-\r
-package jalview.gui;\r
-\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
-import java.awt.*;\r
-import java.awt.image.*;\r
-import jalview.datamodel.*;\r
-\r
-public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener\r
-{\r
- boolean active = false;\r
- Image image;\r
- AlignmentPanel ap ;\r
- boolean resizing = false;\r
- int oldY, mouseX;\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
- int selectedRow = 0;\r
- int scrollOffset = 0;\r
-\r
- public AnnotationLabels(AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
-\r
- java.net.URL url = getClass().getResource("/images/idwidth.gif");\r
- Image temp = null;\r
- if (url != null)\r
- temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);\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
- BufferedImage bi = new BufferedImage(temp.getHeight(this), temp.getWidth(this),\r
- 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 void setScrollOffset(int y)\r
- {\r
- scrollOffset = y;\r
- repaint();\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
-\r
- if(evt.getActionCommand().equals(ADDNEW))\r
- {\r
- String label = JOptionPane.showInputDialog(this, "Label for annotation");\r
- if(label==null)\r
- label = "";\r
- ap.av.alignment.addAnnotation(new AlignmentAnnotation\r
- (label,\r
- "New description",\r
- new Annotation[ap.av.alignment.getWidth()]));\r
- }\r
- else if(evt.getActionCommand().equals(HIDE))\r
- {\r
- aa[selectedRow].visible = false;\r
- }\r
- else if(evt.getActionCommand().equals(DELETE))\r
- {\r
- ap.av.alignment.deleteAnnotation(aa[selectedRow]);\r
- }\r
- else if(evt.getActionCommand().equals(SHOWALL))\r
- {\r
- for(int i=0; i<aa.length; i++)\r
- aa[i].visible = true;\r
- }\r
-\r
- ap.annotationPanel.adjustPanelHeight();\r
- ap.RefreshPanels();\r
-\r
- }\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- int y = evt.getY() - scrollOffset;\r
-\r
- if (SwingUtilities.isRightMouseButton(evt))\r
- {\r
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\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
- return;\r
- }\r
-\r
- int height = 0;\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if(!aa[i].visible)\r
- continue;\r
-\r
- height += aa[i].height;\r
- if(y<height)\r
- {\r
- selectedRow = i;\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
- pop.show(this, evt.getX(), evt.getY());\r
- return;\r
- }\r
-\r
- oldY = evt.getY();\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt){ active = false; repaint(); }\r
- public void mouseEntered(MouseEvent evt) { active = true; repaint();}\r
- public void mouseExited(MouseEvent evt) { active = false; repaint();}\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- active = true;\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,d.height - dif));\r
- d = ap.annotationSpaceFillerHolder.getPreferredSize();\r
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,d.height - dif));\r
- ap.RefreshPanels();\r
- }\r
- ap.addNotify();\r
- }\r
-\r
- public void mouseMoved(MouseEvent evt) {}\r
- public void mouseClicked(MouseEvent evt) {}\r
-\r
- public void paintComponent(Graphics g1)\r
- {\r
- Graphics2D g = (Graphics2D)g1;\r
- g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
-\r
- drawComponent(g);\r
- }\r
-\r
- public void drawComponent(Graphics2D g)\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 = ap.av.alignment.getAlignmentAnnotation();\r
- int y = g.getFont().getSize();\r
- int x = 0;\r
-\r
- if(aa!=null)\r
- for(int i=0; i<aa.length; i++)\r
- {\r
- if(!aa[i].visible)\r
- continue;\r
-\r
- x = getWidth() - fm.stringWidth(aa[i].label)-3;\r
-\r
- g.drawString(aa[i].label, x, y);\r
-\r
- y+=aa[i].height;\r
- }\r
-\r
- if (active)\r
- {\r
- if (image != null)\r
- g.drawImage(image, 2, 0, this);\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
-\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.MediaTracker;
+import java.awt.RenderingHints;
+import java.awt.Toolkit;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.geom.AffineTransform;
+import java.awt.image.BufferedImage;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.regex.Pattern;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AnnotationLabels extends JPanel implements MouseListener,
+ MouseMotionListener, ActionListener
+{
+ private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
+ .compile("<");
+
+ String TOGGLE_LABELSCALE = MessageManager
+ .getString("label.scale_label_to_column");
+
+ String ADDNEW = MessageManager.getString("label.add_new_row");
+
+ String EDITNAME = MessageManager
+ .getString("label.edit_label_description");
+
+ String HIDE = MessageManager.getString("label.hide_row");
+
+ String DELETE = MessageManager.getString("label.delete_row");
+
+ String SHOWALL = MessageManager.getString("label.show_all_hidden_rows");
+
+ String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
+
+ String COPYCONS_SEQ = MessageManager
+ .getString("label.copy_consensus_sequence");
+
+ boolean resizePanel = false;
+
+ Image image;
+
+ AlignmentPanel ap;
+
+ AlignViewport av;
+
+ boolean resizing = false;
+
+ MouseEvent dragEvent;
+
+ int oldY;
+
+ int selectedRow;
+
+ private 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 = bi;
+
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ addMouseWheelListener(ap.getAnnotationPanel());
+ }
+
+ 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.getAlignment()
+ .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!
