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remove conflict on javascript api
author
jprocter
<Jim Procter>
Thu, 11 Oct 2007 11:18:44 +0000
(11:18 +0000)
committer
jprocter
<Jim Procter>
Thu, 11 Oct 2007 11:18:44 +0000
(11:18 +0000)
src/jalview/bin/JalviewLite.java
patch
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diff --git
a/src/jalview/bin/JalviewLite.java
b/src/jalview/bin/JalviewLite.java
index
c9977fd
..
c61c516
100755
(executable)
--- a/
src/jalview/bin/JalviewLite.java
+++ b/
src/jalview/bin/JalviewLite.java
@@
-48,9
+48,9
@@
public class JalviewLite
*/
public String getSelectedSequences()
{
*/
public String getSelectedSequences()
{
- return getSelectedSequences(currentAlignFrame);
+ return getSelectedSequencesFrom(currentAlignFrame);
}
}
- public String getSelectedSequences(AlignFrame alf)
+ public String getSelectedSequencesFrom(AlignFrame alf)
{
StringBuffer result = new StringBuffer("");
{
StringBuffer result = new StringBuffer("");
@@
-71,17
+71,17
@@
public class JalviewLite
public String getAlignment(String format)
{
public String getAlignment(String format)
{
- return getAlignment(currentAlignFrame, format, "true");
+ return getAlignmentFrom(currentAlignFrame, format, "true");
}
}
- public String getAlignment(AlignFrame alf, String format)
+ public String getAlignmentFrom(AlignFrame alf, String format)
{
{
- return getAlignment(alf, format, "true");
+ return getAlignmentFrom(alf, format, "true");
}
public String getAlignment(String format, String suffix)
{
}
public String getAlignment(String format, String suffix)
{
- return getAlignment(currentAlignFrame, format, suffix);
+ return getAlignmentFrom(currentAlignFrame, format, suffix);
}
}
- public String getAlignment(AlignFrame alf, String format, String suffix)
+ public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
{
try
{
{
try
{
@@
-100,9
+100,9
@@
public class JalviewLite
public void loadAnnotation(String annotation)
{
public void loadAnnotation(String annotation)
{
- loadAnnotation(currentAlignFrame, annotation);
+ loadAnnotationFrom(currentAlignFrame, annotation);
}
}
- public void loadAnnotation(AlignFrame alf, String annotation)
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
if (new AnnotationFile().readAnnotationFile(
alf.getAlignViewport().getAlignment(), annotation,
{
if (new AnnotationFile().readAnnotationFile(
alf.getAlignViewport().getAlignment(), annotation,
@@
-119,34
+119,34
@@
public class JalviewLite
public String getFeatures(String format)
{
public String getFeatures(String format)
{
- return getFeatures(currentAlignFrame, format);
+ return getFeaturesFrom(currentAlignFrame, format);
}
}
- public String getFeatures(AlignFrame alf, String format)
+ public String getFeaturesFrom(AlignFrame alf, String format)
{
return alf.outputFeatures(false, format);
}
public String getAnnotation()
{
{
return alf.outputFeatures(false, format);
}
public String getAnnotation()
{
- return getAnnotation(currentAlignFrame);
+ return getAnnotationFrom(currentAlignFrame);
}
}
- public String getAnnotation(AlignFrame alf)
+ public String getAnnotationFrom(AlignFrame alf)
{
return alf.outputAnnotations(false);
}
public AlignFrame newView()
{
{
return alf.outputAnnotations(false);
}
public AlignFrame newView()
{
- return newView(currentAlignFrame);
+ return newViewFrom(currentAlignFrame);
}
public AlignFrame newView(String name)
{
}
public AlignFrame newView(String name)
{
- return newView(currentAlignFrame, name);
+ return newViewFrom(currentAlignFrame, name);
}
}
- public AlignFrame newView(AlignFrame alf)
+ public AlignFrame newViewFrom(AlignFrame alf)
{
return alf.newView(null);
}
{
return alf.newView(null);
}
- public AlignFrame newView(AlignFrame alf, String name)
+ public AlignFrame newViewFrom(AlignFrame alf, String name)
{
return alf.newView(name);
}
{
return alf.newView(name);
}
@@
-797,7
+797,16
@@
public class JalviewLite
String lst = ArraytotabbedList(currentAlignFrame.getFeatureGroups());
return lst;
}
String lst = ArraytotabbedList(currentAlignFrame.getFeatureGroups());
return lst;
}
-
+ /**
+ * @param alf alignframe to get feature groups on
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ */
+ public String getFeatureGroupsOn(AlignFrame alf)
+ {
+ String lst = ArraytotabbedList(alf.getFeatureGroups());
+ return lst;
+ }
/**
* @param visible
* @return
/**
* @param visible
* @return
@@
-808,17
+817,26
@@
public class JalviewLite
return ArraytotabbedList(currentAlignFrame.getFeatureGroupsOfState(visible));
}
/**
return ArraytotabbedList(currentAlignFrame.getFeatureGroupsOfState(visible));
}
/**
+ * @param alf align frame to get groups of state visible
+ * @param visible
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ */
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ {
+ return ArraytotabbedList(alf.getFeatureGroupsOfState(visible));
+ } /**
* @param groups tab separated list of group names
* @param state true or false
* @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[], boolean)
*/
* @param groups tab separated list of group names
* @param state true or false
* @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[], boolean)
*/
- public void setFeatureGroupState(AlignFrame alf, String groups, boolean state)
+ public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state)
{
boolean st = state;//!(state==null || state.equals("") || state.toLowerCase().equals("false"));
alf.setFeatureGroupState(tabbedListToArray(groups), st);
}
public void setFeatureGroupState(String groups, boolean state)
{
{
boolean st = state;//!(state==null || state.equals("") || state.toLowerCase().equals("false"));
alf.setFeatureGroupState(tabbedListToArray(groups), st);
}
public void setFeatureGroupState(String groups, boolean state)
{
- setFeatureGroupState(currentAlignFrame, groups, state);
+ setFeatureGroupStateOn(currentAlignFrame, groups, state);
}
}
}
}