showConservation = false;\r
- }\r
-\r
- if (aa[selectedRow].label.equals("Quality"))\r
- {\r
- ap.av.showQuality = false;\r
- }\r
-\r
- if (aa[selectedRow].label.equals("Consensus"))\r
- {\r
- ap.av.showIdentity = false;\r
- }\r
-\r
- dif = aa[selectedRow].height * -1;\r
- }\r
- else if (evt.getActionCommand().equals(DELETE))\r
- {\r
- ap.av.alignment.deleteAnnotation(aa[selectedRow]);\r
- dif = aa[selectedRow].height * -1;\r
- }\r
- else if (evt.getActionCommand().equals(SHOWALL))\r
- {\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if (!aa[i].visible)\r
- {\r
- dif += aa[i].height;\r
- aa[i].visible = true;\r
- }\r
- }\r
- }\r
- else if (evt.getActionCommand().equals(OUTPUT_TEXT))\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- Desktop.addInternalFrame(cap,\r
- ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,\r
- 100);\r
- cap.setText(aa[selectedRow].toString());\r
- }\r
-\r
-\r
- ap.annotationPanel.adjustPanelHeight();\r
-\r
- Dimension d = ap.annotationScroller.getPreferredSize();\r
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,\r
- d.height + dif));\r
- d = ap.annotationSpaceFillerHolder.getPreferredSize();\r
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,\r
- d.height + dif));\r
-\r
- ap.addNotify();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- oldY = evt.getY();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- active = false;\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- active = true;\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- active = false;\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- active = true;\r
-\r
- Dimension d = ap.annotationScroller.getPreferredSize();\r
- int dif = evt.getY() - oldY;\r
-\r
- dif /= ap.av.charHeight;\r
- dif *= ap.av.charHeight;\r
-\r
- if ((d.height - dif) > 20)\r
- {\r
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,\r
- d.height - dif));\r
- d = ap.annotationSpaceFillerHolder.getPreferredSize();\r
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
- d.width, d.height - dif));\r
- ap.repaint();\r
- }\r
-\r
- ap.addNotify();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseClicked(MouseEvent evt)\r
- {\r
- int y = evt.getY() - scrollOffset;\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
-\r
- if ((aa == null) || (aa.length == 0))\r
- {\r
- JPopupMenu pop = new JPopupMenu("Annotations");\r
- JMenuItem item = new JMenuItem(ADDNEW);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- pop.show(this, evt.getX(), evt.getY());\r
-\r
- return;\r
- }\r
-\r
- int height = 0;\r
-\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if (!aa[i].visible)\r
- {\r
- continue;\r
- }\r
-\r
- height += aa[i].height;\r
-\r
- if (y < height)\r
- {\r
- selectedRow = i;\r
-\r
- break;\r
- }\r
- }\r
-\r
- JPopupMenu pop = new JPopupMenu("Annotations");\r
- JMenuItem item = new JMenuItem(ADDNEW);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(HIDE);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(DELETE);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(SHOWALL);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(OUTPUT_TEXT);\r
- item.addActionListener(this);\r
- pop.add(item);\r
-\r
- if (aa[selectedRow].label.equals("Consensus"))\r
- {\r
- pop.addSeparator();\r
- final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(\r
- "Ignore Gaps In Consensus",\r
- ap.av.getIgnoreGapsConsensus());\r
- cbmi.addActionListener(new ActionListener()\r
- {public void actionPerformed(ActionEvent e)\r
- {\r
- ap.av.setIgnoreGapsConsensus(cbmi.getState());\r
- ap.repaint();\r
- }\r
- });\r
- pop.add(cbmi);\r
-\r
- }\r
-\r
- pop.show(this, evt.getX(), evt.getY());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g1 DOCUMENT ME!\r
- */\r
- public void paintComponent(Graphics g)\r
- {\r
-\r
- int width = getWidth();\r
- if(width==0)\r
- width = ap.calculateIdWidth().width + 4;\r
-\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
-\r
- drawComponent(g2, width);\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- */\r
- public void drawComponent(Graphics g, int width)\r
- {\r
- g.setFont(new Font("Arial", Font.PLAIN, av.getFont().getSize()-2));\r
- FontMetrics fm = g.getFontMetrics(g.getFont());\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getWidth(), getHeight());\r
-\r
- g.translate(0, scrollOffset);\r
- g.setColor(Color.black);\r
-\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- int y = g.getFont().getSize();\r
- int x = 0;\r
