-/*
- * 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.appletgui;
-
-import jalview.analysis.AlignmentUtils;
-import jalview.bin.JalviewLite;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-import jalview.util.ParseHtmlBodyAndLinks;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.FlowLayout;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import java.awt.Image;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.InputEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Vector;
-
-import javax.swing.JCheckBox;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JFrame;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-
-public class AnnotationLabels extends JPanel implements ActionListener,
- MouseListener, MouseMotionListener
-{
- Image image;
-
- boolean active = false;
-
- AlignmentPanel ap;
-
- AlignViewport av;
-
- boolean resizing = false;
-
- int oldY, mouseX;
-
- static String ADDNEW = "Add New Row";
-
- static String EDITNAME = "Edit Label/Description";
-
- static String HIDE = "Hide This Row";
-
- static String SHOWALL = "Show All Hidden Rows";
-
- static String OUTPUT_TEXT = "Show Values In Textbox";
-
- static String COPYCONS_SEQ = "Copy Consensus Sequence";
-
- int scrollOffset = 0;
-
- int selectedRow = -1;
-
- Tooltip tooltip;
-
- private boolean hasHiddenRows;
-
- public AnnotationLabels(AlignmentPanel ap)
- {
- this.ap = ap;
- this.av = ap.av;
- setLayout(null);
-
- /**
- * this retrieves the adjustable height glyph from resources. we don't use
- * it at the moment. 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;
- }
-
- public void setScrollOffset(int y, boolean repaint)
- {
- scrollOffset = y;
- if (repaint)
- {
- repaint();
- }
- }
-
- /**
- *
- * @param y
- * @return -2 if no rows are visible at all, -1 if no visible rows were
- * selected
- */
- int getSelectedRow(int y)
- {
- int row = -2;
- AlignmentAnnotation[] aa = ap.av.getAlignment()
- .getAlignmentAnnotation();
-
- if (aa == null)
- {
- return row;
- }
- int height = 0;
- for (int i = 0; i < aa.length; i++)
- {
- row = -1;
- if (!aa[i].visible)
- {
- continue;
- }
- height += aa[i].height;
- if (y < height)
- {
- row = i;
- break;
- }
- }
-
- return row;
- }
-
- public void actionPerformed(ActionEvent evt)
- {
- AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-
- if (evt.getActionCommand().equals(ADDNEW))
- {
- AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
- new Annotation[ap.av.getAlignment().getWidth()]);
-
- if (!editLabelDescription(newAnnotation))
- {
- return;
- }
-
- ap.av.getAlignment().addAnnotation(newAnnotation);
- ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
- }
- else if (evt.getActionCommand().equals(EDITNAME))
- {
- editLabelDescription(aa[selectedRow]);
- }
- else if (evt.getActionCommand().equals(HIDE))
- {
- aa[selectedRow].visible = false;
- }
- else if (evt.getActionCommand().equals(SHOWALL))
- {
- for (int i = 0; i < aa.length; i++)
- {
- aa[i].visible = (aa[i].annotations == null) ? false : true;
- }
- }
- else if (evt.getActionCommand().equals(OUTPUT_TEXT))
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
- ap.alignFrame);
- JFrame frame = new JFrame();
- frame.add(cap);
- JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
- + " - " + aa[selectedRow].label, 500, 100);
- cap.setText(aa[selectedRow].toString());
- }
- else if (evt.getActionCommand().equals(COPYCONS_SEQ))
- {
- SequenceI cons = av.getConsensusSeq();
- if (cons != null)
- {
- copy_annotseqtoclipboard(cons);
- }
-
- }
- refresh();
- }
-
- /**
- * Adjust size and repaint
- */
- protected void refresh()
- {
- ap.annotationPanel.adjustPanelHeight();
- setSize(getSize().width, ap.annotationPanel.getSize().height);
- ap.validate();
- ap.paintAlignment(true);
- }
-
- boolean editLabelDescription(AlignmentAnnotation annotation)
- {
- JCheckBox padGaps = new JCheckBox("Fill Empty Gaps With \""
- + ap.av.getGapCharacter() + "\"", annotation.padGaps);
-
- EditNameDialog dialog = new EditNameDialog(annotation.label,
- annotation.description, " Annotation Label",
- "Annotation Description", ap.alignFrame,
- "Edit Annotation Name / Description", 500, 180, false);
-
- JPanel empty = new JPanel(new FlowLayout());
- empty.add(padGaps);
- dialog.add(empty);
- dialog.pack();
-
- dialog.setVisible(true);
-
- if (dialog.accept)
- {
- annotation.label = dialog.getName();
- annotation.description = dialog.getDescription();
- annotation.setPadGaps(padGaps.isSelected(), av.getGapCharacter());
- repaint();
- return true;
- }
- else
- {
- return false;
- }
-
- }
-
- boolean resizePanel = false;
-
- public void mouseMoved(MouseEvent evt)
- {
- resizePanel = evt.getY() < 10 && evt.getX() < 14;
- int row = getSelectedRow(evt.getY() + scrollOffset);
-
- if (row > -1)
- {
- ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
