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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git]
/
src
/
jalview
/
gui
/
IdPanel.java
diff --git
a/src/jalview/gui/IdPanel.java
b/src/jalview/gui/IdPanel.java
index
6ae19f0
..
29bb522
100755
(executable)
--- a/
src/jalview/gui/IdPanel.java
+++ b/
src/jalview/gui/IdPanel.java
@@
-152,22
+152,22
@@
public class IdPanel extends JPanel implements MouseListener,
{
if (e.isShiftDown())
{
{
if (e.isShiftDown())
{
- alignPanel.scrollRight(true);
+ av.getRanges().scrollRight(true);
}
else
{
}
else
{
- alignPanel.scrollUp(false);
+ av.getRanges().scrollUp(false);
}
}
else
{
if (e.isShiftDown())
{
}
}
else
{
if (e.isShiftDown())
{
- alignPanel.scrollRight(false);
+ av.getRanges().scrollRight(false);
}
else
{
}
else
{
- alignPanel.scrollUp(true);
+ av.getRanges().scrollUp(true);
}
}
}
}
}
}
@@
-242,13
+242,14
@@
public class IdPanel extends JPanel implements MouseListener,
return;
}
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() >= getHeight())
{
scrollThread = new ScrollThread(true);
}
if (mouseDragging && (e.getY() >= getHeight())
- && (av.getAlignment().getHeight() > av.getEndSeq()))
+ && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
{
scrollThread = new ScrollThread(false);
}
{
scrollThread = new ScrollThread(false);
}
@@
-324,23
+325,19
@@
public class IdPanel extends JPanel implements MouseListener,
{
int seq2 = alignPanel.getSeqPanel().findSeq(e);
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
{
int seq2 = alignPanel.getSeqPanel().findSeq(e);
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
- // build a new links menu based on the current links + any non-positional
- // features
+
+ /*
+ * build a new links menu based on the current links
+ * and any non-positional features
+ */
List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
- SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
- if (sfs != null)
+ for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
{
{
- for (SequenceFeature sf : sfs)
+ if (sf.links != null)
{
{
- if (sf.begin == sf.end && sf.begin == 0)
+ for (String link : sf.links)
{
{
- if (sf.links != null && sf.links.size() > 0)
- {
- for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
- {
- nlinks.add(sf.links.elementAt(l));
- }
- }
+ nlinks.add(link);
}
}
}
}
}
}
@@
-442,9
+439,10
@@
public class IdPanel extends JPanel implements MouseListener,
int index = av.getAlignment().findIndex(list.get(0));
// do we need to scroll the panel?
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);
}
}
}
}
@@
-483,14
+481,14
@@
public class IdPanel extends JPanel implements MouseListener,
while (running)
{
while (running)
{
- if (alignPanel.scrollUp(up))
+ if (av.getRanges().scrollUp(up))
{
// scroll was ok, so add new sequence to selection
{
// scroll was ok, so add new sequence to selection
- int seq = av.getStartSeq();
+ int seq = av.getRanges().getStartSeq();
if (!up)
{
if (!up)
{
- seq = av.getEndSeq();
+ seq = av.getRanges().getEndSeq();
}
if (seq < lastid)
}
if (seq < lastid)