X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=7b491e47e59ec10f8abdb2e39764bc66dff6bcb0;hb=e57f77dc13f5a295cf49a403da05770a68a6e22b;hp=9e0ed33213bf747020bd322ba1ebfe55d5adc915;hpb=c5aa740f1fff4c8caee4ccf0c0e0de517ca4dcb8;p=jalview.git
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 9e0ed33..7b491e4 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,472 +1,657 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import jalview.datamodel.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class IdPanel extends JPanel implements MouseListener,
- MouseMotionListener
-{
- protected IdCanvas idCanvas;
- protected AlignViewport av;
- protected AlignmentPanel alignPanel;
- ScrollThread scrollThread = null;
- int offy;
- int width;
- int lastid = -1;
- boolean mouseDragging = false;
-
- /**
- * Creates a new IdPanel object.
- *
- * @param av DOCUMENT ME!
- * @param parent DOCUMENT ME!
- */
- public IdPanel(AlignViewport av, AlignmentPanel parent)
- {
- this.av = av;
- alignPanel = parent;
- idCanvas = new IdCanvas(av);
- setLayout(new BorderLayout());
- add(idCanvas, BorderLayout.CENTER);
- addMouseListener(this);
- addMouseMotionListener(this);
- ToolTipManager.sharedInstance().registerComponent(this);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseMoved(MouseEvent e)
- {
- int y = e.getY();
-
- if (av.getWrapAlignment())
- {
- y = getWrappedY(y);
- }
-
- final int seq = av.getIndex(y);
- if(seq!=-1)
- {
- StringBuffer tip = new StringBuffer("");
- tip.append(av.alignment.getSequenceAt(seq).getDisplayId(true));
- if (av.alignment.getSequenceAt(seq).getDescription() != null)
- {
- tip.append("
");
- tip.append(av.alignment.getSequenceAt(seq).getDescription());
- tip.append(" |
");
- }
- tip.append("");
- setToolTipText(tip.toString());
- }
-
- if(av.hasHiddenRows)
- {
- if(av.adjustForHiddenSeqs(seq) -
- av.adjustForHiddenSeqs(seq-1)>1)
- {
- JPopupMenu pop = new JPopupMenu();
- JMenuItem item = new JMenuItem("Reveal");
- item.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- av.showSequence(seq);
- alignPanel.repaint();
- if(alignPanel.overviewPanel!=null)
- alignPanel.overviewPanel.updateOverviewImage();
- }
- });
- pop.add(item);
- pop.show(this, e.getX(), e.getY());
- }
- }
- }
-
-
- int getWrappedY(int y)
- {
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
- hgap += av.charHeight;
-
- return y - hgap;
- }
-
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseDragged(MouseEvent e)
- {
- mouseDragging = true;
-
- int y = e.getY();
-
- if (av.getWrapAlignment())
- {
- y = getWrappedY(y);
- }
-
- int seq = av.getIndex(y);
-
- if (seq < 0)
- {
- return;
- }
-
- if (seq < lastid)
- {
- selectSeqs(lastid - 1, seq);
- }
- else if (seq > lastid)
- {
- selectSeqs(lastid + 1, seq);
- }
-
- lastid = seq;
- alignPanel.repaint();
- }
-
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent e)
- {
- if (e.getClickCount() < 2)
- return;
-
- java.util.Vector links = Preferences.sequenceURLLinks;
- if (links == null || links.size() < 1)
- return;
-
- int y = e.getY();
-
- if (av.getWrapAlignment())
- {
- y = getWrappedY(y);
- }
-
- //DEFAULT LINK IS FIRST IN THE LINK LIST
- int seq = av.getIndex(y);
- if(seq==-1)
- return;
-
- String id = av.getAlignment().getSequenceAt(seq).getName();
- if (id.indexOf("|") > -1)
- id = id.substring(id.lastIndexOf("|") + 1);
-
-
- String url = links.elementAt(0).toString();
- url = url.substring(url.indexOf("|")+1);
-
- int index = url.indexOf("$SEQUENCE_ID$");
- url = url.substring(0, index)+ id + url.substring(index+13);
-
- try
- {
- jalview.util.BrowserLauncher.openURL(url);
- }
- catch (Exception ex)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- +"\nAdd the full path to your browser in Preferences.",
- "Web browser not found", JOptionPane.WARNING_MESSAGE );
- ex.printStackTrace();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent e)
- {
- if (scrollThread != null)
- {
- scrollThread.running = false;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseExited(MouseEvent e)
- {
- if (av.getWrapAlignment())
- {
- return;
- }
-
- if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
- {
- scrollThread = new ScrollThread(true);
- }
-
- if (mouseDragging && (e.getY() >= getHeight()) &&
- (av.alignment.getHeight() > av.getEndSeq()))
- {
- scrollThread = new ScrollThread(false);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mousePressed(MouseEvent e)