- av.getAlignment().getAlignmentAnnotation()[row]
- .getDescription(true),
- true, "\n");
- if (tooltip == null)
- {
- tooltip = new Tooltip(phb.getNonHtmlContent(), this);
- }
- else
- {
- tooltip.setTip(phb.getNonHtmlContent());
- }
- }
- else if (tooltip != null)
- {
- tooltip.setTip("");
- }
- }
-
- /**
- * curent drag position
- */
- MouseEvent dragEvent = null;
-
- /**
- * flag to indicate drag events should be ignored
- */
- private boolean dragCancelled = false;
-
- /**
- * clear any drag events in progress
- */
- public void cancelDrag()
- {
- dragEvent = null;
- dragCancelled = true;
- }
-
- public void mouseDragged(MouseEvent evt)
- {
- if (dragCancelled)
- {
- return;
- }
- ;
- dragEvent = evt;
-
- if (resizePanel)
- {
- Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
- .getSize(), f = ap.seqPanelHolder.getSize();
- int dif = evt.getY() - oldY;
-
- dif /= ap.av.getCharHeight();
- dif *= ap.av.getCharHeight();
-
- if ((d.height - dif) > 20 && (f.height + dif) > 20)
- {
- ap.annotationPanel.setSize(d.width, d.height - dif);
- setSize(new Dimension(e.width, d.height - dif));
- ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
- d.height - dif));
- ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
- - dif));
- ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
- av.calcPanelHeight());
- f.height += dif;
- ap.seqPanelHolder.setPreferredSize(f);
- ap.setScrollValues(av.getStartRes(), av.getStartSeq());
- ap.validate();
- // ap.paintAlignment(true);
- ap.addNotify();
- }
-
- }
- else
- {
- int diff;
- if ((diff = 6 - evt.getY()) > 0)
- {
- // nudge scroll up
- ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
- ap.adjustmentValueChanged(null);
-
- }
- else if ((0 < (diff = 6
- - ap.annotationSpaceFillerHolder.getSize().height
- + evt.getY())))
- {
- // nudge scroll down
- ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
- ap.adjustmentValueChanged(null);
- }
- repaint();
- }
- }
-
- public void mouseClicked(MouseEvent evt)
- {
- }
-
- public void mouseReleased(MouseEvent evt)
- {
- if (!resizePanel && !dragCancelled)
- {
- int start = selectedRow;
-
- int end = getSelectedRow(evt.getY() + scrollOffset);
-
- if (start > -1 && 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;
- dragCancelled = false;
- repaint();
- ap.annotationPanel.repaint();
- }
-
- public void mouseEntered(MouseEvent evt)
- {
- if (evt.getY() < 10 && evt.getX() < 14)
- {
- resizePanel = true;
- repaint();
- }
- }
-
- public void mouseExited(MouseEvent evt)
- {
- dragCancelled = false;
-
- if (dragEvent == null)
- {
- resizePanel = false;
- }
- else
- {
- if (!resizePanel)
- {
- dragEvent = null;
- }
- }
- repaint();
- }
-
- public void mousePressed(MouseEvent evt)
- {
- oldY = evt.getY();
- if (resizePanel)
- {
- return;
- }
- dragCancelled = false;
- // todo: move below to mouseClicked ?
- selectedRow = getSelectedRow(evt.getY() + scrollOffset);
-
- AlignmentAnnotation[] aa = ap.av.getAlignment()
- .getAlignmentAnnotation();
-
- // DETECT RIGHT MOUSE BUTTON IN AWT
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
- {
-
- JPopupMenu popup = new JPopupMenu(
- MessageManager.getString("label.annotations"));
-
- JMenuItem item = new JMenuItem(ADDNEW);
- item.addActionListener(this);
- popup.add(item);
- if (selectedRow < 0)
- {
- // this never happens at moment: - see comment on JAL-563
- if (hasHiddenRows)
- {
- item = new JMenuItem(SHOWALL);
- item.addActionListener(this);
- popup.add(item);
- }
- this.add(popup);
- popup.show(this, evt.getX(), evt.getY());
- return;
- }
- // add the rest if there are actually rows to show
- item = new JMenuItem(EDITNAME);
- item.addActionListener(this);
- popup.add(item);
- item = new JMenuItem(HIDE);
- item.addActionListener(this);
- popup.add(item);
-
- /*
- * Hide all <label>:
- */
- if (selectedRow < aa.length)
- {
- if (aa[selectedRow].sequenceRef != null)
- {
- final String label = aa[selectedRow].label;
- JMenuItem hideType = new JMenuItem(
- MessageManager.getString("label.hide_all") + " " + label);
- hideType.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- AlignmentUtils.showOrHideSequenceAnnotations(
- ap.av.getAlignment(), Collections.singleton(label),
- null, false, false);
- refresh();
- }
- });
- popup.add(hideType);
- }
- }
-
- if (hasHiddenRows)
- {
- item = new JMenuItem(SHOWALL);
- item.addActionListener(this);
- popup.add(item);
- }
- this.add(popup);
- item = new JMenuItem(OUTPUT_TEXT);
- item.addActionListener(this);
- popup.add(item);
- if (selectedRow < aa.length)
- {
- if (aa[selectedRow].autoCalculated)
- {
- if (aa[selectedRow].label.indexOf("Consensus") > -1)
- {
- popup.addSeparator();
- 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.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- if (aaa.groupRef != null)
- {
- // TODO: pass on reference to ap so the view can be updated.
- aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
- }
- else
- {
- ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
- }
- ap.paintAlignment(true);
- }
- });
- popup.add(cbmi);
- if (aaa.groupRef != null)
- {
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_histogram"),
- aa[selectedRow].groupRef.isShowConsensusHistogram());
- chist.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent 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());
- }
- });
- popup.add(chist);
- final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_logo"),
- aa[selectedRow].groupRef.isShowSequenceLogo());
- cprofl.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent 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());
- }
- });
-
- popup.add(cprofl);
- final JCheckBoxMenuItem cprofn = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_group_logo"),
- aa[selectedRow].groupRef.isNormaliseSequenceLogo());
- cprofn.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setshowSequenceLogo(true);
- aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- popup.add(cprofn);
- }
- else
- {
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
- chist.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowConsensusHistogram(chist.getState());
- ap.alignFrame.showConsensusHistogram.setState(chist
- .getState()); // TODO: implement
- // ap.updateGUI()/alignFrame.updateGUI
- // for applet
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- popup.add(chist);
- final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
- cprof.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowSequenceLogo(cprof.getState());
- ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
- // implement
- // ap.updateGUI()/alignFrame.updateGUI
- // for
- // applet
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- popup.add(cprof);
- final JCheckBoxMenuItem cprofn = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
- cprofn.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowSequenceLogo(true);
- ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
- // implement
- // ap.updateGUI()/alignFrame.updateGUI
- // for
- // applet
- av.setNormaliseSequenceLogo(cprofn.getState());
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- popup.add(cprofn);
- }
-
- item = new JMenuItem(COPYCONS_SEQ);
- item.addActionListener(this);
- popup.add(item);
- }
- }
- }
- popup.show(this, evt.getX(), evt.getY());
- }
- else
- {
- // selection action.
- 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.av.sendSelection();
- ap.paintAlignment(false);
- PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
- }
- else
- {
- ap.seqPanel.ap.idPanel
- .highlightSearchResults(aa[selectedRow].groupRef
- .getSequences(null));
- }
- return;
- }
- else if (aa[selectedRow].sequenceRef != null)
- {
- if (evt.getClickCount() == 1)
- {
- ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
- .asList(new SequenceI[]
- { aa[selectedRow].sequenceRef }));
- }
- else if (evt.getClickCount() >= 2)
- {
- ap.seqPanel.ap.idPanel.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 (!(evt.isControlDown() || evt.isShiftDown()))
- {
- sg = new SequenceGroup(sg);
- sg.clear();
- sg.addSequence(aa[selectedRow].sequenceRef, false);
- } else {
- if (evt.isControlDown())
- {
- 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();
- }
-
- }
- }
-
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void copy_annotseqtoclipboard(SequenceI sq)
- {
- if (sq == null || sq.getLength() < 1)
- {
- return;
- }
- AlignFrame.copiedSequences = new StringBuffer();
- AlignFrame.copiedSequences.append(sq.getName() + "\t"
- + sq.getStart() + "\t" + sq.getEnd() + "\t"
- + sq.getSequenceAsString() + "\n");
- if (av.hasHiddenColumns())
- {
- AlignFrame.copiedHiddenColumns = new Vector();
- for (int[] region : av.getColumnSelection().getHiddenColumns())
- {
- AlignFrame.copiedHiddenColumns
- .addElement(new int[]
- { region[0], region[1] });
- }
- }
- }
-
- public void update(Graphics g)
- {
- paint(g);
- }
-
- public void paint(Graphics g)
- {
- int w = getSize().width;
- int h = getSize().height;
- if (image == null || w != image.getWidth(this)
- || h != image.getHeight(this))
- {
- image = createImage(w, ap.annotationPanel.getSize().height);
- }
-
- drawComponent(image.getGraphics(), w);
- g.drawImage(image, 0, 0, this);
