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JAL-629 Fix null AlignPanel. More descriptive label of pAE Matrix allows 'Add referen...
author
Ben Soares
<b.soares@dundee.ac.uk>
Mon, 6 Mar 2023 20:43:45 +0000
(20:43 +0000)
committer
Ben Soares
<b.soares@dundee.ac.uk>
Mon, 6 Mar 2023 20:43:45 +0000
(20:43 +0000)
src/jalview/datamodel/ContactMapHolder.java
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src/jalview/gui/StructureChooser.java
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src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
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diff --git
a/src/jalview/datamodel/ContactMapHolder.java
b/src/jalview/datamodel/ContactMapHolder.java
index
5849374
..
a555a17
100644
(file)
--- a/
src/jalview/datamodel/ContactMapHolder.java
+++ b/
src/jalview/datamodel/ContactMapHolder.java
@@
-44,7
+44,7
@@
public class ContactMapHolder implements ContactMapHolderI
aa.graphMin = cm.getMin();
aa.graphMax = cm.getMax();
aa.editable = false;
aa.graphMin = cm.getMin();
aa.graphMax = cm.getMax();
aa.editable = false;
- aa.calcId=cm.getType();
+ aa.calcId = cm.getType();
contactmaps.put(aa.annotationId, cm);
// TODO: contact matrices could be intra or inter - more than one refseq
contactmaps.put(aa.annotationId, cm);
// TODO: contact matrices could be intra or inter - more than one refseq
diff --git
a/src/jalview/gui/StructureChooser.java
b/src/jalview/gui/StructureChooser.java
index
29551b8
..
3fce931
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-1276,7
+1276,7
@@
public class StructureChooser extends GStructureChooser
selectedSequence = userSelectedSeq;
String pdbFilename = selectedPdbFileName;
selectedSequence = userSelectedSeq;
String pdbFilename = selectedPdbFileName;
- StructureChooser.openStructureFileForSequence(ssm, sc, null,
+ StructureChooser.openStructureFileForSequence(ssm, sc, ap,
selectedSequence, true, pdbFilename, tft, paeFilename);
}
SwingUtilities.invokeLater(new Runnable()
selectedSequence, true, pdbFilename, tft, paeFilename);
}
SwingUtilities.invokeLater(new Runnable()
diff --git
a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index
48071bd
..
d1a2e9d
100644
(file)
--- a/
src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/
src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@
-38,12
+38,13
@@
public class PAEContactMatrix implements ContactMatrixI
}
length = _refSeq.getEnd() - _refSeq.getStart() + 1;
}
}
length = _refSeq.getEnd() - _refSeq.getStart() + 1;
}
+
@SuppressWarnings("unchecked")
public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
{
setRefSeq(_refSeq);
// convert the lists to primitive arrays and store
@SuppressWarnings("unchecked")
public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
{
setRefSeq(_refSeq);
// convert the lists to primitive arrays and store
-
+
if (!MapUtils.containsAKey(pae_obj, "predicted_aligned_error", "pae"))
{
parse_version_1_pAE(pae_obj);
if (!MapUtils.containsAKey(pae_obj, "predicted_aligned_error", "pae"))
{
parse_version_1_pAE(pae_obj);
@@
-54,32
+55,35
@@
public class PAEContactMatrix implements ContactMatrixI
parse_version_2_pAE(pae_obj);
}
}
parse_version_2_pAE(pae_obj);
}
}
+
/**
* construct a sequence associated PAE matrix directly from a float array
/**
* construct a sequence associated PAE matrix directly from a float array
+ *
* @param _refSeq
* @param matrix
*/
public PAEContactMatrix(SequenceI _refSeq, float[][] matrix)
{
setRefSeq(_refSeq);
* @param _refSeq
* @param matrix
*/
public PAEContactMatrix(SequenceI _refSeq, float[][] matrix)
{
setRefSeq(_refSeq);
- maxcol=0;
- for (float[] row:matrix)
+ maxcol = 0;
+ for (float[] row : matrix)
{
{
- if (row.length>maxcol)
+ if (row.length > maxcol)
{
{
- maxcol=row.length;
+ maxcol = row.length;
}
}
- maxscore=row[0];
- for (float f:row)
+ maxscore = row[0];
+ for (float f : row)
{
{
- if (maxscore<f) {
- maxscore=f;
+ if (maxscore < f)
+ {
+ maxscore = f;
}
}
}
}
}
}
- maxrow=matrix.length;
+ maxrow = matrix.length;
elements = matrix;
elements = matrix;
-
+
}
/**
}
/**
@@
-94,11
+98,10
@@
public class PAEContactMatrix implements ContactMatrixI
maxscore = ((Double) MapUtils.getFirst(pae_obj,
"max_predicted_aligned_error", "max_pae")).floatValue();
List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
maxscore = ((Double) MapUtils.getFirst(pae_obj,
"max_predicted_aligned_error", "max_pae")).floatValue();
List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
- .getFirst(pae_obj, "predicted_aligned_error", "pae"))
- ;
+ .getFirst(pae_obj, "predicted_aligned_error", "pae"));
elements = new float[scoreRows.size()][scoreRows.size()];
int row = 0, col = 0;
elements = new float[scoreRows.size()][scoreRows.size()];
int row = 0, col = 0;
- for (List<Long> scoreRow:scoreRows)
+ for (List<Long> scoreRow : scoreRows)
{
Iterator<Long> scores = scoreRow.iterator();
while (scores.hasNext())
{
Iterator<Long> scores = scoreRow.iterator();
while (scores.hasNext())
@@
-107,7
+110,7
@@
public class PAEContactMatrix implements ContactMatrixI
if (d instanceof Double)
elements[row][col++] = ((Double) d).longValue();
else
if (d instanceof Double)
elements[row][col++] = ((Double) d).longValue();
else
- elements[row][col++] = (float) ((Long)d).longValue();
+ elements[row][col++] = (float) ((Long) d).longValue();
}
row++;
col = 0;
}
row++;
col = 0;
@@
-172,7
+175,7
@@
public class PAEContactMatrix implements ContactMatrixI
@Override
public int getContactHeight()
{
@Override
public int getContactHeight()
{
- return maxcol-1;
+ return maxcol - 1;
}
@Override
}
@Override
@@
-220,20
+223,26
@@
public class PAEContactMatrix implements ContactMatrixI
@Override
public String getAnnotLabel()
{
@Override
public String getAnnotLabel()
{
- return "pAE Matrix";
+ StringBuilder label = new StringBuilder("pAE Matrix");
+ if (this.getReferenceSeq() != null)
+ label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+ return label.toString();
}
}
- public static final String PAEMATRIX="PAE_MATRIX";
+ public static final String PAEMATRIX = "PAE_MATRIX";
+
@Override
public String getType()
{
return PAEMATRIX;
}
@Override
public String getType()
{
return PAEMATRIX;
}
+
@Override
public int getWidth()
{
return length;
}
@Override
public int getWidth()
{
return length;
}
+
@Override
public int getHeight()
{
@Override
public int getHeight()
{