- {
- if (e.getClickCount() == 2)
- {
- return;
- }
-
- int y = e.getY();
-
- if (av.getWrapAlignment())
- {
- y = getWrappedY(y);
- }
-
- int seq = av.getIndex(y);
-
- if (seq == -1)
- {
- return;
- }
-
- if (javax.swing.SwingUtilities.isRightMouseButton(e))
- {
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
- (Sequence) av.getAlignment().getSequenceAt(seq),
- Preferences.sequenceURLLinks);
- pop.show(this, e.getX(), y);
-
- return;
- }
-
- /* if (!e.isControlDown() && !e.isShiftDown() &&
- (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null))
- {
- System.out.println("no modifiers");
- SequenceGroup selection = new SequenceGroup();
- SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(
- seq));
- selection.setStartRes(0);
- selection.setEndRes(av.alignment.getWidth() - 1);
-
- for (int i = 0; i < sg.getSize(); i++)
- {
- selection.addSequence(sg.getSequenceAt(i), true);
- }
-
- av.setSelectionGroup(selection);
-
- return;
- }*/
-
- if ((av.getSelectionGroup() == null) ||
- ((!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
- {
- av.setSelectionGroup(new SequenceGroup());
- av.getSelectionGroup().setStartRes(0);
- av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
- }
-
-
-
- if (e.isShiftDown() && (lastid != -1))
- {
- selectSeqs(lastid, seq);
- }
- else
- {
- selectSeq(seq);
- }
-
- alignPanel.repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
- */
- void selectSeq(int seq)
- {
- lastid = seq;
-
- SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- */
- void selectSeqs(int start, int end)
- {
- if(av.getSelectionGroup()==null)
- return;
-
- lastid = start;
-
- if (end < start)
- {
- int tmp = start;
- start = end;
- end = tmp;
- lastid = end;
- }
-
- for (int i = start; i <= end; i++)
- {
- av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
- true);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent e)
- {
- if (scrollThread != null)
- {
- scrollThread.running = false;
- }
-
- mouseDragging = false;
- PaintRefresher.Refresh(av.alignment);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param found DOCUMENT ME!
- */
- public void highlightSearchResults(java.util.Vector found)
- {
- idCanvas.setHighlighted(found);
-
- if (found == null)
- {
- return;
- }
-
- int index = av.alignment.findIndex((SequenceI) found.get(0));
-
- // do we need to scroll the panel?
- if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
- {
- alignPanel.setScrollValues(av.getStartRes(), index);
- }
- }
-
- // this class allows scrolling off the bottom of the visible alignment
- class ScrollThread extends Thread
- {
- boolean running = false;
- boolean up = true;
-
- public ScrollThread(boolean up)
- {
- this.up = up;
- start();
- }
-
- public void stopScrolling()
- {
- running = false;
- }
-
- public void run()
- {
- running = true;
-
- while (running)
- {
- if (alignPanel.scrollUp(up))
- {
- // scroll was ok, so add new sequence to selection
- int seq = av.getStartSeq();
-
- if (!up)
- {
- seq = av.getEndSeq();
- }
-
- if (seq < lastid)
- {
- selectSeqs(lastid - 1, seq);
- }
- else if (seq > lastid)
- {
- selectSeqs(lastid + 1, seq);
- }
-
- lastid = seq;
- }
- else
- {
- running = false;
- }
-
- alignPanel.repaint();
-
- try
- {
- Thread.sleep(100);
- }
- catch (Exception ex)
- {
- }
- }
- }
- }
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import java.awt.BorderLayout;
+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.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.List;
+
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.Timer;
+import javax.swing.ToolTipManager;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.SeqPanel.MousePos;
+import jalview.io.SequenceAnnotationReport;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
+
+/**
+ * This panel hosts alignment sequence ids and responds to mouse clicks on them,
+ * as well as highlighting ids matched by a search from the Find menu.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdPanel extends JPanel
+ implements MouseListener, MouseMotionListener, MouseWheelListener
+{
+ private IdCanvas idCanvas;
+
+ protected AlignmentViewport av;
+
+ protected AlignmentPanel alignPanel;
+
+ ScrollThread scrollThread = null;
+
+ int offy;
+
+ // int width;
+ int lastid = -1;
+
+ boolean mouseDragging = false;
+
+ private final SequenceAnnotationReport seqAnnotReport;
+
+ /**
+ * Creates a new IdPanel object.
+ *
+ * @param av
+ * @param parent
+ */
+ public IdPanel(AlignViewport av, AlignmentPanel parent)
+ {
+ this.av = av;
+ alignPanel = parent;
+ setIdCanvas(new IdCanvas(av));
+ seqAnnotReport = new SequenceAnnotationReport(true);
+ setLayout(new BorderLayout());
+ add(getIdCanvas(), BorderLayout.CENTER);
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ addMouseWheelListener(this);
+ ToolTipManager.sharedInstance().registerComponent(this);
+ }
+
+ /**
+ * Responds to mouse movement by setting tooltip text for the sequence id
+ * under the mouse (or possibly annotation label, when in wrapped mode)
+ *
+ * @param e
+ */
+ @Override
+ public void mouseMoved(MouseEvent e)
+ {
+ SeqPanel sp = alignPanel.getSeqPanel();
+ MousePos pos = sp.findMousePosition(e);
+ if (pos.isOverAnnotation())
+ {
+ /*
+ * mouse is over an annotation label in wrapped mode
+ */
+ AlignmentAnnotation[] anns = av.getAlignment()
+ .getAlignmentAnnotation();
+ AlignmentAnnotation annotation = anns[pos.annotationIndex];
+ setToolTipText(AnnotationLabels.getTooltip(annotation));
+ alignPanel.alignFrame.setStatus(
+ AnnotationLabels.getStatusMessage(annotation, anns));
+ }
+ else
+ {
+ int seq = Math.max(0, pos.seqIndex);
+ if (seq < av.getAlignment().getHeight())
+ {
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ StringBuilder tip = new StringBuilder(64);
+ tip.append(sequence.getDisplayId(true)).append(" ");
+ seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
+ av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
+ setToolTipText(JvSwingUtils.wrapTooltip(true, tip.toString()));
+
+ StringBuilder text = new StringBuilder();
+ text.append("Sequence ").append(String.valueOf(seq + 1))
+ .append(" ID: ").append(sequence.getName());
+ alignPanel.alignFrame.setStatus(text.toString());
+ }
+ }
+ }
+
+ /**
+ * Responds to a mouse drag by selecting the sequences under the dragged
+ * region.
+ *
+ * @param e
+ */
+ @Override
+ public void mouseDragged(MouseEvent e)
+ {
+ mouseDragging = true;
+
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+ if (pos.isOverAnnotation())
+ {
+ // mouse is over annotation label in wrapped mode
+ return;
+ }
+
+ int seq = Math.max(0, pos.seqIndex);
+
+ if (seq < lastid)
+ {
+ selectSeqs(lastid - 1, seq);
+ }
+ else if (seq > lastid)
+ {
+ selectSeqs(lastid + 1, seq);
+ }
+
+ lastid = seq;
+ alignPanel.paintAlignment(false, false);
+ }
+
+ /**
+ * Response to the mouse wheel by scrolling the alignment panel.
+ */
+ @Override
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ e.consume();
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
+ {
+ if (e.isShiftDown())
+ {
+ av.getRanges().scrollRight(true);
+ }
+ else
+ {
+ av.getRanges().scrollUp(false);
+ }
+ }
+ else if (wheelRotation < 0)
+ {
+ if (e.isShiftDown())
+ {
+ av.getRanges().scrollRight(false);
+ }
+ else
+ {
+ av.getRanges().scrollUp(true);
+ }
+ }
+ }
+
+ /**
+ * Handle a mouse click event. Currently only responds to a double-click. The
+ * action is to try to open a browser window at a URL that searches for the
+ * selected sequence id. The search URL is configured in Preferences |
+ * Connections | URL link from Sequence ID. For example:
+ *
+ * http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$
+ *
+ * @param e
+ */
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ /*
+ * Ignore single click. Ignore 'left' click followed by 'right' click (user
+ * selects a row then its pop-up menu).
+ */
+ if (e.getClickCount() < 2 || SwingUtilities.isRightMouseButton(e))
+ {
+ // reinstate isRightMouseButton check to ignore mouse-related popup events
+ // note - this does nothing on default MacBookPro force-trackpad config!