- }
-
- public void drawComponent(Graphics g, int width)
- {
- g.setFont(av.getFont());
- FontMetrics fm = g.getFontMetrics(av.getFont());
- g.setColor(Color.white);
- g.fillRect(0, 0, getSize().width, getSize().height);
-
- g.translate(0, -scrollOffset);
- g.setColor(Color.black);
-
- AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
- int y = 0, fy = g.getFont().getSize();
- int x = 0, offset;
-
- if (aa != null)
- {
- hasHiddenRows = false;
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- hasHiddenRows = true;
- continue;
- }
-
- x = width - fm.stringWidth(aa[i].label) - 3;
-
- y += aa[i].height;
- offset = -(aa[i].height - fy) / 2;
-
- g.drawString(aa[i].label, x, y + offset);
- }
- }
- g.translate(0, +scrollOffset);
- if (resizePanel)
- {
- g.setColor(Color.red);
- g.setPaintMode();
- g.drawLine(2, 8, 5, 2);
- g.drawLine(5, 2, 8, 8);
- }
- else if (!dragCancelled && dragEvent != null && aa != null)
- {
- g.setColor(Color.lightGray);
- g.drawString(aa[selectedRow].label, dragEvent.getX(),
- dragEvent.getY());
- }
-
- if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
- {
- g.setColor(Color.black);
- g.drawString(MessageManager.getString("label.right_click"), 2, 8);
- g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
- 18);
- }
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.analysis.AlignmentUtils;\r
+import jalview.bin.JalviewLite;\r
+import jalview.datamodel.AlignmentAnnotation;\r
+import jalview.datamodel.Annotation;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.util.MessageManager;\r
+import jalview.util.ParseHtmlBodyAndLinks;\r
+\r
+import java.awt.Color;\r
+import java.awt.Dimension;\r
+import java.awt.FlowLayout;\r
+import java.awt.FontMetrics;\r
+import java.awt.Graphics;\r
+import java.awt.Image;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.InputEvent;\r
+import java.awt.event.ItemEvent;\r
+import java.awt.event.ItemListener;\r
+import java.awt.event.MouseEvent;\r
+import java.awt.event.MouseListener;\r
+import java.awt.event.MouseMotionListener;\r
+import java.util.Arrays;\r
+import java.util.Collections;\r
+import java.util.Vector;\r
+\r
+import javax.swing.JCheckBox;\r
+import javax.swing.JCheckBoxMenuItem;\r
+import javax.swing.JFrame;\r
+import javax.swing.JMenuItem;\r
+import javax.swing.JPanel;\r
+import javax.swing.JPopupMenu;\r
+\r
+public class AnnotationLabels extends JPanel implements ActionListener,\r
+ MouseListener, MouseMotionListener\r
+{\r
+ Image image;\r
+\r
+ boolean active = false;\r
+\r
+ AlignmentPanel ap;\r
+\r
+ AlignViewport av;\r
+\r
+ boolean resizing = false;\r
+\r
+ int oldY, mouseX;\r
+\r
+ static String ADDNEW = "Add New Row";\r
+\r
+ static String EDITNAME = "Edit Label/Description";\r
+\r
+ static String HIDE = "Hide This Row";\r
+\r
+ static String SHOWALL = "Show All Hidden Rows";\r
+\r
+ static String OUTPUT_TEXT = "Show Values In Textbox";\r
+\r
+ static String COPYCONS_SEQ = "Copy Consensus Sequence";\r
+\r
+ int scrollOffset = 0;\r
+\r
+ int selectedRow = -1;\r
+\r
+ Tooltip tooltip;\r
+\r
+ private boolean hasHiddenRows;\r
+\r
+ public AnnotationLabels(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ this.av = ap.av;\r
+ setLayout(null);\r
+\r
+ /**\r
+ * this retrieves the adjustable height glyph from resources. we don't use\r
+ * it at the moment. java.net.URL url =\r
+ * getClass().getResource("/images/idwidth.gif"); Image temp = null;\r
+ * \r
+ * if (url != null) { temp =\r
+ * java.awt.Toolkit.getDefaultToolkit().createImage(url); }\r
+ * \r
+ * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);\r
+ * mt.waitForID(0); } catch (Exception ex) { }\r
+ * \r
+ * BufferedImage bi = new BufferedImage(temp.getHeight(this),\r
+ * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =\r
+ * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));\r
+ * g.drawImage(temp, 0, -bi.getWidth(this), this); 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
+ public void setScrollOffset(int y, boolean repaint)\r
+ {\r
+ scrollOffset = y;\r
+ if (repaint)\r
+ {\r
+ repaint();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param y\r
+ * @return -2 if no rows are visible at all, -1 if no visible rows were\r
+ * selected\r
+ */\r
+ int getSelectedRow(int y)\r
+ {\r
+ int row = -2;\r
+ AlignmentAnnotation[] aa = ap.av.getAlignment()\r
