X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=8290dcf1d14515177557e449132411fd582c755d;hb=ee6e8272916d66372695723c70ea707b2d5f25a6;hp=59d12d9c84c533e90defb6256113f8c1b57b3f30;hpb=fee1b781ca14aadea5d112fc554fe14879c787c5;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 59d12d9..8290dcf 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.bin.Jalview; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@ -27,21 +28,22 @@ import jalview.datamodel.SequenceI; import jalview.io.SequenceAnnotationReport; import jalview.util.MessageManager; import jalview.util.Platform; -import jalview.util.UrlLink; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; 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 java.util.Vector; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.SwingUtilities; +import javax.swing.Timer; import javax.swing.ToolTipManager; /** @@ -51,8 +53,8 @@ import javax.swing.ToolTipManager; * @author $author$ * @version $Revision$ */ -public class IdPanel extends JPanel implements MouseListener, - MouseMotionListener, MouseWheelListener +public class IdPanel extends JPanel + implements MouseListener, MouseMotionListener, MouseWheelListener { private IdCanvas idCanvas; @@ -111,8 +113,7 @@ public class IdPanel extends JPanel implements MouseListener, SequenceI sequence = av.getAlignment().getSequenceAt(seq); StringBuilder tip = new StringBuilder(64); seqAnnotReport.createTooltipAnnotationReport(tip, sequence, - av.isShowDBRefs(), av.isShowNPFeats(), - sp.seqCanvas.fr.getMinMax()); + av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr); setToolTipText(JvSwingUtils.wrapTooltip(true, sequence.getDisplayId(true) + " " + tip.toString())); } @@ -141,7 +142,7 @@ public class IdPanel extends JPanel implements MouseListener, } lastid = seq; - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -151,26 +152,27 @@ public class IdPanel extends JPanel implements MouseListener, public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); - if (e.getWheelRotation() > 0) + double wheelRotation = e.getPreciseWheelRotation(); + if (wheelRotation > 0) { if (e.isShiftDown()) { - alignPanel.scrollRight(true); + av.getRanges().scrollRight(true); } else { - alignPanel.scrollUp(false); + av.getRanges().scrollUp(false); } } - else + else if (wheelRotation < 0) { if (e.isShiftDown()) { - alignPanel.scrollRight(false); + av.getRanges().scrollRight(false); } else { - alignPanel.scrollUp(true); + av.getRanges().scrollUp(true); } } } @@ -199,56 +201,10 @@ public class IdPanel extends JPanel implements MouseListener, return; } - Vector links = Preferences.sequenceURLLinks; - if (links == null || links.size() < 1) - { - return; - } - int seq = alignPanel.getSeqPanel().findSeq(e); - String url = null; - int i = 0; String id = av.getAlignment().getSequenceAt(seq).getName(); - while (url == null && i < links.size()) - { - // DEFAULT LINK IS FIRST IN THE LINK LIST - // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED - url = links.elementAt(i++).toString(); - jalview.util.UrlLink urlLink = null; - try - { - urlLink = new UrlLink(url); - } catch (Exception foo) - { - jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'", - foo); - url = null; - continue; - } + String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id); - if (urlLink.usesDBAccession()) - { - // this URL requires an accession id, not the name of a sequence - url = null; - continue; - } - - if (!urlLink.isValid()) - { - jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); - url = null; - continue; - } - - String urls[] = urlLink.makeUrls(id, true); - if (urls == null || urls[0] == null || urls[0].length() < 4) - { - url = null; - continue; - } - // just take first URL made from regex - url = urls[1]; - } try { jalview.util.BrowserLauncher.openURL(url); @@ -263,17 +219,24 @@ public class IdPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * On (re-)entering the panel, stop any scrolling * * @param e - * DOCUMENT ME! */ @Override public void mouseEntered(MouseEvent e) { + stopScrolling(); + } + + /** + * Interrupts the scroll thread if one is running + */ + void stopScrolling() + { if (scrollThread != null) { - scrollThread.running = false; + scrollThread.stopScrolling(); } } @@ -291,15 +254,70 @@ public class IdPanel extends JPanel implements MouseListener, return; } - if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0)) + if (mouseDragging) { - scrollThread = new ScrollThread(true); + /* + * 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); + } } + } - if (mouseDragging && (e.getY() >= getHeight()) - && (av.getAlignment().getHeight() > av.getEndSeq())) + /** + * Starts scrolling either up or down + * + * @param up + */ + void startScrolling(boolean up) + { + scrollThread = new ScrollThread(up); + if (!Jalview.isJS()) + { + /* + * Java - run in a new thread + */ + scrollThread.start(); + } + else { - scrollThread = new ScrollThread(false); + /* + * 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) + { + // finished and nulled itself + t.stop(); + } + } + }); + t.start(); } } @@ -341,8 +359,8 @@ public class IdPanel extends JPanel implements MouseListener, } if ((av.getSelectionGroup() == null) - || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() && av - .getSelectionGroup() != null)) + || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() + && av.getSelectionGroup() != null)) { av.setSelectionGroup(new SequenceGroup()); av.getSelectionGroup().setStartRes(0); @@ -361,7 +379,7 @@ public class IdPanel extends JPanel implements MouseListener, av.isSelectionGroupChanged(true); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -373,28 +391,25 @@ public class IdPanel extends JPanel implements MouseListener, { int seq2 = alignPanel.getSeqPanel().findSeq(e); Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2); - // build a new links menu based on the current links + any non-positional - // features - Vector nlinks = new Vector(Preferences.sequenceURLLinks); - SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures(); - if (sfs != null) + + /* + * build a new links menu based on the current links + * and any non-positional features + */ + List nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); + List features = sq.getFeatures().getNonPositionalFeatures(); + for (SequenceFeature sf : features) { - for (SequenceFeature sf : sfs) + if (sf.links != null) { - if (sf.begin == sf.end && sf.begin == 0) + for (String link : sf.links) { - if (sf.links != null && sf.links.size() > 0) - { - for (int l = 0, lSize = sf.links.size(); l < lSize; l++) - { - nlinks.addElement(sf.links.elementAt(l)); - } - } + nlinks.add(link); } } } - PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks, + PopupMenu pop = new PopupMenu(alignPanel, sq, features, Preferences.getGroupURLLinks()); pop.show(this, e.getX(), e.getY()); } @@ -443,8 +458,8 @@ public class IdPanel extends JPanel implements MouseListener, for (int i = start; i <= end; i++) { - av.getSelectionGroup().addSequence( - av.getAlignment().getSequenceAt(i), i == end); + av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), + i == end); } } @@ -457,10 +472,7 @@ public class IdPanel extends JPanel implements MouseListener, @Override public void mouseReleased(MouseEvent e) { - if (scrollThread != null) - { - scrollThread.running = false; - } + stopScrolling(); mouseDragging = false; PaintRefresher.Refresh(this, av.getSequenceSetId()); @@ -491,9 +503,10 @@ public class IdPanel extends JPanel implements MouseListener, int index = av.getAlignment().findIndex(list.get(0)); // do we need to scroll the panel? - if ((av.getStartSeq() > index) || (av.getEndSeq() < index)) + if ((av.getRanges().getStartSeq() > index) + || (av.getRanges().getEndSeq() < index)) { - alignPanel.setScrollValues(av.getStartRes(), index); + av.getRanges().setStartSeq(index); } } @@ -507,24 +520,42 @@ public class IdPanel extends JPanel implements MouseListener, this.idCanvas = idCanvas; } - // this class allows scrolling off the bottom of the visible alignment + /** + * Performs scrolling of the visible alignment up or down, adding newly + * visible sequences to the current selection + */ class ScrollThread extends Thread { - boolean running = false; + private boolean running = false; - boolean up = true; + 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)); start(); } + /** + * 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() { @@ -532,34 +563,7 @@ public class IdPanel extends JPanel implements MouseListener, 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.paintAlignment(false); - + running = scrollOnce(); try { Thread.sleep(100); @@ -567,6 +571,27 @@ public class IdPanel extends JPanel implements MouseListener, { } } + 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; } } }