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JAL-2982 use configured background colour in PCA image export
[jalview.git]
/
src
/
jalview
/
gui
/
AppVarna.java
diff --git
a/src/jalview/gui/AppVarna.java
b/src/jalview/gui/AppVarna.java
index
99bcff4
..
ea16f23
100644
(file)
--- a/
src/jalview/gui/AppVarna.java
+++ b/
src/jalview/gui/AppVarna.java
@@
-23,6
+23,7
@@
package jalview.gui;
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.ColumnSelection;
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.RnaViewerModel;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.RnaViewerModel;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
@@
-60,12
+61,12
@@
import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
import fr.orsay.lri.varna.models.rna.ModeleBase;
import fr.orsay.lri.varna.models.rna.RNA;
import fr.orsay.lri.varna.models.rna.ModeleBase;
import fr.orsay.lri.varna.models.rna.RNA;
-public class AppVarna extends JInternalFrame implements SelectionListener,
- SecondaryStructureListener, InterfaceVARNASelectionListener,
- VamsasSource
+public class AppVarna extends JInternalFrame
+ implements SelectionListener, SecondaryStructureListener,
+ InterfaceVARNASelectionListener, VamsasSource
{
{
- private static final byte[] PAIRS = new byte[]
- { '(', ')', '[', ']', '{', '}', '<', '>' };
+ private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{',
+ '}', '<', '>' };
private AppVarnaBinding vab;
private AppVarnaBinding vab;
@@
-176,10
+177,12
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
{
this(ap);
{
this(ap);
- String sname = aa.sequenceRef == null ? "secondary structure (alignment)"
+ String sname = aa.sequenceRef == null
+ ? "secondary structure (alignment)"
: seq.getName() + " structure";
String theTitle = sname
: seq.getName() + " structure";
String theTitle = sname
- + (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
+ + (aa.sequenceRef == null ? " trimmed to " + seq.getName()
+ : "");
theTitle = MessageManager.formatMessage("label.varna_params",
new String[]
{ theTitle });
theTitle = MessageManager.formatMessage("label.varna_params",
new String[]
{ theTitle });
@@
-190,12
+193,12
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
addModel(gappedModel, gappedTitle);
String trimmedTitle = "trimmed " + sname;
addModel(gappedModel, gappedTitle);
String trimmedTitle = "trimmed " + sname;
- RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, false);
+ RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null,
+ false);
addModel(trimmedModel, trimmedTitle);
vab.setSelectedIndex(0);
}
addModel(trimmedModel, trimmedTitle);
vab.setSelectedIndex(0);
}
-
/**
* Constructor that links the viewer to a parent panel (but has no structures
* yet - use addModel to add them)
/**
* Constructor that links the viewer to a parent panel (but has no structures
* yet - use addModel to add them)
@@
-402,7
+405,7
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
@Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
@Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
- SelectionSource source)
+ HiddenColumns hidden, SelectionSource source)
{
if (source != ap.av)
{
{
if (source != ap.av)
{
@@
-425,8
+428,8
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
end = shift.shift(end);
}
selectionHighlighter.highlightRegion(rna, start, end);
end = shift.shift(end);
}
selectionHighlighter.highlightRegion(rna, start, end);
- selectionHighlighter.getLastHighlight().setOutlineColor(
- seqsel.getOutlineColour());
+ selectionHighlighter.getLastHighlight()
+ .setOutlineColor(seqsel.getOutlineColour());
// TODO - translate column markings to positions on structure if present.
vab.updateSelectedRNA(rna);
}
// TODO - translate column markings to positions on structure if present.
vab.updateSelectedRNA(rna);
}
@@
-461,7
+464,8
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
}
@Override
}
@Override
- public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
+ public void onSelectionChanged(BaseList arg0, BaseList arg1,
+ BaseList arg2)
{
// TODO translate selected regions in VARNA to a selection on the
// alignpanel.
{
// TODO translate selected regions in VARNA to a selection on the
// alignpanel.
@@
-578,7
+582,8
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
{
if (!model.ann.isValidStruc())
{
{
if (!model.ann.isValidStruc())
{
- throw new IllegalArgumentException("Invalid RNA structure annotation");
+ throw new IllegalArgumentException(
+ "Invalid RNA structure annotation");
}
/*
}
/*
@@
-623,11
+628,10
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
ShiftList offset = new ShiftList();
int ofstart = -1;
int sleng = seq.getLength();
ShiftList offset = new ShiftList();
int ofstart = -1;
int sleng = seq.getLength();
- char[] seqChars = seq.getSequence();
for (int i = 0; i < sleng; i++)
{
for (int i = 0; i < sleng; i++)
{
- if (Comparison.isGap(seqChars[i]))
+ if (Comparison.isGap(seq.getCharAt(i)))
{
if (ofstart == -1)
{
{
if (ofstart == -1)
{
@@
-677,7
+681,6
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
vab.setSelectedIndex(selectedIndex);
}
vab.setSelectedIndex(selectedIndex);
}
-
/**
* Add a model with associated Varna session file
*
/**
* Add a model with associated Varna session file
*
@@
-689,7
+692,8
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
{
if (!model.ann.isValidStruc())
{
{
if (!model.ann.isValidStruc())
{
- throw new IllegalArgumentException("Invalid RNA structure annotation");
+ throw new IllegalArgumentException(
+ "Invalid RNA structure annotation");
}
try
}
try
@@
-716,7
+720,6
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
}
}
}
}
-
/**
* Replace everything except RNA secondary structure characters with a period
*
/**
* Replace everything except RNA secondary structure characters with a period
*