+ .getAlignmentAnnotation();\r
+\r
+ if (aa == null)\r
+ {\r
+ return row;\r
+ }\r
+ int height = 0;\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ row = -1;\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
+ height += aa[i].height;\r
+ if (y < height)\r
+ {\r
+ row = i;\r
+ break;\r
+ }\r
+ }\r
+\r
+ return row;\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();\r
+\r
+ if (evt.getActionCommand().equals(ADDNEW))\r
+ {\r
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,\r
+ new Annotation[ap.av.getAlignment().getWidth()]);\r
+\r
+ if (!editLabelDescription(newAnnotation))\r
+ {\r
+ return;\r
+ }\r
+\r
+ ap.av.getAlignment().addAnnotation(newAnnotation);\r
+ ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);\r
+ }\r
+ else if (evt.getActionCommand().equals(EDITNAME))\r
+ {\r
+ editLabelDescription(aa[selectedRow]);\r
+ }\r
+ else if (evt.getActionCommand().equals(HIDE))\r
+ {\r
+ aa[selectedRow].visible = false;\r
+ }\r
+ else if (evt.getActionCommand().equals(SHOWALL))\r
+ {\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ aa[i].visible = (aa[i].annotations == null) ? false : true;\r
+ }\r
+ }\r
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false,\r
+ ap.alignFrame);\r
+ JFrame frame = new JFrame();\r
+ frame.add(cap);\r
+ JalviewLite.addFrame(frame, ap.alignFrame.getTitle()\r
+ + " - " + aa[selectedRow].label, 500, 100);\r
+ cap.setText(aa[selectedRow].toString());\r
+ }\r
+ else if (evt.getActionCommand().equals(COPYCONS_SEQ))\r
+ {\r
+ SequenceI cons = av.getConsensusSeq();\r
+ if (cons != null)\r
+ {\r
+ copy_annotseqtoclipboard(cons);\r
+ }\r
+\r
+ }\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * Adjust size and repaint\r
+ */\r
+ protected void refresh()\r
+ {\r
+ ap.annotationPanel.adjustPanelHeight();\r
+ setSize(getSize().width, ap.annotationPanel.getSize().height);\r
+ ap.validate();\r
+ ap.paintAlignment(true);\r
+ }\r
+\r
+ boolean editLabelDescription(AlignmentAnnotation annotation)\r
+ {\r
+ JCheckBox padGaps = new JCheckBox("Fill Empty Gaps With \""\r
+ + ap.av.getGapCharacter() + "\"", annotation.padGaps);\r
+\r
+ EditNameDialog dialog = new EditNameDialog(annotation.label,\r
+ annotation.description, " Annotation Label",\r
+ "Annotation Description", ap.alignFrame,\r
+ "Edit Annotation Name / Description", 500, 180, false);\r
+\r
+ JPanel empty = new JPanel(new FlowLayout());\r
+ empty.add(padGaps);\r
+ dialog.add(empty);\r
+ dialog.pack();\r
+\r
+ dialog.setVisible(true);\r
+\r
+ if (dialog.accept)\r
+ {\r
+ annotation.label = dialog.getName();\r
+ annotation.description = dialog.getDescription();\r
+ annotation.setPadGaps(padGaps.isSelected(), av.getGapCharacter());\r
+ repaint();\r
+ return true;\r
+ }\r
+ else\r
+ {\r
+ return false;\r
+ }\r
+\r
+ }\r
+\r
+ boolean resizePanel = false;\r
+\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ resizePanel = evt.getY() < 10 && evt.getX() < 14;\r
+ int row = getSelectedRow(evt.getY() + scrollOffset);\r
+\r
+ if (row > -1)\r
+ {\r
+ ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(\r
+ av.getAlignment().getAlignmentAnnotation()[row]\r
+ .getDescription(true),\r
+ true, "\n");\r
+ if (tooltip == null)\r
+ {\r
+ tooltip = new Tooltip(phb.getNonHtmlContent(), this);\r
+ }\r
+ else\r
+ {\r
+ tooltip.setTip(phb.getNonHtmlContent());\r
+ }\r
+ }\r
+ else if (tooltip != null)\r
+ {\r
+ tooltip.setTip("");\r
+ }\r
+ }\r
+\r
+ /**\r
+ * curent drag position\r
+ */\r
+ MouseEvent dragEvent = null;\r
+\r
+ /**\r
+ * flag to indicate drag events should be ignored\r
+ */\r
+ private boolean dragCancelled = false;\r
+\r
+ /**\r
+ * clear any drag events in progress\r
+ */\r
+ public void cancelDrag()\r
+ {\r
+ dragEvent = null;\r
+ dragCancelled = true;\r
+ }\r
+\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ if (dragCancelled)\r
+ {\r
+ return;\r
+ }\r
+ ;\r
+ dragEvent = evt;\r
+\r
+ if (resizePanel)\r
+ {\r
+ Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder\r
+ .getSize(), f = ap.seqPanelHolder.getSize();\r
+ int dif = evt.getY() - oldY;\r
+\r
+ dif /= ap.av.getCharHeight();\r
+ dif *= ap.av.getCharHeight();\r
+\r
+ if ((d.height - dif) > 20 && (f.height + dif) > 20)\r
+ {\r
+ ap.annotationPanel.setSize(d.width, d.height - dif);\r
+ setSize(new Dimension(e.width, d.height - dif));\r
+ ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,\r
