+/*
+ * 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 java.util.Locale;
+
+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.workers.InformationThread;
+
+import java.awt.Color;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+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.util.Arrays;
+import java.util.Collections;
+import java.util.Iterator;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
+/**
+ * The panel that holds the labels for alignment annotations, providing
+ * tooltips, context menus, drag to reorder rows, and drag to adjust panel
+ * height
+ */
+public class AnnotationLabels extends JPanel
+ implements MouseListener, MouseMotionListener, ActionListener
+{
+ private static final String HTML_END_TAG = "</html>";
+
+ private static final String HTML_START_TAG = "<html>";
+
+ /**
+ * width in pixels within which height adjuster arrows are shown and active
+ */
+ private static final int HEIGHT_ADJUSTER_WIDTH = 50;
+
+ /**
+ * height in pixels for allowing height adjuster to be active
+ */
+ private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+
+ private static final Font font = new Font("Arial", Font.PLAIN, 11);
+
+ private static final String TOGGLE_LABELSCALE = MessageManager
+ .getString("label.scale_label_to_column");
+
+ private static final String ADDNEW = MessageManager
+ .getString("label.add_new_row");
+
+ private static final String EDITNAME = MessageManager
+ .getString("label.edit_label_description");
+
+ private static final String HIDE = MessageManager
+ .getString("label.hide_row");
+
+ private static final String DELETE = MessageManager
+ .getString("label.delete_row");
+
+ private static final String SHOWALL = MessageManager
+ .getString("label.show_all_hidden_rows");
+
+ private static final String OUTPUT_TEXT = MessageManager
+ .getString("label.export_annotation");
+
+ private static final String COPYCONS_SEQ = MessageManager
+ .getString("label.copy_consensus_sequence");
+
+ private final boolean debugRedraw = false;
+
+ private AlignmentPanel ap;
+
+ AlignViewport av;
+
+ private MouseEvent dragEvent;
+
+ private int oldY;
+
+ private int selectedRow;
+
+ private int scrollOffset = 0;
+
+ private boolean hasHiddenRows;
+
+ private boolean resizePanel = false;
+
+ /**
+ * Creates a new AnnotationLabels object
+ *
+ * @param ap
+ */
+ public AnnotationLabels(AlignmentPanel ap)
+ {
+
+ this.ap = ap;
+ av = ap.av;
+ ToolTipManager.sharedInstance().registerComponent(this);
+
+ 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();
+
+ String action = evt.getActionCommand();
+ if (ADDNEW.equals(action))
+ {
+ /*
+ * non-returning dialog
+ */
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
+ null, new Annotation[ap.av.getAlignment().getWidth()]);
+ editLabelDescription(newAnnotation, true);
+ }
+ else if (EDITNAME.equals(action))
+ {
+ /*
+ * non-returning dialog
+ */
+ editLabelDescription(aa[selectedRow], false);
+ }
+ else if (HIDE.equals(action))
+ {
+ aa[selectedRow].visible = false;
+ }
+ else if (DELETE.equals(action))
+ {
+ ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
+ ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
+ }
+ else if (SHOWALL.equals(action))
+ {
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (!aa[i].visible && aa[i].annotations != null)
+ {
+ aa[i].visible = true;
+ }
+ }
+ }
+ else if (OUTPUT_TEXT.equals(action))
+ {
+ new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]);
+ }
+ else if (COPYCONS_SEQ.equals(action))
+ {
+ 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 (TOGGLE_LABELSCALE.equals(action))
+ {
+ aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
+ }
+
+ ap.refresh(true);
+ }
+
+ /**
+ * Shows a dialog where the annotation name and description may be edited. If
+ * parameter addNew is true, then on confirmation, a new AlignmentAnnotation
+ * is added, else an existing annotation is updated.
