X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=1d37d083cdffb33e606c6ea4eddf98d958b6a334;hb=4f77328104498504339216829abf5ea87e2791ec;hp=b973913802ed7d06bd0c9190d708155de885c4a6;hpb=7d4f1d8e997964bef5c351d04fbdafe4401cf5d7;p=jalview.git
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index b973913..1d37d08 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,119 +1,162 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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 .
+ * 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;
-
-public class IdPanel extends Panel implements MouseListener,
- MouseMotionListener
+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 urlList = new HashMap<>();
+ 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 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)
@@ -251,36 +274,41 @@ public class IdPanel extends Panel implements MouseListener,
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.getModifiersEx()
+ & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_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 nlinks;
+ if (urlProvider != null)
{
- nlinks.addElement(links.elementAt(l));
+ nlinks = urlProvider.getLinksForMenu();
}
- SequenceFeature sf[] = sq.getSequenceFeatures();
- for (int sl=0;sf!=null && sl();
+ }
+
+ 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 list)
{
- idCanvas.setHighlighted(found);
+ idCanvas.setHighlighted(list);
- if (found == null)
+ if (list == null || list.isEmpty())
{
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);
}
}
@@ -382,9 +417,9 @@ public class IdPanel extends Panel implements MouseListener,
boolean up = true;
- public ScrollThread(boolean up)
+ public ScrollThread(boolean isUp)
{
- this.up = up;
+ this.up = isUp;
start();
}
@@ -393,25 +428,26 @@ public class IdPanel extends Panel implements MouseListener,
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);
}
@@ -423,7 +459,7 @@ public class IdPanel extends Panel implements MouseListener,
running = false;
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
try
{
Thread.sleep(100);
@@ -433,5 +469,4 @@ public class IdPanel extends Panel implements MouseListener,
}
}
}
-
}