From: gmungoc Date: Tue, 5 Dec 2017 09:25:37 +0000 (+0000) Subject: Merge branch 'develop' into features/JAL-1793VCF X-Git-Tag: Release_2_11_0~91 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=56e67e558885f901e565620b3710e42909a68d29;hp=-c;p=jalview.git Merge branch 'develop' into features/JAL-1793VCF --- 56e67e558885f901e565620b3710e42909a68d29 diff --combined src/jalview/gui/SeqPanel.java index d5a13f3,61cac46..fb6efe5 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@@ -59,6 -59,7 +59,6 @@@ import java.awt.event.MouseListener import java.awt.event.MouseMotionListener; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; -import java.util.ArrayList; import java.util.Collections; import java.util.List; @@@ -75,11 -76,12 +75,11 @@@ import javax.swing.ToolTipManager public class SeqPanel extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener, SequenceListener, SelectionListener - { - /** DOCUMENT ME!! */ + private static final int MAX_TOOLTIP_LENGTH = 300; + public SeqCanvas seqCanvas; - /** DOCUMENT ME!! */ public AlignmentPanel ap; /* @@@ -146,33 -148,35 +146,33 @@@ SearchResultsI lastSearchResults; /** - * Creates a new SeqPanel object. + * Creates a new SeqPanel object * - * @param avp - * DOCUMENT ME! - * @param p - * DOCUMENT ME! + * @param viewport + * @param alignPanel */ - public SeqPanel(AlignViewport av, AlignmentPanel ap) + public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel) { linkImageURL = getClass().getResource("/images/link.gif"); seqARep = new SequenceAnnotationReport(linkImageURL.toString()); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); - this.av = av; + this.av = viewport; setBackground(Color.white); - seqCanvas = new SeqCanvas(ap); + seqCanvas = new SeqCanvas(alignPanel); setLayout(new BorderLayout()); add(seqCanvas, BorderLayout.CENTER); - this.ap = ap; + this.ap = alignPanel; - if (!av.isDataset()) + if (!viewport.isDataset()) { addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); - ssm = av.getStructureSelectionManager(); + ssm = viewport.getStructureSelectionManager(); ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } @@@ -359,8 -363,11 +359,11 @@@ int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); + // TODO: once JAL-2759 is ready, change this loop to something more + // efficient while (!hidden.isVisible(seqCanvas.cursorX) - && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) + && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0 + && dx != 0) { seqCanvas.cursorX += dx; } @@@ -831,7 -838,7 +834,7 @@@ List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); seqARep.appendFeatures(tooltipText, pos, features, - this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); + this.ap.getSeqPanel().seqCanvas.fr); } if (tooltipText.length() == 6) // { @@@ -840,11 -847,6 +843,11 @@@ } else { + if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant + { + tooltipText.setLength(MAX_TOOLTIP_LENGTH); + tooltipText.append("..."); + } String textString = tooltipText.toString(); if (lastTooltip == null || !lastTooltip.equals(textString)) { @@@ -1823,10 -1825,21 +1826,10 @@@ final int column = findColumn(evt); final int seq = findSeq(evt); SequenceI sequence = av.getAlignment().getSequenceAt(seq); - List allFeatures = ap.getFeatureRenderer() + List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); - List links = new ArrayList<>(); - for (SequenceFeature sf : allFeatures) - { - if (sf.links != null) - { - for (String link : sf.links) - { - links.add(link); - } - } - } - PopupMenu pop = new PopupMenu(ap, null, links); + PopupMenu pop = new PopupMenu(ap, null, features); pop.show(this, evt.getX(), evt.getY()); }