+ *
+ * @param annotation
+ * @param addNew
+ */
+ void editLabelDescription(AlignmentAnnotation annotation, boolean addNew)
+ {
+ String name = MessageManager.getString("label.annotation_name");
+ String description = MessageManager
+ .getString("label.annotation_description");
+ String title = MessageManager
+ .getString("label.edit_annotation_name_description");
+ EditNameDialog dialog = new EditNameDialog(annotation.label,
+ annotation.description, name, description);
+
+ dialog.showDialog(ap.alignFrame, title, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ annotation.label = dialog.getName();
+ String text = dialog.getDescription();
+ if (text != null && text.length() == 0)
+ {
+ text = null;
+ }
+ annotation.description = text;
+ if (addNew)
+ {
+ ap.av.getAlignment().addAnnotation(annotation);
+ ap.av.getAlignment().setAnnotationIndex(annotation, 0);
+ }
+ ap.refresh(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;
+ }
+ final AlignmentAnnotation ann = aa[selectedRow];
+ final boolean isSequenceAnnotation = ann.sequenceRef != null;
+ 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);
+ 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)
+ && !(InformationThread.HMM_CALC_ID.equals(ann.getCalcId())))
+ {
+ 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)
+ {
+ addConsensusMenuOptions(ap, aa[selectedRow], pop);
+
+ final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+ consclipbrd.addActionListener(this);
+ pop.add(consclipbrd);
+ }
+ else if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+ {
+ addHmmerMenu(pop, ann);
+ }
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ }
+
+ /**
+ * Adds context menu options for (alignment or group) Hmmer annotation
+ *
+ * @param pop
+ * @param ann
+ */
+ protected void addHmmerMenu(JPopupMenu pop, final AlignmentAnnotation ann)
+ {
+ final boolean isGroupAnnotation = ann.groupRef != null;
+ pop.addSeparator();
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString(
+ "label.ignore_below_background_frequency"),
+ isGroupAnnotation
+ ? ann.groupRef
+ .isIgnoreBelowBackground()
+ : ap.av.isIgnoreBelowBackground());
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (isGroupAnnotation)
+ {
+ if (!ann.groupRef.isUseInfoLetterHeight())
+ {
+ ann.groupRef.setIgnoreBelowBackground(cbmi.getState());
+ // todo and recompute group annotation
+ }
+ }
+ else if (!ap.av.isInfoLetterHeight())
+ {
+ ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
+ // todo and recompute annotation
+ }
+ ap.alignmentChanged(); // todo not like this
+ }
+ });
+ pop.add(cbmi);
+ final JCheckBoxMenuItem letterHeight = new JCheckBoxMenuItem(
+ MessageManager.getString("label.use_info_for_height"),
+ isGroupAnnotation ? ann.groupRef.isUseInfoLetterHeight()
+ : ap.av.isInfoLetterHeight());
+ letterHeight.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (isGroupAnnotation)
+ {
+ ann.groupRef.setInfoLetterHeight((letterHeight.getState()));
+ ann.groupRef.setIgnoreBelowBackground(true);
+ // todo and recompute group annotation
+ }
+ else
+ {
+ ap.av.setInfoLetterHeight(letterHeight.getState(), ap);
+ ap.av.setIgnoreBelowBackground(true, ap);
+ // todo and recompute annotation
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(letterHeight);
+ if (isGroupAnnotation)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ ann.groupRef.isShowInformationHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setShowInformationHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ ann.groupRef.isShowHMMSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setShowHMMSequenceLogo(cprofl.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ ann.groupRef.isNormaliseHMMSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef
+ .setNormaliseHMMSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ ann.groupRef.setShowHMMSequenceLogo(true);
+ ap.repaint();
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowInformationHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowInformationHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ av.isShowHMMSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowHMMSequenceLogo(cprof.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseHMMSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowHMMSequenceLogo(true);
+ av.setNormaliseHMMSequenceLogo(cprofnorm.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofnorm);
+ }
+ }
+
+ /**
+ * A helper method that adds menu options for calculation and visualisation of
+ * group and/or alignment consensus annotation to a popup menu. This is
+ * designed to be reusable for either unwrapped mode (popup menu is shown on
+ * component AnnotationLabels), or wrapped mode (popup menu is shown on
+ * IdPanel when the mouse is over an annotation label).
