import java.io.File;
import java.net.URL;
import java.security.AccessControlException;
+import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
boolean loadedInline;
- /**
- * current set of model filenames loaded in the Jmol instance
- */
- String[] modelFileNames = null;
-
StringBuffer resetLastRes = new StringBuffer();
public Viewer viewer;
} catch (InterruptedException i)
{
}
- ;
}
+
+ /*
+ * get the distinct structure files modelled
+ * (a file with multiple chains may map to multiple sequences)
+ */
String[] files = getPdbFile();
if (!waitForFileLoad(files))
{
}
}
StringBuilder command = new StringBuilder(256);
+ // command.append("set spinFps 10;\n");
+
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
if (pdbfnum == refStructure || selcom[pdbfnum] == null
}
if (modelFileNames == null)
{
- String mset[] = new String[viewer.ms.mc];
- _modelFileNameMap = new int[mset.length];
+ List<String> mset = new ArrayList<String>();
+ _modelFileNameMap = new int[viewer.ms.mc];
String m = viewer.ms.getModelFileName(0);
if (m != null)
{
- mset[0] = m;
+ String filePath = m;
try
{
- mset[0] = new File(m).getAbsolutePath();
+ filePath = new File(m).getAbsolutePath();
} catch (AccessControlException x)
{
// usually not allowed to do this in applet
.println("jmolBinding: Using local file string from Jmol: "
+ m);
}
- if (mset[0].indexOf("/file:") != -1)
+ if (filePath.indexOf("/file:") != -1)
{
// applet path with docroot - discard as format won't match pdbfile
- mset[0] = m;
+ filePath = m;
}
+ mset.add(filePath);
_modelFileNameMap[0] = 0; // filename index for first model is always 0.
}
int j = 1;
- for (int i = 1; i < mset.length; i++)
+ for (int i = 1; i < viewer.ms.mc; i++)
{
m = viewer.ms.getModelFileName(i);
- mset[j] = m;
+ String filePath = m;
if (m != null)
{
try
{
- mset[j] = new File(m).getAbsolutePath();
+ filePath = new File(m).getAbsolutePath();
} catch (AccessControlException x)
{
// usually not allowed to do this in applet, so keep raw handle
// System.err.println("jmolBinding: Using local file string from Jmol: "+m);
}
}
- _modelFileNameMap[j] = i; // record the model index for the filename
- // skip any additional models in the same file (NMR structures)
- if ((mset[j] == null ? mset[j] != mset[j - 1]
- : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
+
+ /*
+ * add this model unless it is read from a structure file we have
+ * already seen (example: 2MJW is an NMR structure with 10 models)
+ */
+ if (!mset.contains(filePath))
{
+ mset.add(filePath);
+ _modelFileNameMap[j] = i; // record the model index for the filename
j++;
}
}
- modelFileNames = new String[j];
- System.arraycopy(mset, 0, modelFileNames, 0, j);
+ modelFileNames = mset.toArray(new String[mset.size()]);
}
return modelFileNames;
}
protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
PDBEntry[] pdbs, SequenceI[][] seqsForPdbs, AlignmentPanel ap)
{
+ PDBEntry[] pdbsForFile = getUniquePdbFiles(pdbs);
JalviewStructureDisplayI sview = null;
if (viewerType.equals(ViewerType.JMOL))
{
- sview = new AppJmol(ap, pdbs, ap.av.collateForPDB(pdbs));
+ sview = new AppJmol(ap, pdbsForFile, ap.av.collateForPDB(pdbsForFile));
}
else if (viewerType.equals(ViewerType.CHIMERA))
{
- sview = new ChimeraViewFrame(pdbs, ap.av.collateForPDB(pdbs), ap);
+ sview = new ChimeraViewFrame(pdbsForFile,
+ ap.av.collateForPDB(pdbsForFile), ap);
}
else
{
return sview;
}
+ /**
+ * Convert the array of PDBEntry into an array with no filename repeated
