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JAL-2446 merged to spike branch
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentAnnotation.java
diff --git
a/src/jalview/datamodel/AlignmentAnnotation.java
b/src/jalview/datamodel/AlignmentAnnotation.java
index
9272b0c
..
56bfd74
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentAnnotation.java
+++ b/
src/jalview/datamodel/AlignmentAnnotation.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-96,14
+96,13
@@
public class AlignmentAnnotation
* Updates the _rnasecstr field Determines the positions that base pair and
* the positions of helices based on secondary structure from a Stockholm file
*
* Updates the _rnasecstr field Determines the positions that base pair and
* the positions of helices based on secondary structure from a Stockholm file
*
- * @param RNAannot
+ * @param rnaAnnotation
*/
*/
- private void _updateRnaSecStr(CharSequence RNAannot)
+ private void _updateRnaSecStr(CharSequence rnaAnnotation)
{
try
{
{
try
{
- bps = Rna.getModeleBP(RNAannot);
- _rnasecstr = Rna.getBasePairs(bps);
+ _rnasecstr = Rna.getHelixMap(rnaAnnotation);
invalidrnastruc = -1;
} catch (WUSSParseException px)
{
invalidrnastruc = -1;
} catch (WUSSParseException px)
{
@@
-114,8
+113,6
@@
public class AlignmentAnnotation
{
return;
}
{
return;
}
- Rna.HelixMap(_rnasecstr);
- // setRNAStruc(RNAannot);
if (_rnasecstr != null && _rnasecstr.length > 0)
{
if (_rnasecstr != null && _rnasecstr.length > 0)
{
@@
-170,10
+167,14
@@
public class AlignmentAnnotation
*/
private Map<Integer, Annotation> sequenceMapping;
*/
private Map<Integer, Annotation> sequenceMapping;
- /** DOCUMENT ME!! */
+ /**
+ * lower range for quantitative data
+ */
public float graphMin;
public float graphMin;
- /** DOCUMENT ME!! */
+ /**
+ * Upper range for quantitative data
+ */
public float graphMax;
/**
public float graphMax;
/**
@@
-269,12
+270,6
@@
public class AlignmentAnnotation
}
}
}
}
- // JBPNote: what does this do ?
- public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
- {
- bps = Rna.getModeleBP(RNAannot);
- }
-
/**
* Creates a new AlignmentAnnotation object.
*
/**
* Creates a new AlignmentAnnotation object.
*
@@
-863,6
+858,10
@@
public class AlignmentAnnotation
@Override
public String toString()
{
@Override
public String toString()
{
+ if (annotations == null)
+ {
+ return "";
+ }
StringBuilder buffer = new StringBuilder(256);
for (int i = 0; i < annotations.length; i++)
StringBuilder buffer = new StringBuilder(256);
for (int i = 0; i < annotations.length; i++)
@@
-1142,14
+1141,14
@@
public class AlignmentAnnotation
* @param colSel
*/
public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
* @param colSel
*/
public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
- ColumnSelection colSel)
+ HiddenColumns hidden)
{
this(alignmentAnnotation);
if (annotations == null)
{
return;
}
{
this(alignmentAnnotation);
if (annotations == null)
{
return;
}
- colSel.makeVisibleAnnotation(this);
+ hidden.makeVisibleAnnotation(this);
}
public void setPadGaps(boolean padgaps, char gapchar)
}
public void setPadGaps(boolean padgaps, char gapchar)
@@
-1486,4
+1485,13
@@
public class AlignmentAnnotation
{
return counter++;
}
{
return counter++;
}
+
+ /**
+ *
+ * @return true for rows that have a range of values in their annotation set
+ */
+ public boolean isQuantitative()
+ {
+ return graphMin < graphMax;
+ }
}
}