+ d.height - dif));\r
+ ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height\r
+ - dif));\r
+ ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,\r
+ av.calcPanelHeight());\r
+ f.height += dif;\r
+ ap.seqPanelHolder.setPreferredSize(f);\r
+ ap.setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ ap.validate();\r
+ // ap.paintAlignment(true);\r
+ ap.addNotify();\r
+ }\r
+\r
+ }\r
+ else\r
+ {\r
+ int diff;\r
+ if ((diff = 6 - evt.getY()) > 0)\r
+ {\r
+ // nudge scroll up\r
+ ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);\r
+ ap.adjustmentValueChanged(null);\r
+\r
+ }\r
+ else if ((0 < (diff = 6\r
+ - ap.annotationSpaceFillerHolder.getSize().height\r
+ + evt.getY())))\r
+ {\r
+ // nudge scroll down\r
+ ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);\r
+ ap.adjustmentValueChanged(null);\r
+ }\r
+ repaint();\r
+ }\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ if (!resizePanel && !dragCancelled)\r
+ {\r
+ int start = selectedRow;\r
+\r
+ int end = getSelectedRow(evt.getY() + scrollOffset);\r
+\r
+ if (start > -1 && start != end)\r
+ {\r
+ // Swap these annotations\r
+ AlignmentAnnotation startAA = ap.av.getAlignment()\r
+ .getAlignmentAnnotation()[start];\r
+ if (end == -1)\r
+ {\r
+ end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;\r
+ }\r
+ AlignmentAnnotation endAA = ap.av.getAlignment()\r
+ .getAlignmentAnnotation()[end];\r
+\r
+ ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;\r
+ ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;\r
+ }\r
+ }\r
+ resizePanel = false;\r
+ dragEvent = null;\r
+ dragCancelled = false;\r
+ repaint();\r
+ ap.annotationPanel.repaint();\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ if (evt.getY() < 10 && evt.getX() < 14)\r
+ {\r
+ resizePanel = true;\r
+ repaint();\r
+ }\r
+ }\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ dragCancelled = false;\r
+\r
+ if (dragEvent == null)\r
+ {\r
+ resizePanel = false;\r
+ }\r
+ else\r
+ {\r
+ if (!resizePanel)\r
+ {\r
+ dragEvent = null;\r
+ }\r
+ }\r
+ repaint();\r
+ }\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ oldY = evt.getY();\r
+ if (resizePanel)\r
+ {\r
+ return;\r
+ }\r
+ dragCancelled = false;\r
+ // todo: move below to mouseClicked ?\r
+ selectedRow = getSelectedRow(evt.getY() + scrollOffset);\r
+\r
+ AlignmentAnnotation[] aa = ap.av.getAlignment()\r
+ .getAlignmentAnnotation();\r
+\r
+ // DETECT RIGHT MOUSE BUTTON IN AWT\r
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)\r
+ {\r
+\r
+ JPopupMenu popup = new JPopupMenu(\r
+ MessageManager.getString("label.annotations"));\r
+\r
+ JMenuItem item = new JMenuItem(ADDNEW);\r
+ item.addActionListener(this);\r
+ popup.add(item);\r
+ if (selectedRow < 0)\r
+ {\r
+ // this never happens at moment: - see comment on JAL-563\r
+ if (hasHiddenRows)\r
+ {\r
+ item = new JMenuItem(SHOWALL);\r
+ item.addActionListener(this);\r
+ popup.add(item);\r
+ }\r
+ this.add(popup);\r
+ popup.show(this, evt.getX(), evt.getY());\r
+ return;\r
+ }\r
+ // add the rest if there are actually rows to show\r
+ item = new JMenuItem(EDITNAME);\r
+ item.addActionListener(this);\r
+ popup.add(item);\r
+ item = new JMenuItem(HIDE);\r
+ item.addActionListener(this);\r
+ popup.add(item);\r
+\r
+ /*\r
+ * Hide all <label>:\r
+ */\r
+ if (selectedRow < aa.length)\r
+ {\r
+ if (aa[selectedRow].sequenceRef != null)\r
+ {\r
+ final String label = aa[selectedRow].label;\r
+ JMenuItem hideType = new JMenuItem(\r
+ MessageManager.getString("label.hide_all") + " " + label);\r
+ hideType.addActionListener(new ActionListener()\r
+ {\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ AlignmentUtils.showOrHideSequenceAnnotations(\r
+ ap.av.getAlignment(), Collections.singleton(label),\r
+ null, false, false);\r
+ refresh();\r
+ }\r
+ });\r
+ popup.add(hideType);\r
+ }\r
+ }\r
+\r
+ if (hasHiddenRows)\r
+ {\r
+ item = new JMenuItem(SHOWALL);\r
+ item.addActionListener(this);\r
+ popup.add(item);\r
+ }\r
+ this.add(popup);\r
+ item = new JMenuItem(OUTPUT_TEXT);\r
+ item.addActionListener(this);\r
+ popup.add(item);\r
+ if (selectedRow < aa.length)\r
+ {\r
+ if (aa[selectedRow].autoCalculated)\r
+ {\r
+ if (aa[selectedRow].label.indexOf("Consensus") > -1)\r
+ {\r
+ popup.addSeparator();\r
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(\r