-\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
- x = width - fm.stringWidth(aa[i].label) - 3;\r
-\r
- if (aa[i].isGraph)\r
- {\r
- y += (aa[i].height / 3);\r
- }\r
-\r
- g.drawString(aa[i].label, x, y);\r
-\r
- if (aa[i].isGraph)\r
- {\r
- y += ((2 * aa[i].height) / 3);\r
- }\r
- else\r
- {\r
- y += aa[i].height;\r
- }\r
- }\r
- }\r
-\r
- if (active)\r
- {\r
- if (image != null)\r
- {\r
- g.drawImage(image, 2, 0, this);\r
- }\r
- }\r
-\r
- if ((aa == null) || (aa.length < 1))\r
- {\r
- g.drawString("Right click", 2, 8);\r
- g.drawString("to add annotation", 2, 18);\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.event.*;
+import java.awt.image.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.io.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AnnotationLabels
+ extends JPanel implements MouseListener,
+ MouseMotionListener, ActionListener
+{
+ 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);
+ }
+
+ 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 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)
+ {
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (!aa[i].visible)
+ {
+ continue;
+ }
+
+ height += aa[i].height;
+
+ if (y < height)
+ {
+ selectedRow = i;
+
+ break;
+ }
+ }
+ }
+ }
+
+ /**
+ * 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))
+ {
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
+ null,
+ new Annotation[ap.av.alignment.getWidth()]);
+
+ if (!editLabelDescription(newAnnotation))
+ {
+ return;
+ }
+
+ 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("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 && aa[i].annotations!=null)
+ {
+ dif += aa[i].height;
+ aa[i].visible = true;
+ }
+ }
+ }
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+ {
+ new AnnotationExporter().exportAnnotations(
+ ap,
+ new AlignmentAnnotation[]
+ {aa[selectedRow]},
+ null
+ );
+ }
+ else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+ {
+ SequenceI cons = av.getConsensusSeq();
+ if (cons != null)
+ {
+ copy_annotseqtoclipboard(cons);
+ }
+
+ }
+
+ 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;
+ }
+
+ annotation.label = dialog.getName();
+
+ String text = dialog.getDescription();
+ if (text!=null && text.length() == 0)
+ {
+ text = null;
+ }
+ 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)
+ {
+ //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;
+ }
+
+ 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)
+ {
+ 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)
+ {
+ 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);
+ }
+
+ ap.addNotify();
+ }
+ else
+ {
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent evt)
+ {
+ resizePanel = evt.getY() < 10;
+
+ getSelectedRow(evt.getY() - scrollOffset);
+
+ if (selectedRow > -1
+ && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
+ {
+ String desc = ap.av.alignment.
+ getAlignmentAnnotation()[selectedRow].description;
+
+ if (desc != null && !desc.equals("New description"))
+ {
+ setToolTipText(ap.av.alignment.
+ getAlignmentAnnotation()[selectedRow].description);
+ }
+ }
+
+ }
+
+ /**
+ * 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(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)
+ {
+ 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.getSequenceAsString()));
+
+ 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; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+ {
+ int[] region = (int[])
+ av.getColumnSelection().getHiddenColumns().elementAt(i);
+
+ 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)
+ {
+
+ 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);
+ }
+
+ drawComponent(g2, width);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void drawComponent(Graphics g, int width)
+ {
+ if (av.getFont().getSize() < 10)
+ {
+ g.setFont(font);
+ }
+ else
+ {
+ g.setFont(av.getFont());
+ }
+
+ 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 = 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);
+
+ if (!aa[i].visible)
+ {
+ continue;
+ }
+
+
+ y += aa[i].height;
+
+ offset = -aa[i].height/2;
+
+ if(aa[i].hasText)
+ {
+ offset += fm.getHeight()/2;
+ offset -= fm.getDescent();
+ }
+ else
+ offset += fm.getDescent();
+
+ x = width - fm.stringWidth(aa[i].label) - 3;
+
+ 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,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
+ {
+ 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);
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff