-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class IdPanel extends JPanel implements MouseListener,\r
- MouseMotionListener\r
-{\r
- protected IdCanvas idCanvas;\r
- protected AlignViewport av;\r
- protected AlignmentPanel alignPanel;\r
- ScrollThread scrollThread = null;\r
- int offy;\r
- int width;\r
- int lastid = -1;\r
- boolean mouseDragging = false;\r
-\r
- /**\r
- * Creates a new IdPanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param parent DOCUMENT ME!\r
- */\r
- public IdPanel(AlignViewport av, AlignmentPanel parent)\r
- {\r
- this.av = av;\r
- alignPanel = parent;\r
- idCanvas = new IdCanvas(av);\r
- setLayout(new BorderLayout());\r
- add(idCanvas, BorderLayout.CENTER);\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mouseMoved(MouseEvent e)\r
- {\r
- int y = e.getY();\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- y = getWrappedY(y);\r
- }\r
-\r
- int seq = av.getIndex(y);\r
- if(seq!=-1)\r
- {\r
- StringBuffer tip = new StringBuffer("<html>");\r
- tip.append(av.alignment.getSequenceAt(seq).getDisplayId(true));\r
- if (av.alignment.getSequenceAt(seq).getDescription() != null)\r
- {\r
- tip.append("<table width=250 border=0><tr><td><i>");\r
- tip.append(av.alignment.getSequenceAt(seq).getDescription());\r
- tip.append("</i></td></tr></table>");\r
- }\r
- tip.append("</html>");\r
- setToolTipText(tip.toString());\r
- }\r
-\r
- }\r
-\r
- int getWrappedY(int y)\r
- {\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- hgap += av.charHeight;\r
-\r
- return y - hgap;\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mouseDragged(MouseEvent e)\r
- {\r
- mouseDragging = true;\r
-\r
- int y = e.getY();\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- y = getWrappedY(y);\r
- }\r
-\r
- int seq = av.getIndex(y);\r
-\r
- if (seq < 0)\r
- {\r
- return;\r
- }\r
-\r
- if (seq < lastid)\r
- {\r
- selectSeqs(lastid - 1, seq);\r
- }\r
- else if (seq > lastid)\r
- {\r
- selectSeqs(lastid + 1, seq);\r
- }\r
-\r
- lastid = seq;\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- if (e.getClickCount() < 2)\r
- return;\r
-\r
- java.util.Vector links = Preferences.sequenceURLLinks;\r
- if (links == null || links.size() < 1)\r
- return;\r
-\r
- int y = e.getY();\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- y = getWrappedY(y);\r
- }\r
-\r
- //DEFAULT LINK IS FIRST IN THE LINK LIST\r
- int seq = av.getIndex(y);\r
- String id = av.getAlignment().getSequenceAt(seq).getName();\r
- if (id.indexOf("|") > -1)\r
- id = id.substring(id.lastIndexOf("|") + 1);\r
-\r
-\r
- String url = links.elementAt(0).toString();\r
- url = url.substring(url.indexOf("|")+1);\r
-\r
- int index = url.indexOf("$SEQUENCE_ID$");\r
- url = url.substring(0, index)+ id + url.substring(index+13);\r
-\r
- try\r
- {\r
- jalview.util.BrowserLauncher.openURL(url);\r
- }\r
- catch (Exception ex)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Unixers: Couldn't find default web browser."\r
- +"\nAdd the full path to your browser in Preferences.",\r
- "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mouseEntered(MouseEvent e)\r
- {\r
- if (scrollThread != null)\r
- {\r
- scrollThread.running = false;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mouseExited(MouseEvent e)\r
- {\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
-\r
- if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))\r
- {\r
- scrollThread = new ScrollThread(true);\r
- }\r
-\r
- if (mouseDragging && (e.getY() >= getHeight()) &&\r
- (av.alignment.getHeight() > av.getEndSeq()))\r
- {\r
- scrollThread = new ScrollThread(false);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mousePressed(MouseEvent e)\r
- {\r
- if (e.getClickCount() == 2)\r
- {\r
- return;\r
- }\r
-\r
- int y = e.getY();\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- y = getWrappedY(y);\r
- }\r
-\r
- int seq = av.getIndex(y);\r
-\r
- if (seq == -1)\r
- {\r
- return;\r
- }\r
-\r
- if (javax.swing.SwingUtilities.isRightMouseButton(e))\r
- {\r
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,\r
- (Sequence) av.getAlignment().getSequenceAt(seq));\r
- pop.show(this, e.getX(), y);\r
-\r
- return;\r
- }\r
-\r
- if (!e.isControlDown() && !e.isShiftDown() &&\r
- (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null))\r
- {\r
- SequenceGroup selection = new SequenceGroup();\r
- SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(\r
- seq));\r
- selection.setStartRes(0);\r
- selection.setEndRes(av.alignment.getWidth() - 1);\r
-\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- selection.addSequence(sg.getSequenceAt(i), true);\r
- }\r
-\r
- av.setSelectionGroup(selection);\r
-\r
- return;\r
- }\r
-\r
- if ((av.getSelectionGroup() == null) ||\r
- (!e.isControlDown() && (av.getSelectionGroup() != null)))\r
- {\r
- av.setSelectionGroup(new SequenceGroup());\r
- }\r
-\r
- av.getSelectionGroup().setStartRes(0);\r
- av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);\r
-\r
- if (e.isShiftDown() && (lastid != -1))\r
- {\r
- selectSeqs(lastid, seq);\r
- }\r
- else\r
- {\r
- selectSeq(seq);\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq DOCUMENT ME!\r
- */\r
- void selectSeq(int seq)\r
- {\r
- lastid = seq;\r
-\r
- SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);\r
- av.getSelectionGroup().addOrRemove(pickedSeq, true);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- */\r
- void selectSeqs(int start, int end)\r
- {\r
- if(av.getSelectionGroup()==null)\r
- return;\r
-\r
- lastid = start;\r
-\r
- if (end < start)\r
- {\r
- int tmp = start;\r
- start = end;\r
- end = tmp;\r
- lastid = end;\r
- }\r
-\r
- for (int i = start; i <= end; i++)\r
- {\r
- av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),\r
- true);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mouseReleased(MouseEvent e)\r
- {\r
- if (scrollThread != null)\r
- {\r
- scrollThread.running = false;\r
- }\r
-\r
- mouseDragging = false;\r
- PaintRefresher.Refresh(av.alignment);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param found DOCUMENT ME!\r
- */\r
- public void highlightSearchResults(java.util.Vector found)\r
- {\r
- idCanvas.setHighlighted(found);\r
-\r
- if (found == null)\r
- {\r
- return;\r
- }\r
-\r
- int index = av.alignment.findIndex((SequenceI) found.get(0));\r
-\r
- // do we need to scroll the panel?\r
- if ((av.getStartSeq() > index) || (av.getEndSeq() < index))\r
- {\r
- alignPanel.setScrollValues(av.getStartRes(), index);\r
- }\r
- }\r
-\r
- // this class allows scrolling off the bottom of the visible alignment\r
- class ScrollThread extends Thread\r
- {\r
- boolean running = false;\r
- boolean up = true;\r
-\r
- public ScrollThread(boolean up)\r
- {\r
- this.up = up;\r
- start();\r
- }\r
-\r
- public void stopScrolling()\r
- {\r
- running = false;\r
- }\r
-\r
- public void run()\r
- {\r
- running = true;\r
-\r
- while (running)\r
- {\r
- if (alignPanel.scrollUp(up))\r
- {\r
- // scroll was ok, so add new sequence to selection\r
- int seq = av.getStartSeq();\r
-\r
- if (!up)\r
- {\r
- seq = av.getEndSeq();\r
- }\r
-\r
- if (seq < lastid)\r
- {\r
- selectSeqs(lastid - 1, seq);\r
- }\r
- else if (seq > lastid)\r
- {\r
- selectSeqs(lastid + 1, seq);\r
- }\r
-\r
- lastid = seq;\r
- }\r
- else\r
- {\r
- running = false;\r
- }\r
-\r
- alignPanel.repaint();\r
-\r
- try\r
- {\r
- Thread.sleep(100);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import 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<SequenceI> 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;
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff