/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.awt.*;
-import java.awt.event.*;
-import java.util.Vector;
-
-import jalview.datamodel.*;
-import jalview.util.UrlLink;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.applet.AppletUrlProviderFactory;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Panel;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
public class IdPanel extends Panel implements MouseListener,
MouseMotionListener
protected IdCanvas idCanvas;
- protected AlignViewport av;
+ protected AlignmentViewport av;
protected AlignmentPanel alignPanel;
ScrollThread scrollThread = null;
- int offy;
-
- int width;
-
int lastid = -1;
boolean mouseDragging = false;
- java.util.Vector links = new java.util.Vector();
+ UrlProviderI urlProvider = null;
- public IdPanel(AlignViewport av, AlignmentPanel parent)
+ public IdPanel(AlignViewport viewport, AlignmentPanel parent)
{
- this.av = av;
+ this.av = viewport;
alignPanel = parent;
- idCanvas = new IdCanvas(av);
+ idCanvas = new IdCanvas(viewport);
setLayout(new BorderLayout());
add(idCanvas, BorderLayout.CENTER);
idCanvas.addMouseListener(this);
idCanvas.addMouseMotionListener(this);
String label, url;
- if (av.applet != null)
+ // TODO: add in group link parameter
+
+ // make a list of label,url pairs
+ HashMap<String, String> urlList = new HashMap<String, String>();
+ if (viewport.applet != null)
{
for (int i = 1; i < 10; i++)
{
- label = av.applet.getParameter("linkLabel_" + i);
- url = av.applet.getParameter("linkURL_" + i);
+ label = viewport.applet.getParameter("linkLabel_" + i);
+ url = viewport.applet.getParameter("linkURL_" + i);
- if (label != null && url != null)
+ // only add non-null parameters
+ if (label != null)
{
- links.addElement(label + "|" + url);
+ urlList.put(label, url);
}
+ }
+ if (!urlList.isEmpty())
+ {
+ // set default as first entry in list
+ String defaultUrl = viewport.applet.getParameter("linkLabel_1");
+ UrlProviderFactoryI factory = new AppletUrlProviderFactory(
+ defaultUrl, urlList);
+ urlProvider = factory.createUrlProvider();
}
}
- if (links.size() < 1)
- {
- links = new java.util.Vector();
- links
- .addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
- }
}
Tooltip tooltip;
+ @Override
public void mouseMoved(MouseEvent e)
{
int seq = alignPanel.seqPanel.findSeq(e);
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-
- // look for non-pos features
- StringBuffer tooltiptext = new StringBuffer();
-
+ StringBuffer tooltiptext = new StringBuffer();
+ if (sequence == null)
+ {
+ return;
+ }
if (sequence.getDescription() != null)
{
tooltiptext.append(sequence.getDescription());
tooltiptext.append("\n");
}
-
- SequenceFeature sf[] = sequence.getSequenceFeatures();
- for (int sl=0;sf!=null && sl<sf.length;sl++)
+
+ for (SequenceFeature sf : sequence.getFeatures()
+ .getNonPositionalFeatures())
{
- if (sf[sl].begin==sf[sl].end && sf[sl].begin==0)
+ boolean nl = false;
+ if (sf.getFeatureGroup() != null)
+ {
+ tooltiptext.append(sf.getFeatureGroup());
+ nl = true;
+ }
+ if (sf.getType() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getType());
+ nl = true;
+ }
+ if (sf.getDescription() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getDescription());
+ nl = true;
+ }
+ if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f)
+ {
+ tooltiptext.append(" Score = ");
+ tooltiptext.append(sf.getScore());
+ nl = true;
+ }
+ if (sf.getStatus() != null && sf.getStatus().length() > 0)
+ {
+ tooltiptext.append(" (");
+ tooltiptext.append(sf.getStatus());
+ tooltiptext.append(")");
+ nl = true;
+ }
+ if (nl)
{
- boolean nl=false;
- if (sf[sl].getFeatureGroup()!=null) { tooltiptext.append(sf[sl].getFeatureGroup()); nl=true;};
- if (sf[sl].getType()!=null) { tooltiptext.append(" "); tooltiptext.append(sf[sl].getType()); nl=true;};
- if (sf[sl].getDescription()!=null) { tooltiptext.append(" "); tooltiptext.append(sf[sl].getDescription()); nl=true;};
- if (sf[sl].getScore()!=Float.NaN && sf[sl].getScore()!=0f) { tooltiptext.append(" Score = "); tooltiptext.append(sf[sl].getScore()); nl=true;};
- if (sf[sl].getStatus()!=null && sf[sl].getStatus().length()>0) { tooltiptext.append(" ("); tooltiptext.append(sf[sl].getStatus()); tooltiptext.append(")");nl=true;};
- if (nl) {tooltiptext.append("\n"); }
+ tooltiptext.append("\n");
}
}
-
- if (tooltiptext.length()==0)
+
+ if (tooltiptext.length() == 0)
{
// nothing to display - so clear tooltip if one is visible
if (tooltip != null)
tooltip.setTip(sequence.getDisplayId(true) + "\n"
+ tooltiptext.toString());
}
- tooltiptext=null;
+ tooltiptext = null;
}
+ @Override
public void mouseDragged(MouseEvent e)
{
mouseDragging = true;
alignPanel.paintAlignment(false);
}
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() < 2)
return;
}
- // DEFAULT LINK IS FIRST IN THE LINK LIST
+ // get the sequence details
int seq = alignPanel.seqPanel.findSeq(e);
