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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git]
/
src
/
jalview
/
appletgui
/
IdPanel.java
diff --git
a/src/jalview/appletgui/IdPanel.java
b/src/jalview/appletgui/IdPanel.java
index
80f03a1
..
a5c2e5a
100755
(executable)
--- a/
src/jalview/appletgui/IdPanel.java
+++ b/
src/jalview/appletgui/IdPanel.java
@@
-34,6
+34,7
@@
import java.awt.event.InputEvent;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
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;
import java.util.HashMap;
import java.util.List;
@@
-55,11
+56,11
@@
public class IdPanel extends Panel implements MouseListener,
UrlProviderI urlProvider = null;
UrlProviderI urlProvider = null;
- public IdPanel(AlignViewport av, AlignmentPanel parent)
+ public IdPanel(AlignViewport viewport, AlignmentPanel parent)
{
{
- this.av = av;
+ this.av = viewport;
alignPanel = parent;
alignPanel = parent;
- idCanvas = new IdCanvas(av);
+ idCanvas = new IdCanvas(viewport);
setLayout(new BorderLayout());
add(idCanvas, BorderLayout.CENTER);
idCanvas.addMouseListener(this);
setLayout(new BorderLayout());
add(idCanvas, BorderLayout.CENTER);
idCanvas.addMouseListener(this);
@@
-70,12
+71,12
@@
public class IdPanel extends Panel implements MouseListener,
// make a list of label,url pairs
HashMap<String, String> urlList = new HashMap<String, String>();
// make a list of label,url pairs
HashMap<String, String> urlList = new HashMap<String, String>();
- if (av.applet != null)
+ if (viewport.applet != null)
{
for (int i = 1; i < 10; i++)
{
{
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);
// only add non-null parameters
if (label != null)
// only add non-null parameters
if (label != null)
@@
-87,7
+88,7
@@
public class IdPanel extends Panel implements MouseListener,
if (!urlList.isEmpty())
{
// set default as first entry in list
if (!urlList.isEmpty())
{
// set default as first entry in list
- String defaultUrl = av.applet.getParameter("linkLabel_1");
+ String defaultUrl = viewport.applet.getParameter("linkLabel_1");
UrlProviderFactoryI factory = new AppletUrlProviderFactory(
defaultUrl, urlList);
urlProvider = factory.createUrlProvider();
UrlProviderFactoryI factory = new AppletUrlProviderFactory(
defaultUrl, urlList);
urlProvider = factory.createUrlProvider();
@@
-217,6
+218,10
@@
public class IdPanel extends Panel implements MouseListener,
String id = sq.getName();
// get the default url with the sequence details filled in
String id = sq.getName();
// 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
String url = urlProvider.getPrimaryUrl(id);
String target = urlProvider.getPrimaryTarget(id);
try
@@
-281,7
+286,15
@@
public class IdPanel extends Panel implements MouseListener,
* build a new links menu based on the current links
* and any non-positional features
*/
* build a new links menu based on the current links
* and any non-positional features
*/
- List<String> nlinks = urlProvider.getLinksForMenu();
+ List<String> nlinks;
+ if (urlProvider != null)
+ {
+ nlinks = urlProvider.getLinksForMenu();
+ }
+ else
+ {
+ nlinks = new ArrayList<String>();
+ }
for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
{
for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
{
@@
-391,7
+404,7
@@
public class IdPanel extends Panel implements MouseListener,
if (av.getRanges().getStartSeq() > index
|| av.getRanges().getEndSeq() < index)
{
if (av.getRanges().getStartSeq() > index
|| av.getRanges().getEndSeq() < index)
{
- alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
+ av.getRanges().setStartSeq(index);
}
}
}
}
@@
-402,9
+415,9
@@
public class IdPanel extends Panel implements MouseListener,
boolean up = true;
boolean up = true;
- public ScrollThread(boolean up)
+ public ScrollThread(boolean isUp)
{
{
- this.up = up;
+ this.up = isUp;
start();
}
start();
}
@@
-419,7
+432,7
@@
public class IdPanel extends Panel implements MouseListener,
running = true;
while (running)
{
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.getRanges().getStartSeq();
{
// scroll was ok, so add new sequence to selection
int seq = av.getRanges().getStartSeq();