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doco writing.
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
a76106b
..
87cd9a9
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-195,6
+195,11
@@
public class AlignFrame
return jalview.bin.Cache.getProperty("VERSION");
\r
}
\r
\r
return jalview.bin.Cache.getProperty("VERSION");
\r
}
\r
\r
+ public FeatureRenderer getFeatureRenderer()
\r
+ {
\r
+ return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
\r
+ }
\r
+
\r
\r
public void fetchSequence_actionPerformed(ActionEvent e)
\r
{
\r
\r
public void fetchSequence_actionPerformed(ActionEvent e)
\r
{
\r
@@
-707,8
+712,9
@@
public class AlignFrame
String newtitle = new String("Copied sequences");
\r
\r
//>>>This is a fix for the moment, until a better solution is found!!<<<
\r
String newtitle = new String("Copied sequences");
\r
\r
//>>>This is a fix for the moment, until a better solution is found!!<<<
\r
- FeatureRenderer fr = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
\r
- fr.featureColours = alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
\r
+
\r
\r
if (title.startsWith("Copied sequences"))
\r
{
\r
\r
if (title.startsWith("Copied sequences"))
\r
{
\r
@@
-801,7
+807,7
@@
public class AlignFrame
\r
//Jalview no longer allows deletion of residues.
\r
//Check here whether any residues are in selection area
\r
\r
//Jalview no longer allows deletion of residues.
\r
//Check here whether any residues are in selection area
\r
- if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
\r
+ /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
\r
{
\r
for (int i = 0; i < sg.sequences.size(); i++)
\r
{
\r
{
\r
for (int i = 0; i < sg.sequences.size(); i++)
\r
{
\r
@@
-822,7
+828,7
@@
public class AlignFrame
j++;
\r
}while(j<=sg.getEndRes());
\r
}
\r
j++;
\r
}while(j<=sg.getEndRes());
\r
}
\r
- }
\r
+ }*/
\r
\r
\r
addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
\r
\r
addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
@@
-1207,8
+1213,8
@@
public class AlignFrame
\r
viewport.padGaps = padGapsMenuitem.isSelected();
\r
\r
\r
viewport.padGaps = padGapsMenuitem.isSelected();
\r
\r
- if (viewport.padGaps)
\r
- alignmentChanged();
\r
+ // if (viewport.padGaps)
\r
+ alignmentChanged();
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
@@
-2355,6
+2361,7
@@
public class AlignFrame
{
\r
// Add any Multiple Sequence Alignment Services
\r
final JMenu msawsmenu = new JMenu("Alignment");
\r
{
\r
// Add any Multiple Sequence Alignment Services
\r
final JMenu msawsmenu = new JMenu("Alignment");
\r
+ final AlignFrame af = this;
\r
for (int i = 0, j = msaws.size(); i < j; i++)
\r
{
\r
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
for (int i = 0, j = msaws.size(); i < j; i++)
\r
{
\r
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
@@
-2366,7
+2373,7
@@
public class AlignFrame
{
\r
SequenceI[] msa = gatherSequencesForAlignment();
\r
new jalview.ws.MsaWSClient(sh, title, msa,
\r
{
\r
SequenceI[] msa = gatherSequencesForAlignment();
\r
new jalview.ws.MsaWSClient(sh, title, msa,
\r
- false, true, viewport.getAlignment().getDataset());
\r
+ false, true, viewport.getAlignment().getDataset(), af);
\r
\r
}
\r
\r
\r
}
\r
\r
@@
-2383,7
+2390,7
@@
public class AlignFrame
{
\r
SequenceI[] msa = gatherSequencesForAlignment();
\r
new jalview.ws.MsaWSClient(sh, title, msa,
\r
{
\r
SequenceI[] msa = gatherSequencesForAlignment();
\r
new jalview.ws.MsaWSClient(sh, title, msa,
\r
- true, true, viewport.getAlignment().getDataset());
\r
+ true, true, viewport.getAlignment().getDataset(), af);
\r
\r
}
\r
\r
\r
}
\r
\r