X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=fe05c4d9ba31187bdc41fe4f2769442a524d8708;hb=8edebdd9789b2d93fb8f9db24b8be2c1e6317690;hp=6aad6c5d753b2ed4925728ce01f2691df9480a3c;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 6aad6c5..fe05c4d 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -20,13 +20,16 @@ */ package jalview.gui; +import jalview.bin.Cache; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.SequenceAnnotationReport; +import jalview.util.BrowserLauncher; import jalview.util.MessageManager; import jalview.util.UrlLink; +import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; import java.awt.event.MouseEvent; @@ -54,7 +57,7 @@ public class IdPanel extends JPanel implements MouseListener, { private IdCanvas idCanvas; - protected AlignViewport av; + protected AlignmentViewport av; protected AlignmentPanel alignPanel; @@ -110,7 +113,7 @@ public class IdPanel extends JPanel implements MouseListener, StringBuffer tip = new StringBuffer(64); seqAnnotReport .createSequenceAnnotationReport(tip, sequence, - av.isShowDbRefs(), av.isShowNpFeats(), + av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr.getMinMax()); setToolTipText("" + sequence.getDisplayId(true) + " " + tip.toString() + ""); @@ -211,13 +214,13 @@ public class IdPanel extends JPanel implements MouseListener, // 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; + UrlLink urlLink = null; try { urlLink = new UrlLink(url); } catch (Exception foo) { - jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'", + Cache.log.error("Exception for URLLink '" + url + "'", foo); url = null; continue; @@ -225,7 +228,7 @@ public class IdPanel extends JPanel implements MouseListener, ; if (!urlLink.isValid()) { - jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); + Cache.log.error(urlLink.getInvalidMessage()); url = null; continue; } @@ -241,7 +244,7 @@ public class IdPanel extends JPanel implements MouseListener, } try { - jalview.util.BrowserLauncher.openURL(url); + BrowserLauncher.openURL(url); } catch (Exception ex) { JOptionPane @@ -323,8 +326,7 @@ public class IdPanel extends JPanel implements MouseListener, // build a new links menu based on the current links + any non-positional // features Vector nlinks = new Vector(Preferences.sequenceURLLinks); - SequenceFeature sf[] = sq == null ? null : sq.getDatasetSequence() - .getSequenceFeatures(); + SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures(); for (int sl = 0; sf != null && sl < sf.length; sl++) { if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) @@ -339,7 +341,7 @@ public class IdPanel extends JPanel implements MouseListener, } } - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq, + PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks, new Vector(Preferences.getGroupURLLinks())); pop.show(this, e.getX(), e.getY()); @@ -363,6 +365,9 @@ public class IdPanel extends JPanel implements MouseListener, { selectSeq(seq); } + // TODO is this addition ok here? + av.isSelectionGroupChanged(true); + alignPanel.paintAlignment(true); }