-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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 = "Export Annotation";\r
- boolean resizePanel = false;\r
- Image image;\r
- AlignmentPanel ap;\r
- AlignViewport av;\r
- boolean resizing = false;\r
- MouseEvent dragEvent;\r
- int oldY;\r
- int selectedRow;\r
- int scrollOffset = 0;\r
- Font font = new Font("Arial", Font.PLAIN, 11);\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
- void getSelectedRow(int y)\r
- {\r
- int height = 0;\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\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
- height += aa[i].height;\r
-\r
- if (y < height)\r
- {\r
- selectedRow = i;\r
-\r
- break;\r
- }\r
- }\r
- }\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
- AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label,\r
- "New description",\r
- new Annotation[ap.av.alignment.getWidth()]);\r
-\r
- ap.av.alignment.addAnnotation(newAnnotation);\r
- ap.av.alignment.setAnnotationIndex(newAnnotation, 0);\r
- if (aa != null)\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
- new AnnotationExporter().exportAnnotations(\r
- ap,\r
- new AlignmentAnnotation[]\r
- {aa[selectedRow]}\r
- );\r
- }\r
-\r
-\r
- ap.annotationPanel.adjustPanelHeight();\r
- ap.annotationScroller.validate();\r
- ap.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- getSelectedRow(evt.getY() - scrollOffset);\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
- int start = selectedRow;\r
- getSelectedRow(evt.getY() - scrollOffset);\r
- int end = selectedRow;\r
-\r
- if(start!=end)\r
- {\r
- //Swap these annotations\r
- AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start];\r
- AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];\r
-\r
-\r
- ap.av.alignment.getAlignmentAnnotation()[end] = startAA;\r
- ap.av.alignment.getAlignmentAnnotation()[start] = endAA;\r
- }\r
-\r
- resizePanel = false;\r
- dragEvent = null;\r
- repaint();\r
- ap.annotationPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- if(evt.getY()<10)\r
- {\r
- resizePanel = true;\r
- repaint();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- if(dragEvent == null)\r
- {\r
- resizePanel = false;\r
- repaint();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- dragEvent = evt;\r
-\r
- if (resizePanel)\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
- else\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- resizePanel = evt.getY()<10;\r
-\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseClicked(MouseEvent evt)\r
- {\r
- if(!SwingUtilities.isRightMouseButton(evt))\r
- return;\r
-\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
-\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
- if(av.antiAlias)\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
- if(av.getFont().getSize()<10)\r
- g.setFont(font);\r
- else\r
- g.setFont(av.getFont());\r
-\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 fontHeight = g.getFont().getSize();\r
- int y = fontHeight;\r
- int x = 0;\r
- int graphExtras = 0;\r
-\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].graph>0)\r
- {\r
- graphExtras = y;\r
-\r
- y += (aa[i].height / 3);\r
-\r
- if(aa[i].graphGroup<0)\r
- graphExtras = y + fontHeight;\r
- }\r
-\r
- if(aa[i].graphGroup>-1)\r
- {\r
- int groupSize = 0;\r
- for (int gg = 0; gg < aa.length; gg++)\r
- {\r
- if (aa[gg].graphGroup == aa[i].graphGroup)\r
- groupSize++;\r
- }\r
-\r
- if(groupSize * (fontHeight+8) < aa[i].height)\r
- graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2;\r
-\r
- for(int gg=0; gg<aa.length; gg++)\r
- {\r
- if(aa[gg].graphGroup==aa[i].graphGroup)\r
- {\r
- x = width - fm.stringWidth(aa[gg].label) - 3;\r
- g.drawString(aa[gg].label, x, graphExtras );\r
- if(aa[gg].annotations[0]!=null)\r
- g.setColor(aa[gg].annotations[0].colour);\r
-\r
- g.drawLine( x, graphExtras+3,\r
- x+fm.stringWidth(aa[gg].label),\r
- graphExtras+3);\r
-\r
- g.setColor(Color.black);\r
- graphExtras += fontHeight+8;\r
- }\r
- }\r
- }\r
- else\r
- g.drawString(aa[i].label, x, y);\r
-\r
- if (aa[i].graph>0)\r
- {\r
- /* if (aa[i].graphLines != null)\r
- {\r
- for (int gl = 0; gl < aa[i].graphLines.size(); gl++)\r
- {\r
- x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;\r
- g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);\r
- g.setColor(aa[i].getGraphLine(gl).colour);\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setStroke(new BasicStroke(1,\r
- BasicStroke.CAP_SQUARE,\r
- BasicStroke.JOIN_ROUND, 3f,\r
- new float[]\r
- {5f, 3f}, 0f));\r
-\r
- graphExtras += 3;\r
-\r
- g.drawLine(x, graphExtras,\r
- x+fm.stringWidth(aa[i].label),\r
- graphExtras);\r
- g2.setStroke(new BasicStroke());\r
- }\r
- }*/\r
- y += ((2 * aa[i].height) / 3);\r
- }\r
- else\r
- {\r
- y += aa[i].height;\r
- }\r
- }\r
- }\r
-\r
- if (resizePanel)\r
- {\r
- g.drawImage(image, 2, 0 - scrollOffset, this);\r
- }\r
- else if (dragEvent != null && aa!=null)\r
- {\r
- g.setColor(Color.lightGray);\r
- g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset);\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 (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+import java.util.regex.Pattern;
+
+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 TOGGLE_LABELSCALE = "Scale Label to Column";
+
+ 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);
+
+ private boolean hasHiddenRows;
+
+ /**
+ * 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();
+ }
+
+ /**
+ * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
+ * y
+ *
+ * @param y
+ * coordinate position to search for a row
+ */
+ void getSelectedRow(int y)
+ {
+ int height = 0;
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ selectedRow = -2;
+ if (aa != null)
+ {
+ for (int i = 0; i < aa.length; i++)
+ {
+ selectedRow = -1;
+ 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)
+ {
+ 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);
+ }
+ else if (evt.getActionCommand().equals(EDITNAME))
+ {
+ editLabelDescription(aa[selectedRow]);
+ repaint();
+ }
+ 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; i < aa.length; i++)
+ {
+ if (!aa[i].visible && aa[i].annotations != null)
+ {
+ aa[i].visible = true;
+ }
+ }
+ }
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+ {
+ new AnnotationExporter().exportAnnotations(ap,
+ new AlignmentAnnotation[]
+ { aa[selectedRow] }, null, null);
+ }
+ else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+ {
+ SequenceI cons = null;
+ if (aa[selectedRow].groupRef != null)
+ {
+ cons = aa[selectedRow].groupRef.getConsensusSeq();
+ }
+ else
+ {
+ cons = av.getConsensusSeq();
+ }
+ if (cons != null)
+ {
+ copy_annotseqtoclipboard(cons);
+ }
+
+ }
+ else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
+ {
+ aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
+ }
+
+ ap.validateAnnotationDimensions(false);
+ ap.addNotify();
+ ap.repaint();
+ //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",
+ ap.alignFrame);
+
+ 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];
+ if (end == -1)
+ {
+ end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+ }
+ 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)
+ {
+ AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
+
+ StringBuffer desc = new StringBuffer();
+ if (aa.description != null
+ && !aa.description.equals("New description"))
+ {
+ // TODO: we could refactor and merge this code with the code in jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature tooltips
+ desc.append(aa.getDescription(true).trim());
+ // check to see if the description is an html fragment.
+ if (desc.length()<6 || (desc.substring(0,6).toLowerCase().indexOf("<html>")<0))
+ {
+ // clean the description ready for embedding in html
+ desc = new StringBuffer(Pattern.compile("<").matcher(desc).replaceAll("<"));
+ desc.insert(0, "<html>");
+ } else {
+ // remove terminating html if any
+ int i=desc.substring(desc.length()-7).toLowerCase().lastIndexOf("</html>");
+ if (i>-1) {
+ desc.setLength(desc.length()-7+i);
+ }
+ }
+ if (aa.hasScore())
+ {
+ desc.append("<br/>");
+ }
+
+
+ } else {
+ // begin the tooltip's html fragment
+ desc.append("<html>");
+ }
+ if (aa.hasScore())
+ {
+ // TODO: limit precision of score to avoid noise from imprecise doubles (64.7 becomes 64.7+/some tiny value).
