X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=b5569c3ba2c9a7ee430475a29847b2cac81fdc4c;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d50f06c337743f9a929f0d2600b4f4f31a04f644;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index d50f06c..b5569c3 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -27,6 +27,7 @@ import jalview.datamodel.SequenceI; import jalview.io.SequenceAnnotationReport; import jalview.util.MessageManager; import jalview.util.UrlLink; +import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; import java.awt.event.MouseEvent; @@ -54,7 +55,7 @@ public class IdPanel extends JPanel implements MouseListener, { private IdCanvas idCanvas; - protected AlignViewport av; + protected AlignmentViewport av; protected AlignmentPanel alignPanel; @@ -108,10 +109,9 @@ public class IdPanel extends JPanel implements MouseListener, { SequenceI sequence = av.getAlignment().getSequenceAt(seq); StringBuffer tip = new StringBuffer(64); - seqAnnotReport - .createSequenceAnnotationReport(tip, sequence, - av.isShowDbRefs(), av.isShowNpFeats(), - sp.seqCanvas.fr.getMinMax()); + seqAnnotReport.createSequenceAnnotationReport(tip, sequence, + av.isShowDBRefs(), av.isShowNPFeats(), + sp.seqCanvas.fr.getMinMax()); setToolTipText("" + sequence.getDisplayId(true) + " " + tip.toString() + ""); } @@ -244,11 +244,10 @@ public class IdPanel extends JPanel implements MouseListener, jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - MessageManager.getString("label.web_browser_not_found_unix"), - MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), + JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } } @@ -323,8 +322,7 @@ 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) @@ -363,6 +361,9 @@ public class IdPanel extends JPanel implements MouseListener, { selectSeq(seq); } + // TODO is this addition ok here? + av.isSelectionGroupChanged(true); + alignPanel.paintAlignment(true); }