X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=4cc4a3a5d5e1fa4961532d1a75fb8cb4e47aee4f;hb=5078a67d8357697791d2e71f9df95a46e762aa2e;hp=d2832f84f93305d101787cbc5974a6179c36c1fb;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index d2832f8..4cc4a3a 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,28 +1,43 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * 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;
+import jalview.datamodel.Sequence;
+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
@@ -30,21 +45,17 @@ public class IdPanel extends Panel implements MouseListener,
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)
{
@@ -58,6 +69,9 @@ public class IdPanel extends Panel implements MouseListener,
String label, url;
// TODO: add in group link parameter
+
+ // make a list of label,url pairs
+ HashMap urlList = new HashMap();
if (av.applet != null)
{
for (int i = 1; i < 10; i++)
@@ -65,22 +79,27 @@ public class IdPanel extends Panel implements MouseListener,
label = av.applet.getParameter("linkLabel_" + i);
url = av.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 = av.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);
@@ -123,7 +142,7 @@ public class IdPanel extends Panel implements MouseListener,
nl = true;
}
;
- if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
+ if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f)
{
tooltiptext.append(" Score = ");
tooltiptext.append(sf[sl].getScore());
@@ -169,6 +188,7 @@ public class IdPanel extends Panel implements MouseListener,
tooltiptext = null;
}
+ @Override
public void mouseDragged(MouseEvent e)
{
mouseDragging = true;
@@ -188,6 +208,7 @@ public class IdPanel extends Panel implements MouseListener,
alignPanel.paintAlignment(false);
}
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() < 2)
@@ -195,55 +216,24 @@ public class IdPanel extends Panel implements MouseListener,
return;
}
- // DEFAULT LINK IS FIRST IN THE LINK LIST
+ // get the sequence details
int seq = alignPanel.seqPanel.findSeq(e);
SequenceI sq = av.getAlignment().getSequenceAt(seq);
- if (sq==null)
+ if (sq == null)
{
return;
}
String id = sq.getName();
- String target = null;
- String url = null;
- int i = 0;
- while (url == null && i < links.size())
+ // get the default url with the sequence details filled in
+ if (urlProvider == null)
{
- // 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;
- }
-
- 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];
+ return;
}
+ String url = urlProvider.getPrimaryUrl(id);
+ String target = urlProvider.getPrimaryTarget(id);
try
{
-
alignPanel.alignFrame.showURL(url, target);
} catch (Exception ex)
{
@@ -251,6 +241,7 @@ public class IdPanel extends Panel implements MouseListener,
}
}
+ @Override
public void mouseEntered(MouseEvent e)
{
if (scrollThread != null)
@@ -259,6 +250,7 @@ public class IdPanel extends Panel implements MouseListener,
}
}
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
@@ -266,18 +258,19 @@ public class IdPanel extends Panel 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() >= 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)
@@ -288,7 +281,7 @@ 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);
@@ -296,15 +289,19 @@ public class IdPanel extends Panel implements MouseListener,
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++)
+ List nlinks;
+ if (urlProvider != null)
{
- nlinks.addElement(links.elementAt(l));
+ nlinks = urlProvider.getLinksForMenu();
}
- SequenceFeature sf[] = sq==null ? null:sq.getSequenceFeatures();
+ else
+ {
+ nlinks = new ArrayList();
+ }
+ 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)
@@ -313,7 +310,7 @@ public class IdPanel extends Panel implements MouseListener,
{
for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
{
- nlinks.addElement(sf[sl].links.elementAt(l));
+ nlinks.add(sf[sl].links.elementAt(l));
}
}
}
@@ -326,12 +323,12 @@ public class IdPanel extends Panel implements MouseListener,
}
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)
@@ -350,7 +347,7 @@ public class IdPanel extends Panel implements MouseListener,
{
lastid = seq;
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, false);
+ av.getSelectionGroup().addOrRemove(pickedSeq, true);
}
void selectSeqs(int start, int end)
@@ -377,11 +374,12 @@ public class IdPanel extends Panel implements MouseListener,
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)
@@ -400,21 +398,22 @@ public class IdPanel extends Panel implements MouseListener,
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)
+ if (av.getRanges().getStartSeq() > index
+ || av.getRanges().getEndSeq() < index)
{
- alignPanel.setScrollValues(av.getStartRes(), index);
+ alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
}
}
@@ -436,6 +435,7 @@ public class IdPanel extends Panel implements MouseListener,
running = false;
}
+ @Override
public void run()
{
running = true;
@@ -444,17 +444,17 @@ public class IdPanel extends Panel implements MouseListener,
if (alignPanel.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);
}
@@ -476,5 +476,4 @@ public class IdPanel extends Panel implements MouseListener,
}
}
}
-
}