- String id = av.getAlignment().getSequenceAt(seq).getName();
-
- String target = null;
- String url = null;
- int i = 0;
- 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);
- target = urlLink.getTarget();
- } catch (Exception foo)
- {
- System.err.println("Exception for URLLink '" + url + "'");
- foo.printStackTrace();
- url = null;
- continue;
- }
- ;
- if (!urlLink.isValid())
- {
- System.err.println(urlLink.getInvalidMessage());
- url = null;
- continue;
- }
+ SequenceI sq = av.getAlignment().getSequenceAt(seq);
+ if (sq == null)
+ {
+ return;
+ }
+ String id = sq.getName();
- String urls[] = urlLink.makeUrls(id, true);
- if (urls == null || urls[0] == null || urls[0].length() < 1)
- {
- url = null;
- continue;
- }
- // just take first URL made from regex
- url = urls[1];
+ // get the default url with the sequence details filled in
+ if (urlProvider == null)
+ {
+ return;
}
+ String url = urlProvider.getPrimaryUrl(id);
+ String target = urlProvider.getPrimaryTarget(id);
try
{
-
alignPanel.alignFrame.showURL(url, target);
} catch (Exception ex)
{
}
}
+ @Override
public void mouseEntered(MouseEvent e)
{
if (scrollThread != null)
}
}
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
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() >= getSize().height
- && av.alignment.getHeight() > av.getEndSeq())
+ && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
{
scrollThread = new ScrollThread(false);
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
if (e.getClickCount() > 1)
int y = e.getY();
if (av.getWrapAlignment())
{
- y -= 2 * av.charHeight;
+ y -= 2 * av.getCharHeight();
}
int seq = alignPanel.seqPanel.findSeq(e);
if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- Sequence sq = (Sequence) av
- .getAlignment().getSequenceAt(seq);
- // build a new links menu based on the current links + any non-positional features
- Vector nlinks = new Vector();
- for (int l=0,lSize=links.size();l<lSize; l++)
+ SequenceI sq = av.getAlignment().getSequenceAt(seq);
+
+ /*
+ * build a new links menu based on the current links
+ * and any non-positional features
+ */
+ List<String> nlinks;
+ if (urlProvider != null)
{
- nlinks.addElement(links.elementAt(l));
+ nlinks = urlProvider.getLinksForMenu();
}
- SequenceFeature sf[] = sq.getSequenceFeatures();
- for (int sl=0;sf!=null && sl<sf.length;sl++)
+ else
+ {
+ nlinks = new ArrayList<String>();
+ }
+
+ for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
{
- if (sf[sl].begin==sf[sl].end && sf[sl].begin==0)
+ if (sf.links != null)
{
- if (sf[sl].links!=null && sf[sl].links.size()>0)
+ for (String link : sf.links)
{
- for (int l=0, lSize=sf[sl].links.size(); l<lSize; l++)
- {
- nlinks.addElement(sf[sl].links.elementAt(l));
- }
+ nlinks.add(link);
}
}
}
-
+
APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
this.add(popup);
popup.show(this, e.getX(), e.getY());
}
if ((av.getSelectionGroup() == null)
- || ((!e.isControlDown() && !e.isShiftDown()) && av
- .getSelectionGroup() != null))
+ || ((!jalview.util.Platform.isControlDown(e) && !e
+ .isShiftDown()) && av.getSelectionGroup() != null))
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
- av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+ av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
}
if (e.isShiftDown() && lastid != -1)
{
lastid = seq;
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, false);
+ av.getSelectionGroup().addOrRemove(pickedSeq, true);
}
void selectSeqs(int start, int end)
end = tmp;
lastid = end;
}
-
+ if (av.getSelectionGroup() == null)
+ {
+ av.setSelectionGroup(new SequenceGroup());
+ }
for (int i = start; i <= end; i++)
{
av.getSelectionGroup().addSequence(
- av.getAlignment().getSequenceAt(i), false);
+ av.getAlignment().getSequenceAt(i), i == end);
}
}
+ @Override
public void mouseReleased(MouseEvent e)
{
if (scrollThread != null)
mouseDragging = false;
PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // always send selection message when mouse is released
+ av.sendSelection();
}
- public void highlightSearchResults(java.util.Vector found)
+ public void highlightSearchResults(List<SequenceI> list)
{
- idCanvas.setHighlighted(found);
+ idCanvas.setHighlighted(list);
- if (found == null)
+ if (list == null)
{
return;
}
- int index = av.alignment.findIndex((SequenceI) found.elementAt(0));
+ 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);
}
}
boolean up = true;
- public ScrollThread(boolean up)
+ public ScrollThread(boolean isUp)
{
- this.up = up;
+ this.up = isUp;
start();
}
running = false;
}
+ @Override
public void run()
{
running = true;
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)
{
selectSeqs(lastid - 1, seq);
}
- else if (seq > lastid && seq < av.alignment.getHeight())
+ else if (seq > lastid && seq < av.getAlignment().getHeight())
{
selectSeqs(lastid + 1, seq);
}
}
}
}
-
}
git://source.jalview.org / jalview.git / blobdiff