+ MessageManager.getString("label.ignore_gaps_consensus"),\r
+ (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef\r
+ .getIgnoreGapsConsensus() : ap.av\r
+ .isIgnoreGapsConsensus());\r
+ final AlignmentAnnotation aaa = aa[selectedRow];\r
+ cbmi.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ if (aaa.groupRef != null)\r
+ {\r
+ // TODO: pass on reference to ap so the view can be updated.\r
+ aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());\r
+ }\r
+ else\r
+ {\r
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);\r
+ }\r
+ ap.paintAlignment(true);\r
+ }\r
+ });\r
+ popup.add(cbmi);\r
+ if (aaa.groupRef != null)\r
+ {\r
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(\r
+ MessageManager.getString("label.show_group_histogram"),\r
+ aa[selectedRow].groupRef.isShowConsensusHistogram());\r
+ chist.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ // TODO: pass on reference\r
+ // to ap\r
+ // so the\r
+ // view\r
+ // can be\r
+ // updated.\r
+ aaa.groupRef.setShowConsensusHistogram(chist.getState());\r
+ ap.repaint();\r
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());\r
+ }\r
+ });\r
+ popup.add(chist);\r
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(\r
+ MessageManager.getString("label.show_group_logo"),\r
+ aa[selectedRow].groupRef.isShowSequenceLogo());\r
+ cprofl.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ // TODO: pass on reference\r
+ // to ap\r
+ // so the\r
+ // view\r
+ // can be\r
+ // updated.\r
+ aaa.groupRef.setshowSequenceLogo(cprofl.getState());\r
+ ap.repaint();\r
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());\r
+ }\r
+ });\r
+\r
+ popup.add(cprofl);\r
+ final JCheckBoxMenuItem cprofn = new JCheckBoxMenuItem(\r
+ MessageManager.getString("label.normalise_group_logo"),\r
+ aa[selectedRow].groupRef.isNormaliseSequenceLogo());\r
+ cprofn.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ // TODO: pass on reference\r
+ // to ap\r
+ // so the\r
+ // view\r
+ // can be\r
+ // updated.\r
+ aaa.groupRef.setshowSequenceLogo(true);\r
+ aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());\r
+ ap.repaint();\r
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());\r
+ }\r
+ });\r
+ popup.add(cprofn);\r
+ }\r
+ else\r
+ {\r
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(\r
+ MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());\r
+ chist.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ // TODO: pass on reference\r
+ // to ap\r
+ // so the\r
+ // view\r
+ // can be\r
+ // updated.\r
+ av.setShowConsensusHistogram(chist.getState());\r
+ ap.alignFrame.showConsensusHistogram.setState(chist\r
+ .getState()); // TODO: implement\r
+ // ap.updateGUI()/alignFrame.updateGUI\r
+ // for applet\r
+ ap.repaint();\r
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());\r
+ }\r
+ });\r
+ popup.add(chist);\r
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(\r
+ MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());\r
+ cprof.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ // TODO: pass on reference\r
+ // to ap\r
+ // so the\r
+ // view\r
+ // can be\r
+ // updated.\r
+ av.setShowSequenceLogo(cprof.getState());\r
+ ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:\r
+ // implement\r
+ // ap.updateGUI()/alignFrame.updateGUI\r
+ // for\r
+ // applet\r
+ ap.repaint();\r
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());\r
+ }\r
+ });\r
+ popup.add(cprof);\r
+ final JCheckBoxMenuItem cprofn = new JCheckBoxMenuItem(\r
+ MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());\r
+ cprofn.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ // TODO: pass on reference\r
+ // to ap\r
+ // so the\r
+ // view\r
+ // can be\r
+ // updated.\r
+ av.setShowSequenceLogo(true);\r
+ ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:\r
+ // implement\r
+ // ap.updateGUI()/alignFrame.updateGUI\r
+ // for\r
+ // applet\r
+ av.setNormaliseSequenceLogo(cprofn.getState());\r
+ ap.repaint();\r
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());\r
+ }\r
+ });\r
+ popup.add(cprofn);\r
+ }\r
+\r
+ item = new JMenuItem(COPYCONS_SEQ);\r
+ item.addActionListener(this);\r
+ popup.add(item);\r
+ }\r
+ }\r
+ }\r
+ popup.show(this, evt.getX(), evt.getY());\r
+ }\r
+ else\r
+ {\r
+ // selection action.\r
+ if (selectedRow > -1 && selectedRow < aa.length)\r
+ {\r
