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());
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);
void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
{
+ int boarderBottomOffset = 5;
long pSessionId = System.currentTimeMillis();
headless = (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true"));
}
im = new jalview.util.ImageMaker(this, type, imageAction,
- aDimension.getWidth(), aDimension.getHeight(), file,
+ aDimension.getWidth(), aDimension.getHeight()
+ + boarderBottomOffset, file,
imageTitle, alignFrame, pSessionId, headless);
if (av.getWrapAlignment())
{
if (im.getGraphics() != null)
{
printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
- aDimension.getHeight(), 0);
+ aDimension.getHeight() + boarderBottomOffset, 0);
im.writeImage();
}
}
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);
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" })
{
System.out.println("CalcId: " + aa.getCalcId());
+ if (StructureImportSettings.getDefaultPDBFileParser().equals(
+ StructureParser.JALVIEW_PARSER))
+ {
assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ }
}
}
}
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("TYR: 314 1gaqA", sf[295].getDescription());
+ assertEquals("TYR:314 1gaqA", sf[295].getDescription());
/*
* 1GAQ/B
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("ALA: 98 1gaqB", sf[97].getDescription());
+ assertEquals("ALA:98 1gaqB", sf[97].getDescription());
/*
* 1GAQ/C
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("TYR: 314 1gaqC", sf[295].getDescription());
+ assertEquals("TYR:314 1gaqC", sf[295].getDescription());
}
@Test(groups = { "Functional" })
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
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());
}
}