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JAL-2349 JAL-3855 ContactListI.getPosition() to recover original position passed...
author
Jim Procter
<j.procter@dundee.ac.uk>
Thu, 20 Oct 2022 15:28:00 +0000
(16:28 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Thu, 20 Oct 2022 15:28:00 +0000
(16:28 +0100)
src/jalview/datamodel/ContactListI.java
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src/jalview/datamodel/ContactListImpl.java
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src/jalview/datamodel/ContactListProviderI.java
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src/jalview/datamodel/ContactMatrix.java
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src/jalview/datamodel/SeqDistanceContactMatrix.java
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src/jalview/gui/AnnotationPanel.java
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src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
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test/jalview/datamodel/ContactMatrixTest.java
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diff --git
a/src/jalview/datamodel/ContactListI.java
b/src/jalview/datamodel/ContactListI.java
index
72dbf2e
..
ac06adb
100644
(file)
--- a/
src/jalview/datamodel/ContactListI.java
+++ b/
src/jalview/datamodel/ContactListI.java
@@
-1,6
+1,5
@@
package jalview.datamodel;
package jalview.datamodel;
-
public interface ContactListI extends ContactListProviderI
{
public interface ContactListI extends ContactListProviderI
{
diff --git
a/src/jalview/datamodel/ContactListImpl.java
b/src/jalview/datamodel/ContactListImpl.java
index
561048e
..
beb557f
100644
(file)
--- a/
src/jalview/datamodel/ContactListImpl.java
+++ b/
src/jalview/datamodel/ContactListImpl.java
@@
-21,6
+21,12
@@
public class ContactListImpl implements ContactListI
}
@Override
}
@Override
+ public int getPosition()
+ {
+ return clist.getPosition();
+ }
+
+ @Override
public double getContactAt(int column)
{
return clist.getContactAt(column);
public double getContactAt(int column)
{
return clist.getContactAt(column);
diff --git
a/src/jalview/datamodel/ContactListProviderI.java
b/src/jalview/datamodel/ContactListProviderI.java
index
37c4e07
..
f027e01
100644
(file)
--- a/
src/jalview/datamodel/ContactListProviderI.java
+++ b/
src/jalview/datamodel/ContactListProviderI.java
@@
-4,6
+4,13
@@
public interface ContactListProviderI
{
/**
{
/**
+ *
+ * @return position index for this contact List (usually sequence position or
+ * alignment column)
+ */
+ int getPosition();
+
+ /**
* dimension of list where getContactAt(column<getContactHeight()) may return
* a value
*
* dimension of list where getContactAt(column<getContactHeight()) may return
* a value
*
diff --git
a/src/jalview/datamodel/ContactMatrix.java
b/src/jalview/datamodel/ContactMatrix.java
index
07934a1
..
2968ab9
100644
(file)
--- a/
src/jalview/datamodel/ContactMatrix.java
+++ b/
src/jalview/datamodel/ContactMatrix.java
@@
-87,6
+87,12
@@
public class ContactMatrix implements ContactMatrixI
int p = column;
@Override
int p = column;
@Override
+ public int getPosition()
+ {
+ return p;
+ }
+
+ @Override
public int getContactHeight()
{
return width;
public int getContactHeight()
{
return width;
diff --git
a/src/jalview/datamodel/SeqDistanceContactMatrix.java
b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index
bb2299b
..
4b23f04
100644
(file)
--- a/
src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/
src/jalview/datamodel/SeqDistanceContactMatrix.java
@@
-26,6
+26,7
@@
public class SeqDistanceContactMatrix implements ContactMatrixI
{
return width;
}
{
return width;
}
+
@Override
public ContactListI getContactList(final int column)
{
@Override
public ContactListI getContactList(final int column)
{
@@
-60,6
+61,12
@@
public class SeqDistanceContactMatrix implements ContactMatrixI
}
@Override
}
@Override
+ public int getPosition()
+ {
+ return p;
+ }
+
+ @Override
public double getContactAt(int column)
{
return Math.abs(column - p);
public double getContactAt(int column)
{
return Math.abs(column - p);
diff --git
a/src/jalview/gui/AnnotationPanel.java
b/src/jalview/gui/AnnotationPanel.java
index
2149266
..
615fbdd
100755
(executable)
--- a/
src/jalview/gui/AnnotationPanel.java
+++ b/
src/jalview/gui/AnnotationPanel.java
@@
-1101,8
+1101,8
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset,
rowAndOffset);
ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset,
rowAndOffset);
ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
- tooltip = "Contact from " + ci.cStart + " to " + ci.cEnd
- + "<br/>Mean:" + cr.getMean();
+ tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
+ + " - " + ci.cEnd + "]" + "<br/>Mean:" + cr.getMean();
// ap.getStructureSelectionManager().mouseOverSequence(ann.sequenceRef,
// new int[] {column, ci.cStart,ci.cEnd}, -1, null)
// ap.getStructureSelectionManager().mouseOverSequence(ann.sequenceRef,
// new int[] {column, ci.cStart,ci.cEnd}, -1, null)
diff --git
a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index
3a8e26a
..
8fde1e8
100644
(file)
--- a/
src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/
src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@
-126,6
+126,12
@@
public class PAEContactMatrix implements ContactMatrixI
return new ContactListImpl(new ContactListProviderI()
{
@Override
return new ContactListImpl(new ContactListProviderI()
{
@Override
+ public int getPosition()
+ {
+ return _column;
+ }
+
+ @Override
public int getContactHeight()
{
return maxcol - 1;
public int getContactHeight()
{
return maxcol - 1;
diff --git
a/test/jalview/datamodel/ContactMatrixTest.java
b/test/jalview/datamodel/ContactMatrixTest.java
index
f0861e9
..
5d8b8d1
100644
(file)
--- a/
test/jalview/datamodel/ContactMatrixTest.java
+++ b/
test/jalview/datamodel/ContactMatrixTest.java
@@
-18,7
+18,8
@@
public class ContactMatrixTest
/**
* standard asserts for ContactMatrixI
*/
/**
* standard asserts for ContactMatrixI
*/
- public static void testContactMatrixI(ContactMatrixI cm, boolean symmetric)
+ public static void testContactMatrixI(ContactMatrixI cm,
+ boolean symmetric)
{
// assume contact matrix is square for text
ContactListI clist = cm.getContactList(1);
{
// assume contact matrix is square for text
ContactListI clist = cm.getContactList(1);
@@
-81,6
+82,12
@@
public class ContactMatrixTest
double[] val = { 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7 };
@Override
double[] val = { 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7 };
@Override
+ public int getPosition()
+ {
+ return 0;
+ }
+
+ @Override
public int getContactHeight()
{
return val.length;
public int getContactHeight()
{
return val.length;