+ *
+ * @param ap
+ * @param ann
+ * @param pop
+ */
+ static void addConsensusMenuOptions(AlignmentPanel ap,
+ AlignmentAnnotation ann, JPopupMenu pop)
+ {
+ pop.addSeparator();
+
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = ann;
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (aaa.groupRef != null)
+ {
+ aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+ ap.getAnnotationPanel()
+ .paint(ap.getAnnotationPanel().getGraphics());
+ }
+ else
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(cbmi);
+
+ if (aaa.groupRef != null)
+ {
+ /*
+ * group consensus options
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ ann.groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aaa.groupRef.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ ann.groupRef.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aaa.groupRef.setshowSequenceLogo(cprofl.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ ann.groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ aaa.groupRef.setshowSequenceLogo(true);
+ ap.repaint();
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ /*
+ * alignment consensus options
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ ap.av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ ap.av.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ ap.av.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.setShowSequenceLogo(true);
+ ap.av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ }
+ });
+ pop.add(cprofnorm);
+ }
+ }
+
+ /**
+ * Reorders annotation rows after a drag of a label
+ *
+ * @param evt
+ */
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger())
+ {
+ showPopupMenu(evt);
+ return;
+ }
+
+ int start = selectedRow;
+ getSelectedRow(evt.getY() - getScrollOffset());
+ int end = selectedRow;
+
+ /*
+ * if dragging to resize instead, start == end
+ */
+ 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();
+ }
+
+ /**
+ * Removes the height adjuster image on leaving the panel, unless currently
+ * dragging it
+ */
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ if (resizePanel && dragEvent == null)
+ {
+ resizePanel = false;
+ repaint();
+ }
+ }
+
+ /**
+ * A mouse drag may be either an adjustment of the panel height (if flag
+ * resizePanel is set on), or a reordering of the annotation rows. The former
+ * is dealt with by this method, the latter in mouseReleased.
+ *
+ * @param evt
+ */
+ @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, false);
+ }
+
+ ap.addNotify();
+ }
+ else
+ {
+ repaint();
+ }
+ }
+
+ /**
+ * Updates the tooltip as the mouse moves over the labels
+ *
+ * @param evt
+ */
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ showOrHideAdjuster(evt);
+
+ getSelectedRow(evt.getY() - getScrollOffset());
+
+ if (selectedRow > -1 && ap.av.getAlignment()
+ .getAlignmentAnnotation().length > selectedRow)
+ {
+ AlignmentAnnotation[] anns = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ AlignmentAnnotation aa = anns[selectedRow];
+
+ String desc = getTooltip(aa);
+ this.setToolTipText(desc);
+ String msg = getStatusMessage(aa, anns);
+ ap.alignFrame.setStatus(msg);
+ }
+ }
+
+ /**
+ * Constructs suitable text to show in the status bar when over an annotation
+ * label, containing the associated sequence name (if any), and the annotation
+ * labels (or all labels for a graph group annotation)
+ *
+ * @param aa
+ * @param anns
+ * @return
+ */
+ static String getStatusMessage(AlignmentAnnotation aa,
+ AlignmentAnnotation[] anns)
+ {
+ if (aa == null)
+ {
+ return null;
+ }
+
+ StringBuilder msg = new StringBuilder(32);
+ if (aa.sequenceRef != null)
+ {
+ msg.append(aa.sequenceRef.getName()).append(" : ");
+ }
+
+ if (aa.graphGroup == -1)
+ {
+ msg.append(aa.label);
+ }
+ else if (anns != null)
+ {
+ boolean first = true;
+ for (int i = anns.length - 1; i >= 0; i--)
+ {
+ if (anns[i].graphGroup == aa.graphGroup)
+ {
+ if (!first)
+ {
+ msg.append(", ");
+ }
+ msg.append(anns[i].label);
+ first = false;
+ }
+ }
+ }
+
+ return msg.toString();
+ }
+
+ /**
+ * Answers a tooltip, formatted as html, containing the annotation description
+ * (prefixed by associated sequence id if applicable), and the annotation
+ * (non-positional) score if it has one. Answers null if neither description
+ * nor score is found.
