X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=8f24f119390027cc8e9c1f0981f502dbfdc0b9c7;hb=4ff572f7cf17f5ca9c23f82bbe41005af8af55cc;hp=44a03ecaef810a93012ca9cb9a69d5b560f9924d;hpb=5d01e85b903f9ce67b2b4a32e9e7a02f57d9f2e9;p=jalview.git
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 44a03ec..8f24f11 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,43 +1,57 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
- *
- * 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 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.appletgui;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.util.UrlLink;
-
-public class IdPanel
- extends Panel implements MouseListener, MouseMotionListener
+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.List;
+import java.util.Vector;
+
+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();
public IdPanel(AlignViewport av, AlignmentPanel parent)
@@ -51,6 +65,7 @@ public class IdPanel
idCanvas.addMouseMotionListener(this);
String label, url;
+ // TODO: add in group link parameter
if (av.applet != null)
{
for (int i = 1; i < 10; i++)
@@ -65,41 +80,112 @@ public class IdPanel
}
}
+ {
+ // upgrade old SRS link
+ int srsPos = links
+ .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ if (srsPos > -1)
+ {
+ links.setElementAt(
+ "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+ srsPos);
+ }
+ }
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");
+ links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
}
}
Tooltip tooltip;
+
public void mouseMoved(MouseEvent e)
{
int seq = alignPanel.seqPanel.findSeq(e);
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- if (sequence.getDescription() == null)
+ // look for non-pos features
+ StringBuffer tooltiptext = new StringBuffer();
+ if (sequence != null)
+ {
+ 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++)
+ {
+ if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ {
+ 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 (!Float.isNaN(sf[sl].getScore()) && 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");
+ }
+ }
+ }
+ }
+ if (tooltiptext.length() == 0)
{
+ // nothing to display - so clear tooltip if one is visible
if (tooltip != null)
{
tooltip.setVisible(false);
}
tooltip = null;
+ tooltiptext = null;
return;
}
-
if (tooltip == null)
{
- tooltip = new Tooltip(
- sequence.getDisplayId(true)
- + "\n" + sequence.getDescription(), idCanvas);
+ tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
+ + tooltiptext.toString(), idCanvas);
}
else
{
- tooltip.setTip(sequence.getDisplayId(true)
- + "\n" + sequence.getDescription());
+ tooltip.setTip(sequence.getDisplayId(true) + "\n"
+ + tooltiptext.toString());
}
+ tooltiptext = null;
}
public void mouseDragged(MouseEvent e)
@@ -128,13 +214,18 @@ public class IdPanel
return;
}
- //DEFAULT LINK IS FIRST IN THE LINK LIST
+ // DEFAULT LINK IS FIRST IN THE LINK LIST
int seq = alignPanel.seqPanel.findSeq(e);
- String id = av.getAlignment().getSequenceAt(seq).getName();
-
+ SequenceI sq = av.getAlignment().getSequenceAt(seq);
+ if (sq == null)
+ {
+ return;
+ }
+ String id = sq.getName();
+
String target = null;
String url = null;
- int i=0;
+ int i = 0;
while (url == null && i < links.size())
{
// DEFAULT LINK IS FIRST IN THE LINK LIST
@@ -161,7 +252,7 @@ public class IdPanel
}
String urls[] = urlLink.makeUrls(id, true);
- if (urls == null || urls[0]==null || urls[0].length()<1)
+ if (urls == null || urls[0] == null || urls[0].length() < 1)
{
url = null;
continue;
@@ -173,8 +264,7 @@ public class IdPanel
{
alignPanel.alignFrame.showURL(url, target);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
@@ -200,8 +290,8 @@ public class IdPanel
scrollThread = new ScrollThread(true);
}
- if (mouseDragging && e.getY() >= getSize().height &&
- av.alignment.getHeight() > av.getEndSeq())
+ if (mouseDragging && e.getY() >= getSize().height
+ && av.getAlignment().getHeight() > av.getEndSeq())
{
scrollThread = new ScrollThread(false);
}
@@ -217,28 +307,50 @@ public class IdPanel
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)
+ if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- APopupMenu popup = new APopupMenu(alignPanel,
- (Sequence) av.getAlignment().
- getSequenceAt(seq), links);
+ 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++)
+ {
+ nlinks.addElement(links.elementAt(l));
+ }
+ 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)
+ {
+ if (sf[sl].links != null && sf[sl].links.size() > 0)
+ {
+ for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
+ {
+ nlinks.addElement(sf[sl].links.elementAt(l));
+ }
+ }
+ }
+ }
+
+ APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
this.add(popup);
popup.show(this, e.getX(), e.getY());
return;
}
- if ( (av.getSelectionGroup() == null) ||
- ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
+ if ((av.getSelectionGroup() == null)
+ || ((!e.isControlDown() && !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)
@@ -257,7 +369,7 @@ public class IdPanel
{
lastid = seq;
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, false);
+ av.getSelectionGroup().addOrRemove(pickedSeq, true);
}
void selectSeqs(int start, int end)
@@ -277,10 +389,14 @@ public class IdPanel
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.getSelectionGroup().addSequence(
+ av.getAlignment().getSequenceAt(i), i == end);
}
}
@@ -299,18 +415,20 @@ public class IdPanel
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 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)
@@ -320,11 +438,12 @@ public class IdPanel
}
// this class allows scrolling off the bottom of the visible alignment
- class ScrollThread
- extends Thread
+ class ScrollThread extends Thread
{
boolean running = false;
+
boolean up = true;
+
public ScrollThread(boolean up)
{
this.up = up;
@@ -354,7 +473,7 @@ public class IdPanel
{
selectSeqs(lastid - 1, seq);
}
- else if (seq > lastid && seq < av.alignment.getHeight())
+ else if (seq > lastid && seq < av.getAlignment().getHeight())
{
selectSeqs(lastid + 1, seq);
}
@@ -370,11 +489,10 @@ public class IdPanel
try
{
Thread.sleep(100);
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
}
}
}
-
}