+ */
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+
+ boolean fullRepaint = false;
+ if (evt.getActionCommand().equals(ADDNEW))
+ {
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
+ null, new Annotation[ap.av.getAlignment().getWidth()]);
+
+ if (!editLabelDescription(newAnnotation))
+ {
+ return;
+ }
+
+ ap.av.getAlignment().addAnnotation(newAnnotation);
+ ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+ fullRepaint = true;
+ }
+ else if (evt.getActionCommand().equals(EDITNAME))
+ {
+ String name = aa[selectedRow].label;
+ editLabelDescription(aa[selectedRow]);
+ if (!name.equalsIgnoreCase(aa[selectedRow].label))
+ {
+ fullRepaint = true;
+ }
+ }
+ else if (evt.getActionCommand().equals(HIDE))
+ {
+ aa[selectedRow].visible = false;
+ }
+ else if (evt.getActionCommand().equals(DELETE))
+ {
+ ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
+ ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
+ fullRepaint = true;
+ }
+ 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;
+ }
+ }
+ fullRepaint = true;
+ }
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+ {
+ new AnnotationExporter().exportAnnotations(ap,
+ new AlignmentAnnotation[] { aa[selectedRow] });
+ }
+ 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.refresh(fullRepaint);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ boolean editLabelDescription(AlignmentAnnotation annotation)
+ {
+ // TODO i18n
+ 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;
+ }
+
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ getSelectedRow(evt.getY() - getScrollOffset());
+ oldY = evt.getY();
+ if (evt.isPopupTrigger())
+ {
+ showPopupMenu(evt);
+ }
+ }
+
+ /**
+ * Build and show the Pop-up menu at the right-click mouse position
+ *
+ * @param evt
+ */
+ void showPopupMenu(MouseEvent evt)
+ {
+ evt.consume();
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.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);
+ // JAL-1264 hide all sequence-specific annotations of this type
+ if (selectedRow < aa.length)
+ {
+ if (aa[selectedRow].sequenceRef != null)
+ {
+ final String label = aa[selectedRow].label;
+ JMenuItem hideType = new JMenuItem();
+ String text = MessageManager.getString("label.hide_all") + " "
+ + label;
+ hideType.setText(text);
+ hideType.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ ap.av.getAlignment(), Collections.singleton(label),
+ null, false, false);
+ // for (AlignmentAnnotation ann : ap.av.getAlignment()
+ // .getAlignmentAnnotation())
+ // {
+ // if (ann.sequenceRef != null && ann.label != null
+ // && ann.label.equals(label))
+ // {
+ // ann.visible = false;
+ // }
+ // }
+ ap.refresh(true);
+ }
+ });
+ pop.add(hideType);
+ }
+ }
+ 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)
+ {
+ final String label = aa[selectedRow].label;
+ 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 (label.indexOf("Consensus") > -1)
+ {
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+ .getIgnoreGapsConsensus() : ap.av
+ .isIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = aa[selectedRow];
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ 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.getAnnotationPanel().paint(
+ ap.getAnnotationPanel().getGraphics());
+ }
+ else
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(cbmi);
+ // av and sequencegroup need to implement same interface for
+ if (aaa.groupRef != null)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ aa[selectedRow].groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ 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(
+ MessageManager.getString("label.show_group_logo"),
+ aa[selectedRow].groupRef.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ 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);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ aaa.groupRef.setshowSequenceLogo(true);
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(true);
+ av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprofnorm);
+ }
+ final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+ consclipbrd.addActionListener(this);
+ pop.add(consclipbrd);
+ }
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger())
+ {
+ showPopupMenu(evt);
+ return;
+ }
+
+ int start = selectedRow;
+ getSelectedRow(evt.getY() - getScrollOffset());
+ int end = selectedRow;
+
+ if (start != end)
+ {
+ // Swap these annotations
+ AlignmentAnnotation startAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[start];
+ if (end == -1)
+ {
+ end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
+ }
+ AlignmentAnnotation endAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[end];
+
+ ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
+ }
+
+ resizePanel = false;
+ dragEvent = null;
+ repaint();
+ ap.getAnnotationPanel().repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ if (evt.getY() < 10)
+ {
+ resizePanel = true;
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ if (dragEvent == null)
+ {
+ resizePanel = false;
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ dragEvent = evt;
+
+ if (resizePanel)
+ {
+ Dimension d = ap.annotationScroller.getPreferredSize();
+ int dif = evt.getY() - oldY;
+
+ dif /= ap.av.getCharHeight();
+ dif *= ap.av.getCharHeight();
+
+ 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!