+ *
+ * @param aa
+ * @return
+ */
+ static String getTooltip(AlignmentAnnotation aa)
+ {
+ if (aa == null)
+ {
+ return null;
+ }
+ StringBuilder tooltip = new StringBuilder();
+ 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
+ String desc = aa.getDescription(true).trim();
+ if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG))
+ {
+ tooltip.append(HTML_START_TAG);
+ desc = desc.replace("<", "<");
+ }
+ else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG))
+ {
+ desc = desc.substring(0, desc.length() - HTML_END_TAG.length());
+ }
+ tooltip.append(desc);
+ }
+ else
+ {
+ // begin the tooltip's html fragment
+ tooltip.append(HTML_START_TAG);
+ }
+ if (aa.hasScore())
+ {
+ if (tooltip.length() > HTML_START_TAG.length())
+ {
+ tooltip.append("<br/>");
+ }
+ // TODO: limit precision of score to avoid noise from imprecise
+ // doubles
+ // (64.7 becomes 64.7+/some tiny value).
+ tooltip.append(" Score: ").append(String.valueOf(aa.score));
+ }
+
+ if (tooltip.length() > HTML_START_TAG.length())
+ {
+ return tooltip.append(HTML_END_TAG).toString();
+ }
+
+ /*
+ * nothing in the tooltip (except "<html>")
+ */
+ return null;
+ }
+
+ /**
+ * Shows the height adjuster image if the mouse moves into the top left
+ * region, or hides it if the mouse leaves the regio
+ *
+ * @param evt
+ */
+ protected void showOrHideAdjuster(MouseEvent evt)
+ {
+ boolean was = resizePanel;
+ resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
+ && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+
+ if (resizePanel != was)
+ {
+ setCursor(Cursor
+ .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR
+ : Cursor.DEFAULT_CURSOR));
+ repaint();
+ }
+ }
+
+ @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
+ || !(Platform.isControlDown(evt) || evt.isShiftDown()))
+ {
+ if (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, 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 (!(Platform.isControlDown(evt) || evt.isShiftDown()))
+ {
+ sg = new SequenceGroup(sg);
+ sg.clear();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
+ else
+ {
+ if (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, 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(AlignSeq.extractGaps(Comparison.GapChars,
+ sq.getSequenceAsString()));
+
+ sq.setDatasetSequence(dseqs[0]);
+ }
+ Alignment ds = new Alignment(dseqs);
+ if (av.hasHiddenColumns())
+ {
+ Iterator<int[]> it = av.getAlignment().getHiddenColumns()
+ .getVisContigsIterator(0, sq.getLength(), false);
+ omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
+ }
+
+ int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
+ if (av.hasHiddenColumns())
+ {
+ alignmentStartEnd = av.getAlignment().getHiddenColumns()
+ .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
+ }
+
+ String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
+ seqs, omitHidden, alignmentStartEnd);
+
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.getInstance());
+
+ HiddenColumns hiddenColumns = null;
+
+ if (av.hasHiddenColumns())
+ {
+ hiddenColumns = new HiddenColumns(
+ av.getAlignment().getHiddenColumns());
+ }
+
+ // what is the dataset of a consensus sequence?
+ // need to flag sequence as special.
+ Desktop.getInstance().jalviewClipboard = new Object[] { seqs, ds,
+ hiddenColumns };
+ }
+
+ @Override
+ public void paintComponent(Graphics g)
+ {
+
+ int width = getWidth();
+ if (width == 0)
+ {
+ width = ap.calculateIdWidth().width;
+ }
+
+ 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);
+ }
+
+ /**
+ * 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 && 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;
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ }
+}