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JAL-1919 Added improvement to ensure consistence of annotations parsed via JmolParser...
author
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Mon, 15 Aug 2016 13:53:58 +0000
(14:53 +0100)
committer
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Mon, 15 Aug 2016 13:53:58 +0000
(14:53 +0100)
src/MCview/Atom.java
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src/jalview/ext/jmol/JmolParser.java
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test/MCview/AtomTest.java
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test/jalview/io/AnnotatedPDBFileInputTest.java
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test/jalview/structure/StructureSelectionManagerTest.java
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diff --git
a/src/MCview/Atom.java
b/src/MCview/Atom.java
index
ab038a0
..
fe6a0ac
100755
(executable)
--- a/
src/MCview/Atom.java
+++ b/
src/MCview/Atom.java
@@
-81,7
+81,7
@@
public class Atom
chain = str.substring(21, 22);
resNumber = Integer.parseInt(str.substring(22, 26).trim());
chain = str.substring(21, 22);
resNumber = Integer.parseInt(str.substring(22, 26).trim());
- resNumIns = str.substring(22, 27);
+ resNumIns = str.substring(22, 27).trim();
insCode = str.substring(26, 27).charAt(0);
this.x = (new Float(str.substring(30, 38).trim()).floatValue());
this.y = (new Float(str.substring(38, 46).trim()).floatValue());
insCode = str.substring(26, 27).charAt(0);
this.x = (new Float(str.substring(30, 38).trim()).floatValue());
this.y = (new Float(str.substring(38, 46).trim()).floatValue());
diff --git
a/src/jalview/ext/jmol/JmolParser.java
b/src/jalview/ext/jmol/JmolParser.java
index
ea969ff
..
848e7db
100644
(file)
--- a/
src/jalview/ext/jmol/JmolParser.java
+++ b/
src/jalview/ext/jmol/JmolParser.java
@@
-217,7
+217,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
curAtom.resNumber = atom.getResno();
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
curAtom.resNumber = atom.getResno();
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
- curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
+ curAtom.resNumIns = ("" + curAtom.resNumber + curAtom.insCode)
+ .trim();
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
// significantAtoms.add(curAtom);
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
// significantAtoms.add(curAtom);
diff --git
a/test/MCview/AtomTest.java
b/test/MCview/AtomTest.java
index
33d332a
..
21a79fe
100644
(file)
--- a/
test/MCview/AtomTest.java
+++ b/
test/MCview/AtomTest.java
@@
-42,7
+42,7
@@
public class AtomTest
assertEquals("GLN", a.resName);
assertEquals("A", a.chain);
assertEquals(48, a.resNumber);
assertEquals("GLN", a.resName);
assertEquals("A", a.chain);
assertEquals(48, a.resNumber);
- assertEquals(" 48 ", a.resNumIns);
+ assertEquals("48", a.resNumIns);
assertEquals(' ', a.insCode);
assertEquals(22.290, a.x, 0.00001);
assertEquals(8.595, a.y, 0.00001);
assertEquals(' ', a.insCode);
assertEquals(22.290, a.x, 0.00001);
assertEquals(8.595, a.y, 0.00001);
diff --git
a/test/jalview/io/AnnotatedPDBFileInputTest.java
b/test/jalview/io/AnnotatedPDBFileInputTest.java
index
e6019aa
..
d3d9ff8
100644
(file)
--- a/
test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/
test/jalview/io/AnnotatedPDBFileInputTest.java
@@
-68,8
+68,8
@@
public class AnnotatedPDBFileInputTest
pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
.get(0).getId();
StructureImportSettings.setDefaultStructureFileFormat("PDB");
pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
.get(0).getId();
StructureImportSettings.setDefaultStructureFileFormat("PDB");
- StructureImportSettings
- .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
@Test(groups = { "Functional" })
}
@Test(groups = { "Functional" })
@@
-101,7
+101,11
@@
public class AnnotatedPDBFileInputTest
{
System.out.println("CalcId: " + aa.getCalcId());
{
System.out.println("CalcId: " + aa.getCalcId());
+ if (StructureImportSettings.getDefaultPDBFileParser().equals(
+ StructureParser.JALVIEW_PARSER))
+ {
assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ }
}
}
}
}
}
}
@@
-118,9
+122,9
@@
public class AnnotatedPDBFileInputTest
SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU: 19 1gaqA", sf[0].getDescription());
+ assertEquals("GLU:19 1gaqA", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqA", sf[295].getDescription());
+ assertEquals("TYR:314 1gaqA", sf[295].getDescription());
/*
* 1GAQ/B
/*
* 1GAQ/B
@@
-128,9
+132,9
@@
public class AnnotatedPDBFileInputTest
sf = al.getSequenceAt(1).getSequenceFeatures();
assertEquals(98, sf.length);
assertEquals("RESNUM", sf[0].getType());
sf = al.getSequenceAt(1).getSequenceFeatures();
assertEquals(98, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("ALA: 1 1gaqB", sf[0].getDescription());
+ assertEquals("ALA:1 1gaqB", sf[0].getDescription());
assertEquals("RESNUM", sf[97].getType());
assertEquals("RESNUM", sf[97].getType());
- assertEquals("ALA: 98 1gaqB", sf[97].getDescription());
+ assertEquals("ALA:98 1gaqB", sf[97].getDescription());
/*
* 1GAQ/C
/*
* 1GAQ/C
@@
-138,9
+142,9
@@
public class AnnotatedPDBFileInputTest
sf = al.getSequenceAt(2).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
sf = al.getSequenceAt(2).getSequenceFeatures();
assertEquals(296, sf.length);
assertEquals("RESNUM", sf[0].getType());
- assertEquals("GLU: 19 1gaqC", sf[0].getDescription());
+ assertEquals("GLU:19 1gaqC", sf[0].getDescription());
assertEquals("RESNUM", sf[295].getType());
assertEquals("RESNUM", sf[295].getType());
- assertEquals("TYR: 314 1gaqC", sf[295].getDescription());
+ assertEquals("TYR:314 1gaqC", sf[295].getDescription());
}
@Test(groups = { "Functional" })
}
@Test(groups = { "Functional" })
diff --git
a/test/jalview/structure/StructureSelectionManagerTest.java
b/test/jalview/structure/StructureSelectionManagerTest.java
index
2074fb4
..
baaa96b
100644
(file)
--- a/
test/jalview/structure/StructureSelectionManagerTest.java
+++ b/
test/jalview/structure/StructureSelectionManagerTest.java
@@
-138,7
+138,7
@@
public class StructureSelectionManagerTest
SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
- assertEquals("GLU: 19 1gaqA", sf.getDescription());
+ assertEquals("GLU:19 1gaqA", sf.getDescription());
/*
* Verify a RESNUM sequence feature in the StructureSelectionManager mapped
/*
* Verify a RESNUM sequence feature in the StructureSelectionManager mapped
@@
-148,6
+148,6
@@
public class StructureSelectionManagerTest
sf = map.sequence.getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
sf = map.sequence.getSequenceFeatures()[0];
assertEquals("RESNUM", sf.getType());
assertEquals("1gaq", sf.getFeatureGroup());
- assertEquals("ALA: 1 1gaqB", sf.getDescription());
+ assertEquals("ALA:1 1gaqB", sf.getDescription());
}
}
}
}