+ *
+ * @param pdbs
+ * @return
+ */
+ static PDBEntry[] getUniquePdbFiles(PDBEntry[] pdbs)
+ {
+ if (pdbs == null)
+ {
+ return null;
+ }
+ List<PDBEntry> uniques = new ArrayList<PDBEntry>();
+ List<String> filesSeen = new ArrayList<String>();
+ for (PDBEntry entry : pdbs)
+ {
+ String file = entry.getFile();
+ if (file == null)
+ {
+ uniques.add(entry);
+ }
+ else if (!filesSeen.contains(file))
+ {
+ uniques.add(entry);
+ filesSeen.add(file);
+ }
+ }
+ return uniques.toArray(new PDBEntry[uniques.size()]);
+ }
+
protected JalviewStructureDisplayI viewStructures(ViewerType viewerType,
PDBEntry pdb, SequenceI[] seqsForPdb, AlignmentPanel ap)
{
--- /dev/null
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+
+import org.testng.annotations.Test;
+
+public class StructureViewerTest
+{
+ @Test(groups = "Functional")
+ public void testGetUniquePdbFiles()
+ {
+ assertNull(StructureViewer.getUniquePdbFiles(null));
+
+ PDBEntry pdbe1 = new PDBEntry("1A70", "A", Type.PDB, "path1");
+ PDBEntry pdbe2 = new PDBEntry("3A6S", "A", Type.PDB, "path2");
+ PDBEntry pdbe3 = new PDBEntry("1A70", "B", Type.PDB, "path1");
+ PDBEntry pdbe4 = new PDBEntry("1GAQ", "A", Type.PDB, null);
+ PDBEntry pdbe5 = new PDBEntry("3A6S", "B", Type.PDB, "path2");
+ PDBEntry pdbe6 = new PDBEntry("1GAQ", "B", Type.PDB, null);
+
+ /*
+ * pdbe2 and pdbe5 get removed as having a duplicate file path
+ */
+ PDBEntry[] uniques = StructureViewer.getUniquePdbFiles(new PDBEntry[] {
+ pdbe1, pdbe2, pdbe3, pdbe4, pdbe5, pdbe6 });
+ assertEquals(uniques,
+ new PDBEntry[] { pdbe1, pdbe2, pdbe4, pdbe6 });
+ }
+}
*/
public class AAStructureBindingModelTest
{
+ /*
+ * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
+ */
private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n"
+ "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n"
+ "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n"
+ "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n"
+ "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n"
- + "ATOM 31 CA LYS A 101 33.323 11.587 43.115 1.00 41.69 C \n";
+ // artificial jump in residue numbering to prove it is correctly
+ // mapped:
+ + "ATOM 31 CA LYS A 102 33.323 11.587 43.115 1.00 41.69 C \n"
+ + "ATOM 1857 CA GLU B 374 9.193 -16.005 95.870 1.00 54.22 C \n"
+ + "ATOM 1866 CA ILE B 375 7.101 -14.921 92.847 1.00 46.82 C \n"
+ + "ATOM 1874 CA VAL B 376 10.251 -13.625 91.155 1.00 47.80 C \n"
+ + "ATOM 1881 CA LYS B 377 11.767 -17.068 91.763 1.00 50.21 C \n"
+ + "ATOM 1890 CA PHE B 378 8.665 -18.948 90.632 1.00 44.85 C \n";
private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
- + "ATOM 2 CA MET A 1 15.366 -11.648 24.854 1.00 32.05 C \n"
- + "ATOM 10 CA LYS A 2 16.846 -9.215 22.340 1.00 25.68 C \n"
- + "ATOM 19 CA LYS A 3 15.412 -6.335 20.343 1.00 19.42 C \n"
- + "ATOM 28 CA LEU A 4 15.629 -5.719 16.616 1.00 15.49 C \n"
- + "ATOM 36 CA GLN A 5 14.412 -2.295 15.567 1.00 12.19 C \n";
+ + "ATOM 2 CA MET B 1 15.366 -11.648 24.854 1.00 32.05 C \n"
+ + "ATOM 10 CA LYS B 2 16.846 -9.215 22.340 1.00 25.68 C \n"
+ + "ATOM 19 CA LYS B 3 15.412 -6.335 20.343 1.00 19.42 C \n"
+ + "ATOM 28 CA LEU B 4 15.629 -5.719 16.616 1.00 15.49 C \n"
+ + "ATOM 36 CA GLN B 5 14.412 -2.295 15.567 1.00 12.19 C \n";
private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n"
- + "ATOM 2 CA SER A 1 29.427 3.330 -6.578 1.00 32.50 C \n"
- + "ATOM 8 CA PRO A 2 29.975 3.340 -2.797 1.00 17.62 C \n"
- + "ATOM 16 CA ALYS A 3 26.958 3.024 -0.410 0.50 8.78 C \n"
- + "ATOM 33 CA ALA A 4 26.790 4.320 3.172 1.00 11.98 C \n"
- + "ATOM 39 CA AVAL A 5 24.424 3.853 6.106 0.50 13.83 C \n";
+ + "ATOM 2 CA SER A 7 29.427 3.330 -6.578 1.00 32.50 C \n"
+ + "ATOM 8 CA PRO A 8 29.975 3.340 -2.797 1.00 17.62 C \n"
+ + "ATOM 16 CA ALYS A 9 26.958 3.024 -0.410 0.50 8.78 C \n"
+ + "ATOM 33 CA ALA A 10 26.790 4.320 3.172 1.00 11.98 C \n"
+ + "ATOM 39 CA AVAL A 12 24.424 3.853 6.106 0.50 13.83 C \n";
AAStructureBindingModel testee;
@BeforeMethod(alwaysRun = true)
public void setUp()
{
- SequenceI seq1 = new Sequence("1YCS", "-VPSQK");
+ SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
+ SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
- al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+ al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
al.setDataset(null);
+ /*
+ * give pdb files the name generated by Jalview for PASTE source
+ */
PDBEntry[] pdbFiles = new PDBEntry[3];
- pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "1YCS.pdb");
- pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "3A6S.pdb");
- pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "1OOT.pdb");
+ pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
+ pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
+ pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
String[][] chains = new String[3][];
SequenceI[][] seqs = new SequenceI[3][];
- seqs[0] = new SequenceI[] { seq1 };
+ seqs[0] = new SequenceI[] { seq1a, seq1b };
seqs[1] = new SequenceI[] { seq2 };
seqs[2] = new SequenceI[] { seq3 };
StructureSelectionManager ssm = new StructureSelectionManager();
- ssm.setMapping(new SequenceI[] { seq1 }, null, PDB_1,
+ ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
AppletFormatAdapter.PASTE);
ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
AppletFormatAdapter.PASTE);
@Override
public String[] getPdbFile()
{
- /*
- * fudge 'filenames' to match those generated when PDBFile parses PASTE
- * data
- */
return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
}
@Test(groups = { "Functional" })
public void testFindSuperposableResidues()
{
- SuperposeData[] structs = new SuperposeData[al.getHeight()];
+ /*
+ * create a data bean to hold data per structure file
+ */
+ SuperposeData[] structs = new SuperposeData[testee.getPdbFile().length];
for (int i = 0; i < structs.length; i++)
{
structs[i] = testee.new SuperposeData(al.getWidth());
*/
assertFalse(matched[0]); // gap in first sequence
assertTrue(matched[1]);
- assertFalse(matched[2]); // gap in second sequence
- assertFalse(matched[3]); // gap in third sequence
+ assertFalse(matched[2]); // gap in third sequence
+ assertFalse(matched[3]); // gap in fourth sequence
assertTrue(matched[4]);
- assertTrue(matched[5]);
+ assertTrue(matched[5]); // gap in second sequence
+
+ assertEquals("1YCS", structs[0].pdbId);
+ assertEquals("3A6S", structs[1].pdbId);
+ assertEquals("1OOT", structs[2].pdbId);
+ assertEquals("A", structs[0].chain); // ? struct has chains A _and_ B
+ assertEquals("B", structs[1].chain);
+ assertEquals("A", structs[2].chain);
+ // the 0's for unsuperposable positions propagate down the columns:
+ assertEquals("[0, 97, 98, 99, 100, 102]",
+ Arrays.toString(structs[0].pdbResNo));
+ assertEquals("[0, 2, 0, 3, 4, 5]", Arrays.toString(structs[1].pdbResNo));
+ assertEquals("[0, 8, 0, 0, 10, 12]",
+ Arrays.toString(structs[2].pdbResNo));
}
@Test(groups = { "Functional" })
git://source.jalview.org / jalview.git / commitdiff