X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=f0aefb1438fc998ff375e38abc873b7797f864dc;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=d68d9a720f13690858d2767bb274e15c96b62dd1;hpb=524cc1554c04aea0eefab3a86382fa698bf4b4fe;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index d68d9a7..f0aefb1 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -27,7 +27,6 @@ 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 java.awt.BorderLayout; @@ -37,9 +36,7 @@ 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.ToolTipManager; @@ -51,8 +48,8 @@ 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; @@ -109,8 +106,8 @@ public class IdPanel extends JPanel implements MouseListener, if (seq > -1 && seq < av.getAlignment().getHeight()) { SequenceI sequence = av.getAlignment().getSequenceAt(seq); - StringBuffer tip = new StringBuffer(64); - seqAnnotReport.createSequenceAnnotationReport(tip, sequence, + StringBuilder tip = new StringBuilder(64); + seqAnnotReport.createTooltipAnnotationReport(tip, sequence, av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr.getMinMax()); setToolTipText(JvSwingUtils.wrapTooltip(true, @@ -141,7 +138,7 @@ public class IdPanel extends JPanel implements MouseListener, } lastid = seq; - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false); } /** @@ -155,22 +152,22 @@ public class IdPanel extends JPanel implements MouseListener, { if (e.isShiftDown()) { - alignPanel.scrollRight(true); + av.getRanges().scrollRight(true); } - else + else if (!av.getWrapAlignment()) { - alignPanel.scrollUp(false); + av.getRanges().scrollUp(false); } } else { if (e.isShiftDown()) { - alignPanel.scrollRight(false); + av.getRanges().scrollRight(false); } - else + else if (!av.getWrapAlignment()) { - alignPanel.scrollUp(true); + av.getRanges().scrollUp(true); } } } @@ -199,66 +196,19 @@ 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; - } - ; - - if (urlLink.usesSeqId()) - { - // this URL requires an accession id, not the name of a sequence - url = null; - continue; - } + String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id); - 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); } catch (Exception ex) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } } @@ -292,13 +242,14 @@ public class IdPanel extends JPanel implements MouseListener, return; } - if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0)) + if (mouseDragging && (e.getY() < 0) + && (av.getRanges().getStartSeq() > 0)) { scrollThread = new ScrollThread(true); } if (mouseDragging && (e.getY() >= getHeight()) - && (av.getAlignment().getHeight() > av.getEndSeq())) + && (av.getAlignment().getHeight() > av.getRanges().getEndSeq())) { scrollThread = new ScrollThread(false); } @@ -342,8 +293,8 @@ 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); @@ -362,7 +313,7 @@ public class IdPanel extends JPanel implements MouseListener, av.isSelectionGroupChanged(true); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false); } /** @@ -374,28 +325,25 @@ 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()); } @@ -444,8 +392,8 @@ 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); } } @@ -492,9 +440,10 @@ 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); } } @@ -533,14 +482,14 @@ public class IdPanel extends JPanel implements MouseListener, while (running) { - if (alignPanel.scrollUp(up)) + if (av.getRanges().scrollUp(up)) { // scroll was ok, so add new sequence to selection - int seq = av.getStartSeq(); + int seq = av.getRanges().getStartSeq(); if (!up) { - seq = av.getEndSeq(); + seq = av.getRanges().getEndSeq(); } if (seq < lastid)