+ */
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ resizePanel = evt.getY() < 10;
+
+ getSelectedRow(evt.getY() - getScrollOffset());
+
+ if (selectedRow > -1
+ && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+ {
+ AlignmentAnnotation aa = ap.av.getAlignment()
+ .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(LEFT_ANGLE_BRACKET_PATTERN.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/>");
+ }
+ // if (aa.hasProperties())
+ // {
+ // desc.append("<table>");
+ // for (String prop : aa.getProperties())
+ // {
+ // desc.append("<tr><td>" + prop + "</td><td>"
+ // + aa.getProperty(prop) + "</td><tr>");
+ // }
+ // desc.append("</table>");
+ // }
+ }
+ 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);
+ }
+ }
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (!evt.isPopupTrigger() && 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.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
+ // process modifiers
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null
+ || sg == aa[selectedRow].groupRef
+ || !(jalview.util.Platform.isControlDown(evt) || evt
+ .isShiftDown()))
+ {
+ if (jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown())
+ {
+ // clone a new selection group from the associated group
+ ap.av.setSelectionGroup(new SequenceGroup(
+ aa[selectedRow].groupRef));
+ }
+ else
+ {
+ // set selection to the associated group so it can be edited
+ ap.av.setSelectionGroup(aa[selectedRow].groupRef);
+ }
+ }
+ else
+ {
+ // modify current selection with associated group
+ int remainToAdd = aa[selectedRow].groupRef.getSize();
+ for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
+ {
+ if (jalview.util.Platform.isControlDown(evt))
+ {
+ sg.addOrRemove(sgs, --remainToAdd == 0);
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
+ sg.addSequence(sgs, --remainToAdd == 0);
+ }
+ }
+ }
+
+ ap.paintAlignment(false);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
+ }
+ else
+ {
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
+ aa[selectedRow].groupRef.getSequences(null));
+ }
+ return;
+ }
+ else if (aa[selectedRow].sequenceRef != null)
+ {
+ if (evt.getClickCount() == 1)
+ {
+ ap.getSeqPanel().ap
+ .getIdPanel()
+ .highlightSearchResults(
+ Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+ }
+ else if (evt.getClickCount() >= 2)
+ {
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg != null)
+ {
+ // we make a copy rather than edit the current selection if no
+ // modifiers pressed
+ // see Enhancement JAL-1557
+ if (!(jalview.util.Platform.isControlDown(evt) || evt
+ .isShiftDown()))
+ {
+ sg = new SequenceGroup(sg);
+ sg.clear();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
+ else
+ {
+ if (jalview.util.Platform.isControlDown(evt))
+ {
+ sg.addOrRemove(aa[selectedRow].sequenceRef, true);
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
+ sg.addSequence(aa[selectedRow].sequenceRef, true);
+ }
+ }
+ }
+ else
+ {
+ sg = new SequenceGroup();
+ sg.setStartRes(0);
+ sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
+ ap.av.setSelectionGroup(sg);
+ ap.paintAlignment(false);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
+ }
+
+ }
+ }
+ return;
+ }
+ }
+
+ /**
+ * 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.getAlignment().getHiddenColumns()
+ .getVisibleSequenceStrings(0,
+ sq.getLength(), seqs);
+ }
+
+ int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
+ List<int[]> hiddenCols = av.getAlignment().getHiddenColumns()
+ .getHiddenRegions();
+ if (hiddenCols != null)
+ {
+ alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
+ hiddenCols);
+ }
+ String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
+ seqs, omitHidden, alignmentStartEnd);
+
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.instance);
+
+ ArrayList<int[]> hiddenColumns = null;
+ if (av.hasHiddenColumns())
+ {
+ hiddenColumns = new ArrayList<int[]>();
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenRegions())
+ {
+ hiddenColumns.add(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!
+ */
+ @Override
+ 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, true, width);
+
+ }
+
+ /**
+ * Draw the full set of annotation Labels for the alignment at the given
+ * cursor
+ *
+ * @param g
+ * Graphics2D instance (needed for font scaling)
+ * @param width
+ * Width for scaling labels
+ *
+ */
+ public void drawComponent(Graphics g, int width)
+ {
+ drawComponent(g, false, width);
+ }
+
+ private final boolean debugRedraw = false;
+
+ /**
+ * Draw the full set of annotation Labels for the alignment at the given
+ * cursor
+ *
+ * @param g
+ * Graphics2D instance (needed for font scaling)
+ * @param clip
+ * - true indicates that only current visible area needs to be
+ * rendered
+ * @param width
+ * Width for scaling labels
+ */
+ public void drawComponent(Graphics g, boolean clip, 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, getScrollOffset());
+ g.setColor(Color.black);
+
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ int fontHeight = g.getFont().getSize();
+ int y = 0;
+ int x = 0;
+ int graphExtras = 0;
+ int offset = 0;
+ Font baseFont = g.getFont();
+ FontMetrics baseMetrics = fm;
+ int ofontH = fontHeight;
+ int sOffset = 0;
+ int visHeight = 0;
+ int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap
+ .getAnnotationPanel().getVisibleVRange() : null;
+ if (clip && visr != null)
+ {
+ sOffset = visr[0];
+ visHeight = visr[1];
+ }
+ boolean visible = true, before = false, after = false;
+ if (aa != null)
+ {
+ hasHiddenRows = false;
+ int olY = 0;
+ for (int i = 0; i < aa.length; i++)
+ {
+ visible = true;
+ if (!aa[i].visible)
+ {
+ hasHiddenRows = true;
+ continue;
+ }
+ olY = y;
+ y += aa[i].height;
+ if (clip)
+ {
+ if (y < sOffset)
+ {
+ if (!before)
+ {
+ if (debugRedraw)
+ {
+ System.out.println("before vis: " + i);
+ }
+ before = true;
+ }
+ // don't draw what isn't visible
+ continue;
+ }
+ if (olY > visHeight)
+ {
+
+ if (!after)
+ {
+ if (debugRedraw)
+ {
+ System.out.println("Scroll offset: " + sOffset
+ + " after vis: " + i);
+ }
+ after = true;
+ }
+ // don't draw what isn't visible
+ continue;
+ }
+ }
+ g.setColor(Color.black);
+
+ 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;
+ // TODO: JAL-1291 revise rendering model so the graphGroup map is
+ // computed efficiently for all visible labels
+ 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;
+ }
+ else
+ {
+ // scale font to fit
+ float h = aa[i].height / (float) groupSize, s;
+ if (h < 9)
+ {
+ visible = false;
+ }
+ else
+ {
+ fontHeight = -8 + (int) h;
+ s = ((float) fontHeight) / (float) ofontH;
+ Font f = baseFont.deriveFont(AffineTransform
+ .getScaleInstance(s, s));
+ g.setFont(f);
+ fm = g.getFontMetrics();
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ }
+ }
+ if (visible)
+ {
+ 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]._linecolour != null)
+ {
+
+ g.setColor(aa[gg]._linecolour);
+ g.drawLine(x, y - graphExtras + 3,
+ x + fm.stringWidth(aa[gg].label), y - graphExtras
+ + 3);
+ }
+
+ g.setColor(Color.black);
+ graphExtras += fontHeight + 8;
+ }
+ }
+ }
+ g.setFont(baseFont);
+ fm = baseMetrics;
+ fontHeight = ofontH;
+ }
+ else
+ {
+ g.drawString(aa[i].label, x, y + offset);
+ }
+ }
+ }
+
+ if (resizePanel)
+ {
+ g.drawImage(image, 2, 0 - getScrollOffset(), this);
+ }
+ else if (dragEvent != null && aa != null)
+ {
+ g.setColor(Color.lightGray);
+ g.drawString(aa[selectedRow].label, dragEvent.getX(),
+ dragEvent.getY() - getScrollOffset());
+ }
+
+ if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
+ {
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
+ }
+ }
+
+ public int getScrollOffset()
+ {
+ return scrollOffset;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff