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fully integrate HMMER3 file format into Jalview
[jalview.git]
/
src
/
jalview
/
gui
/
VamsasApplication.java
diff --git
a/src/jalview/gui/VamsasApplication.java
b/src/jalview/gui/VamsasApplication.java
index
75ddba5
..
d58cb5a
100644
(file)
--- a/
src/jalview/gui/VamsasApplication.java
+++ b/
src/jalview/gui/VamsasApplication.java
@@
-23,6
+23,7
@@
package jalview.gui;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
@@
-43,7
+44,6
@@
import java.util.IdentityHashMap;
import java.util.Iterator;
import javax.swing.JInternalFrame;
import java.util.Iterator;
import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
import uk.ac.vamsas.client.ClientHandle;
import uk.ac.vamsas.client.IClient;
import uk.ac.vamsas.client.ClientHandle;
import uk.ac.vamsas.client.IClient;
@@
-821,7
+821,7
@@
public class VamsasApplication implements SelectionSource, VamsasSource
{
// TODO: rationalise : can only clear a selection over a
// referred to object
{
// TODO: rationalise : can only clear a selection over a
// referred to object
- ssm.sendSelection(null, null, me);
+ ssm.sendSelection(null, null, null, me);
return;
}
Class type = null;
return;
}
Class type = null;
@@
-955,7
+955,7
@@
public class VamsasApplication implements SelectionSource, VamsasSource
}
if (send)
{
}
if (send)
{
- ssm.sendSelection(jselection, colsel, me);
+ ssm.sendSelection(jselection, colsel, null, me);
}
// discard message.
for (int c = 0; c < jvobjs.length; c++)
}
// discard message.
for (int c = 0; c < jvobjs.length; c++)
@@
-1004,7
+1004,8
@@
public class VamsasApplication implements SelectionSource, VamsasSource
@Override
public void selection(SequenceGroup seqsel,
@Override
public void selection(SequenceGroup seqsel,
- ColumnSelection colsel, SelectionSource source)
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
{
if (vobj2jv == null)
{
{
if (vobj2jv == null)
{
@@
-1079,7
+1080,9
@@
public class VamsasApplication implements SelectionSource, VamsasSource
}
else
{
}
else
{
- int[] intervals = colsel.getVisibleContigs(
+ // int[] intervals = colsel.getVisibleContigs(
+ // seqsel.getStartRes(), seqsel.getEndRes() + 1);
+ int[] intervals = hidden.getVisibleContigs(
seqsel.getStartRes(), seqsel.getEndRes() + 1);
for (int iv = 0; iv < intervals.length; iv += 2)
{
seqsel.getStartRes(), seqsel.getEndRes() + 1);
for (int iv = 0; iv < intervals.length; iv += 2)
{