+ return;
+ }
+
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+ int seq = pos.seqIndex;
+ if (pos.isOverAnnotation() || seq < 0)
+ {
+ return;
+ }
+
+ String id = av.getAlignment().getSequenceAt(seq).getName();
+ String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
+
+ try
+ {
+ jalview.util.BrowserLauncher.openURL(url);
+ } catch (Exception ex)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * On (re-)entering the panel, stop any scrolling
+ *
+ * @param e
+ */
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ stopScrolling();
+ }
+
+ /**
+ * Interrupts the scroll thread if one is running
+ */
+ void stopScrolling()
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.stopScrolling();
+ scrollThread = null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging)
+ {
+ /*
+ * on mouse drag above or below the panel, start
+ * scrolling if there are more sequences to show
+ */
+ ViewportRanges ranges = av.getRanges();
+ if (e.getY() < 0 && ranges.getStartSeq() > 0)
+ {
+ startScrolling(true);
+ }
+ else if (e.getY() >= getHeight()
+ && ranges.getEndSeq() <= av.getAlignment().getHeight())
+ {
+ startScrolling(false);
+ }
+ }
+ }
+
+ /**
+ * Starts scrolling either up or down
+ *
+ * @param up
+ */
+ void startScrolling(boolean up)
+ {
+ scrollThread = new ScrollThread(up);
+ if (Platform.isJS())
+ {
+ /*
+ * for JalviewJS using Swing Timer
+ */
+ Timer t = new Timer(20, new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (scrollThread != null)
+ {
+ // if (!scrollOnce() {t.stop();}) gives compiler error :-(
+ scrollThread.scrollOnce();
+ }
+ }
+ });
+ t.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (scrollThread == null)
+ {
+ // IdPanel.stopScrolling called
+ t.stop();
+ }
+ }
+ });
+ t.start();
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ scrollThread.start();
+ }
+ }
+
+ /**
+ * Respond to a mouse press. Does nothing for (left) double-click as this is
+ * handled by mouseClicked().
+ *
+ * Right mouse down - construct and show context menu.
+ *
+ * Ctrl-down or Shift-down - add to or expand current selection group if there
+ * is one.
+ *
+ * Mouse down - select this sequence.
+ *
+ * @param e
+ */
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e))
+ {
+ return;
+ }
+
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+
+ if (e.isPopupTrigger()) // Mac reports this in mousePressed
+ {
+ showPopupMenu(e, pos);
+ return;
+ }
+
+ /*
+ * defer right-mouse click handling to mouseReleased on Windows
+ * (where isPopupTrigger() will answer true)
+ * NB isRightMouseButton is also true for Cmd-click on Mac
+ */
+ if (Platform.isWinRightButton(e))
+ {
+ return;
+ }
+
+ if ((av.getSelectionGroup() == null)
+ || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown()
+ && av.getSelectionGroup() != null))
+ {
+ av.setSelectionGroup(new SequenceGroup());
+ av.getSelectionGroup().setStartRes(0);
+ av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
+ }
+
+ if (e.isShiftDown() && (lastid != -1))
+ {
+ selectSeqs(lastid, pos.seqIndex);
+ }
+ else
+ {
+ selectSeq(pos.seqIndex);
+ }
+
+ av.isSelectionGroupChanged(true);
+
+ alignPanel.paintAlignment(false, false);
+ }
+
+ /**
+ * Build and show the popup-menu at the right-click mouse position
+ *
+ * @param e
+ */
+ void showPopupMenu(MouseEvent e, MousePos pos)
+ {
+ if (pos.isOverAnnotation())
+ {
+ showAnnotationMenu(e, pos);
+ return;
+ }
+
+ Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex);
+ if (sq != null)
+ {
+ PopupMenu pop = new PopupMenu(alignPanel, sq,
+ Preferences.getGroupURLLinks());
+ pop.show(this, e.getX(), e.getY());
+ }
+ }
+
+ /**
+ * On right mouse click on a Consensus annotation label, shows a limited popup
+ * menu, with options to configure the consensus calculation and rendering.
+ *
+ * @param e
+ * @param pos
+ * @see AnnotationLabels#showPopupMenu(MouseEvent)
+ */
+ void showAnnotationMenu(MouseEvent e, MousePos pos)
+ {
+ if (pos.annotationIndex == -1)
+ {
+ return;
+ }
+ AlignmentAnnotation[] anns = this.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (anns == null || pos.annotationIndex >= anns.length)
+ {
+ return;
+ }
+ AlignmentAnnotation ann = anns[pos.annotationIndex];
+ if (!ann.label.contains("Consensus"))
+ {
+ return;
+ }
+
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
+ AnnotationLabels.addConsensusMenuOptions(this.alignPanel, ann, pop);
+ pop.show(this, e.getX(), e.getY());
+ }
+
+ /**
+ * Toggle whether the sequence is part of the current selection group.
