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JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...
[jalview.git]
/
src
/
jalview
/
appletgui
/
IdPanel.java
diff --git
a/src/jalview/appletgui/IdPanel.java
b/src/jalview/appletgui/IdPanel.java
index
80f03a1
..
15e269c
100755
(executable)
--- a/
src/jalview/appletgui/IdPanel.java
+++ b/
src/jalview/appletgui/IdPanel.java
@@
-34,11
+34,12
@@
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;
-public class IdPanel extends Panel implements MouseListener,
- MouseMotionListener
+public class IdPanel extends Panel
+ implements MouseListener, MouseMotionListener
{
protected IdCanvas idCanvas;
{
protected IdCanvas idCanvas;
@@
-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);
@@
-69,13
+70,13
@@
public class IdPanel extends Panel implements MouseListener,
// TODO: add in group link parameter
// make a list of label,url pairs
// TODO: add in group link parameter
// make a list of label,url pairs
- HashMap<String, String> urlList = new HashMap<String, String>();
- if (av.applet != null)
+ HashMap<String, String> urlList = new HashMap<>();
+ 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();
@@
-168,13
+169,14
@@
public class IdPanel extends Panel implements MouseListener,
}
if (tooltip == null)
{
}
if (tooltip == null)
{
- tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
- + tooltiptext.toString(), idCanvas);
+ tooltip = new Tooltip(
+ sequence.getDisplayId(true) + "\n" + tooltiptext.toString(),
+ idCanvas);
}
else
{
}
else
{
- tooltip.setTip(sequence.getDisplayId(true) + "\n"
- + tooltiptext.toString());
+ tooltip.setTip(
+ sequence.getDisplayId(true) + "\n" + tooltiptext.toString());
}
tooltiptext = null;
}
}
tooltiptext = null;
}
@@
-196,7
+198,7
@@
public class IdPanel extends Panel implements MouseListener,
}
lastid = seq;
}
lastid = seq;
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
}
@Override
}
@Override
@@
-217,6
+219,10
@@
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
@@
-273,7
+279,8
@@
public class IdPanel extends Panel implements MouseListener,
int seq = alignPanel.seqPanel.findSeq(e);
int seq = alignPanel.seqPanel.findSeq(e);
- if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((e.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
SequenceI sq = av.getAlignment().getSequenceAt(seq);
{
SequenceI sq = av.getAlignment().getSequenceAt(seq);
@@
-281,7
+288,15
@@
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<>();
+ }
for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
{
for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
{
@@
-301,8
+316,8
@@
public class IdPanel extends Panel implements MouseListener,
}
if ((av.getSelectionGroup() == null)
}
if ((av.getSelectionGroup() == null)
- || ((!jalview.util.Platform.isControlDown(e) && !e
- .isShiftDown()) && av.getSelectionGroup() != null))
+ || ((!jalview.util.Platform.isControlDown(e)
+ && !e.isShiftDown()) && av.getSelectionGroup() != null))
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
@@
-318,7
+333,7
@@
public class IdPanel extends Panel implements MouseListener,
selectSeq(seq);
}
selectSeq(seq);
}
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
}
void selectSeq(int seq)
}
void selectSeq(int seq)
@@
-351,8
+366,8
@@
public class IdPanel extends Panel implements MouseListener,
}
for (int i = start; i <= end; i++)
{
}
for (int i = start; i <= end; i++)
{
- av.getSelectionGroup().addSequence(
- av.getAlignment().getSequenceAt(i), i == end);
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+ i == end);
}
}
}
}
@@
-391,7
+406,7
@@
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
+417,9
@@
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
+434,7
@@
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();
@@
-444,7
+459,7
@@
public class IdPanel extends Panel implements MouseListener,
running = false;
}
running = false;
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
try
{
Thread.sleep(100);
try
{
Thread.sleep(100);