+ desc.append(" Score: " + aa.score);
+ }
+
+ if (desc.length() > 6)
+ {
+ desc.append("</html>");
+ this.setToolTipText(desc.toString());
+ }
+ else
+ this.setToolTipText(null);
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseClicked(MouseEvent evt)
+ {
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ if (SwingUtilities.isLeftMouseButton(evt))
+ {
+ if (selectedRow > -1 && selectedRow < aa.length)
+ {
+ if (aa[selectedRow].groupRef != null)
+ {
+ if (evt.getClickCount() >= 2)
+ {
+ // todo: make the ap scroll to the selection - not necessary, first click highlights/scrolls, second selects
+ ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+ ap.av.setSelectionGroup(// new SequenceGroup(
+ aa[selectedRow].groupRef); // );
+ ap.paintAlignment(false);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
+ }
+ else
+ {
+ ap.seqPanel.ap.idPanel
+ .highlightSearchResults(aa[selectedRow].groupRef
+ .getSequences(null));
+ }
+ return;
+ }
+ else if (aa[selectedRow].sequenceRef != null)
+ {
+ Vector sr = new Vector();
+ sr.addElement(aa[selectedRow].sequenceRef);
+ if (evt.getClickCount() == 1)
+ {
+ ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
+ }
+ else if (evt.getClickCount() >= 2)
+ {
+ ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ ap.av.setSelectionGroup(sg);
+ ap.av.sendSelection();
+ ap.paintAlignment(false);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ }
+
+ }
+ }
+ }
+ if (!SwingUtilities.isRightMouseButton(evt))
+ {
+ return;
+ }
+
+ JPopupMenu pop = new JPopupMenu("Annotations");
+ JMenuItem item = new JMenuItem(ADDNEW);
+ item.addActionListener(this);
+ pop.add(item);
+ if (selectedRow < 0)
+ {
+ if (hasHiddenRows)
+ { // let the user make everything visible again
+ item = new JMenuItem(SHOWALL);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ return;
+ }
+ 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);
+ if (hasHiddenRows)
+ {
+ item = new JMenuItem(SHOWALL);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ item = new JMenuItem(OUTPUT_TEXT);
+ item.addActionListener(this);
+ pop.add(item);
+ // TODO: annotation object should be typed for autocalculated/derived
+ // property methods
+ if (selectedRow < aa.length)
+ {
+ if (!aa[selectedRow].autoCalculated)
+ {
+ if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
+ {
+ // display formatting settings for this row.
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
+ aa[selectedRow].scaleColLabel);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ }
+ else if (aa[selectedRow].label.indexOf("Consensus") > -1)
+ {
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ "Ignore Gaps In Consensus",
+ (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+ .getIgnoreGapsConsensus() : ap.av
+ .getIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = aa[selectedRow];
+ cbmi.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ if (aaa.groupRef != null)
+ {
+ // TODO: pass on reference to ap so the view can be updated.
+ aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+ ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ else
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ }
+ }
+ });
+ pop.add(cbmi);
+ // av and sequencegroup need to implement same interface for
+ if (aaa.groupRef != null)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ "Show Group Histogram",
+ aa[selectedRow].groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ "Show Group Logo",
+ aa[selectedRow].groupRef.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowSequenceLogo(cprofl.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprofl);
+ }
+ else
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ "Show Histogram", av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ "Show Logo", av.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(cprof.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprof);
+ }
+ 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)
+ {
+ hasHiddenRows = false;
+ for (int i = 0; i < aa.length; i++)
+ {
+ g.setColor(Color.black);
+
+ if (!aa[i].visible)
+ {
+ hasHiddenRows = true;
+ 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