+ *
+ * @param seq
+ */
+ void selectSeq(int seq)
+ {
+ lastid = seq;
+
+ SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+ av.getSelectionGroup().addOrRemove(pickedSeq, false);
+ }
+
+ /**
+ * Add contiguous rows of the alignment to the current selection group. Does
+ * nothing if there is no selection group.
+ *
+ * @param start
+ * @param end
+ */
+ void selectSeqs(int start, int end)
+ {
+ if (av.getSelectionGroup() == null)
+ {
+ return;
+ }
+
+ if (end >= av.getAlignment().getHeight())
+ {
+ end = av.getAlignment().getHeight() - 1;
+ }
+
+ lastid = start;
+
+ if (end < start)
+ {
+ int tmp = start;
+ start = end;
+ end = tmp;
+ lastid = end;
+ }
+
+ for (int i = start; i <= end; i++)
+ {
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+ false);
+ }
+ }
+
+ /**
+ * Respond to mouse released. Refreshes the display and triggers broadcast of
+ * the new selection group to any listeners.
+ *
+ * @param e
+ */
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ if (scrollThread != null)
+ {
+ stopScrolling();
+ }
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+
+ mouseDragging = false;
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // always send selection message when mouse is released
+ av.sendSelection();
+
+ if (e.isPopupTrigger()) // Windows reports this in mouseReleased
+ {
+ showPopupMenu(e, pos);
+ }
+ }
+
+ /**
+ * Highlight sequence ids that match the given list, and if necessary scroll
+ * to the start sequence of the list.
+ *
+ * @param list
+ */
+ public void highlightSearchResults(List list)
+ {
+ getIdCanvas().setHighlighted(list);
+
+ if (list == null || list.isEmpty())
+ {
+ return;
+ }
+
+ int index = av.getAlignment().findIndex(list.get(0));
+
+ // do we need to scroll the panel?
+ if ((av.getRanges().getStartSeq() > index)
+ || (av.getRanges().getEndSeq() < index))
+ {
+ av.getRanges().setStartSeq(index);
+ }
+ }
+
+ public IdCanvas getIdCanvas()
+ {
+ return idCanvas;
+ }
+
+ public void setIdCanvas(IdCanvas idCanvas)
+ {
+ this.idCanvas = idCanvas;
+ }
+
+ /**
+ * Performs scrolling of the visible alignment up or down, adding newly
+ * visible sequences to the current selection
+ */
+ class ScrollThread extends Thread
+ {
+ private boolean running = false;
+
+ private boolean up;
+
+ /**
+ * Constructor for a thread that scrolls either up or down
+ *
+ * @param up
+ */
+ public ScrollThread(boolean up)
+ {
+ this.up = up;
+ setName("IdPanel$ScrollThread$" + String.valueOf(up));
+ }
+
+ /**
+ * Sets a flag to stop the scrolling
+ */
+ public void stopScrolling()
+ {
+ running = false;
+ }
+
+ /**
+ * Scrolls the alignment either up or down, one row at a time, adding newly
+ * visible sequences to the current selection. Speed is limited to a maximum
+ * of ten rows per second. The thread exits when the end of the alignment is
+ * reached or a flag is set to stop it by a call to stopScrolling.
+ */
+ @Override
+ public void run()
+ {
+ running = true;
+
+ while (running)
+ {
+ running = scrollOnce();
+ try
+ {
+ Thread.sleep(100);
+ } catch (Exception ex)
+ {
+ }
+ }
+ IdPanel.this.scrollThread = null;
+ }
+
+ /**
+ * Scrolls one row up or down. Answers true if a scroll could be done, false
+ * if not (top or bottom of alignment reached).
+ */
+ boolean scrollOnce()
+ {
+ ViewportRanges ranges = IdPanel.this.av.getRanges();
+ if (ranges.scrollUp(up))
+ {
+ int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq();
+ int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1;
+ IdPanel.this.selectSeqs(fromSeq, toSeq);
+ lastid = toSeq;
+ alignPanel.paintAlignment(false, false);
+ return true;
+ }
+
+ return false;
+ }
+ }
+}