+ if (aa[selectedRow].groupRef != null)\r
+ {\r
+ if (evt.getClickCount() >= 2)\r
+ {\r
+ // todo: make the ap scroll to the selection - not necessary, first\r
+ // click highlights/scrolls, second selects\r
+ ap.seqPanel.ap.idPanel.highlightSearchResults(null);\r
+ ap.av.setSelectionGroup(// new SequenceGroup(\r
+ aa[selectedRow].groupRef); // );\r
+ ap.av.sendSelection();\r
+ ap.paintAlignment(false);\r
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());\r
+ }\r
+ else\r
+ {\r
+ ap.seqPanel.ap.idPanel\r
+ .highlightSearchResults(aa[selectedRow].groupRef\r
+ .getSequences(null));\r
+ }\r
+ return;\r
+ }\r
+ else if (aa[selectedRow].sequenceRef != null)\r
+ {\r
+ if (evt.getClickCount() == 1)\r
+ {\r
+ ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays\r
+ .asList(new SequenceI[]\r
+ { aa[selectedRow].sequenceRef }));\r
+ }\r
+ else if (evt.getClickCount() >= 2)\r
+ {\r
+ ap.seqPanel.ap.idPanel.highlightSearchResults(null);\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg!=null)\r
+ {\r
+ // we make a copy rather than edit the current selection if no modifiers pressed\r
+ // see Enhancement JAL-1557\r
+ if (!(evt.isControlDown() || evt.isShiftDown()))\r
+ {\r
+ sg = new SequenceGroup(sg);\r
+ sg.clear();\r
+ sg.addSequence(aa[selectedRow].sequenceRef, false);\r
+ } else {\r
+ if (evt.isControlDown())\r
+ {\r
+ sg.addOrRemove(aa[selectedRow].sequenceRef, true);\r
+ } else {\r
+ // notionally, we should also add intermediate sequences from last added sequence ?\r
+ sg.addSequence(aa[selectedRow].sequenceRef, true);\r
+ }\r
+ }\r
+ } else {\r
+ sg = new SequenceGroup();\r
+ sg.setStartRes(0);\r
+ sg.setEndRes(ap.av.getAlignment().getWidth()-1);\r
+ sg.addSequence(aa[selectedRow].sequenceRef, false);\r
+ }\r
+ ap.av.setSelectionGroup(sg);\r
+ ap.paintAlignment(false);\r
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());\r
+ ap.av.sendSelection();\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void copy_annotseqtoclipboard(SequenceI sq)\r
+ {\r
+ if (sq == null || sq.getLength() < 1)\r
+ {\r
+ return;\r
+ }\r
+ AlignFrame.copiedSequences = new StringBuffer();\r
+ AlignFrame.copiedSequences.append(sq.getName() + "\t"\r
+ + sq.getStart() + "\t" + sq.getEnd() + "\t"\r
+ + sq.getSequenceAsString() + "\n");\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ AlignFrame.copiedHiddenColumns = new Vector();\r
+ for (int[] region : av.getColumnSelection().getHiddenColumns())\r
+ {\r
+ AlignFrame.copiedHiddenColumns\r
+ .addElement(new int[]\r
+ { region[0], region[1] });\r
+ }\r
+ }\r
+ }\r
+\r
+ public void update(Graphics g)\r
+ {\r
+ paint(g);\r
+ }\r
+\r
+ public void paint(Graphics g)\r
+ {\r
+ int w = getSize().width;\r
+ int h = getSize().height;\r
+ if (image == null || w != image.getWidth(this)\r
+ || h != image.getHeight(this))\r
+ {\r
+ image = createImage(w, ap.annotationPanel.getSize().height);\r
+ }\r
+\r
+ drawComponent(image.getGraphics(), w);\r
+ g.drawImage(image, 0, 0, this);\r
+ }\r
+\r
+ public void drawComponent(Graphics g, int width)\r
+ {\r
+ g.setFont(av.getFont());\r
+ FontMetrics fm = g.getFontMetrics(av.getFont());\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+\r
+ g.translate(0, -scrollOffset);\r
+ g.setColor(Color.black);\r
+\r
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();\r
+ int y = 0, fy = g.getFont().getSize();\r
+ int x = 0, offset;\r
+\r
+ if (aa != null)\r
+ {\r
+ hasHiddenRows = false;\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ hasHiddenRows = true;\r
+ continue;\r
+ }\r
+\r
+ x = width - fm.stringWidth(aa[i].label) - 3;\r
+\r
+ y += aa[i].height;\r
+ offset = -(aa[i].height - fy) / 2;\r
+\r
+ g.drawString(aa[i].label, x, y + offset);\r
+ }\r
+ }\r
+ g.translate(0, +scrollOffset);\r
+ if (resizePanel)\r
+ {\r
+ g.setColor(Color.red);\r
+ g.setPaintMode();\r
+ g.drawLine(2, 8, 5, 2);\r
+ g.drawLine(5, 2, 8, 8);\r
+ }\r
+ else if (!dragCancelled && dragEvent != null && aa != null)\r
+ {\r
+ g.setColor(Color.lightGray);\r
+ g.drawString(aa[selectedRow].label, dragEvent.getX(),\r
+ dragEvent.getY());\r
+ }\r
+\r
+ if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))\r
+ {\r
+ g.setColor(Color.black);\r
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);\r
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,\r
+ 18);\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff