*/
package jalview.ext.jmol;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-
import java.awt.Color;
import java.awt.Container;
import java.awt.event.ComponentEvent;
import java.net.URL;
import java.security.AccessControlException;
import java.util.Hashtable;
+import java.util.List;
import java.util.Map;
import java.util.Vector;
import org.jmol.constant.EnumCallback;
import org.jmol.popup.JmolPopup;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
return;
}
- int index;
- Color col;
jmolHistory(false);
- // TODO: Switch between nucleotide or aa selection expressions
StringBuilder command = new StringBuilder(128);
command.append("select *;color white;");
- for (String res : ResidueProperties.aa3Hash.keySet())
+ List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
+ false);
+ for (String res : residueSet)
{
- index = ResidueProperties.aa3Hash.get(res).intValue();
- if (index > 20)
- {
- continue;
- }
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
+ Color col = cs.findColour(res.charAt(0));
command.append("select " + res + ";color[" + col.getRed() + ","
+ col.getGreen() + "," + col.getBlue() + "];");
}
return;
}
- int index;
- Color col;
// Chimera expects RBG values in the range 0-1
final double normalise = 255D;
viewerCommandHistory(false);
- // TODO: Switch between nucleotide or aa selection expressions
StringBuilder command = new StringBuilder(128);
- command.append("color white;");
- for (String res : ResidueProperties.aa3Hash.keySet())
- {
- index = ResidueProperties.aa3Hash.get(res).intValue();
- if (index > 20)
- {
- continue;
- }
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
+ List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
+ false);
+ for (String res : residueSet)
+ {
+ Color col = cs.findColour(res.charAt(0));
command.append("color " + col.getRed() / normalise + ","
+ col.getGreen() / normalise + "," + col.getBlue()
/ normalise + " ::" + res + ";");
*/
package jalview.schemes;
-import jalview.analysis.scoremodels.FeatureScoreModel;
-import jalview.analysis.scoremodels.PIDScoreModel;
-import jalview.api.analysis.ScoreModelI;
-
import java.awt.Color;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Map;
import java.util.Vector;
+import jalview.analysis.scoremodels.FeatureScoreModel;
+import jalview.analysis.scoremodels.PIDScoreModel;
+import jalview.api.analysis.ScoreModelI;
+
public class ResidueProperties
{
public static Hashtable<String, ScoreModelI> scoreMatrices = new Hashtable();
}
// to here
+ /**
+ * Returns a list of residue characters for the specified inputs
+ *
+ * @param nucleotide
+ * @param includeAmbiguous
+ * @return
+ */
+ public static List<String> getResidues(boolean nucleotide,
+ boolean includeAmbiguous)
+ {
+ List<String> result = new ArrayList<String>();
+ if (nucleotide)
+ {
+ for (String nuc : nucleotideName.keySet())
+ {
+ int val = nucleotideIndex[nuc.charAt(0)];
+ if ((!includeAmbiguous && val > 4) || (val >= maxNucleotideIndex))
+ {
+ continue;
+ }
+ nuc = nuc.toUpperCase();
+ if (!result.contains(nuc))
+ {
+ result.add(nuc);
+ }
+ }
+ } else {
+ /*
+ * Peptide
+ */
+ for (String res : aa3Hash.keySet())
+ {
+ int index = aa3Hash.get(res).intValue();
+ if ((!includeAmbiguous && index >= 20) || index >= maxProteinIndex)
+ {
+ continue;
+ }
+ res = res.toUpperCase();
+ if (!result.contains(res))
+ {
+ result.add(res);
+ }
+ }
+ }
+
+ return result;
+ }
+
}
package jalview.structures.models;
+import java.util.ArrayList;
+import java.util.List;
+
import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
-import java.util.ArrayList;
-import java.util.List;
-
/**
*
* A base class to hold common function for protein structure model binding.
protected boolean colourBySequence = true;
+ private boolean nucleotide;
+
/**
* Constructor
*
{
this.ssm = ssm;
this.sequence = sequenceIs;
+ this.nucleotide = Comparison.isNucleotide(sequenceIs);
this.chains = chains;
this.pdbEntry = pdbentry;
this.protocol = protocol;
}
}
- // TODO Jmol and Chimera seem to expect pdbFile, javascript listener pdbId
protected abstract void highlightAtom(int atomIndex, int pdbResNum,
String chain, String pdbFile);
+ protected boolean isNucleotide()
+ {
+ return this.nucleotide;
+ }
}
\ No newline at end of file
*/
package jalview.util;
+import java.util.ArrayList;
+import java.util.List;
+
import jalview.datamodel.SequenceI;
/**
/**
* Answers true if more than 85% of the sequence residues (ignoring gaps) are
* A, G, C, T or U, else false. This is just a heuristic guess and may give a
- * wrong answer (as AGCT are also animo acid codes).
+ * wrong answer (as AGCT are also amino acid codes).
*
* @param seqs
* @return
int aaCount = 0;
for (SequenceI seq : seqs)
{
+ if (seq == null)
+ {
+ continue;
+ }
+ // TODO could possibly make an informed guess just from the first sequence
+ // to save a lengthy calculation
for (char c : seq.getSequence())
{
if ('a' <= c && c <= 'z')
}
}
+
+ /**
+ * Convenience overload of isNucleotide
+ *
+ * @param seqs
+ * @return
+ */
+ public static boolean isNucleotide(SequenceI[][] seqs)
+ {
+ if (seqs == null)
+ {
+ return false;
+ }
+ List<SequenceI> flattened = new ArrayList<SequenceI>();
+ for (SequenceI[] ss : seqs)
+ {
+ for (SequenceI s : ss) {
+ flattened.add(s);
+ }
+ }
+ final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened.size()]);
+ return isNucleotide(oneDArray);
+ }
}
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
+import java.util.Collections;
+import java.util.List;
+
import org.junit.Test;
public class ResiduePropertiesTest
assertNull(ResidueProperties.codonTranslate("VHD"));
assertNull(ResidueProperties.codonTranslate("WSK"));
}
+
+ @Test
+ public void testGetResidues_nucleotide()
+ {
+ /*
+ * Non-ambiguous only; we don't care about the order of the list, it is just
+ * sorted here to make assertions reliable
+ */
+ List<String> residues = ResidueProperties.getResidues(true, false);
+ Collections.sort(residues);
+ assertEquals("[A, C, G, T, U]", residues.toString());
+
+ /*
+ * Including ambiguity codes I N R X Y
+ */
+ residues = ResidueProperties.getResidues(true, true);
+ Collections.sort(residues);
+ assertEquals("[A, C, G, I, N, R, T, U, X, Y]", residues.toString());
+ }
+
+ @Test
+ public void testGetResidues_peptide()
+ {
+ /*
+ * Non-ambiguous only; we don't care about the order of the list, it is just
+ * sorted here to make assertions reliable
+ */
+ List<String> residues = ResidueProperties.getResidues(false, false);
+ Collections.sort(residues);
+ assertEquals(
+ "[ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL]",
+ residues.toString());
+
+ /*
+ * Including ambiguity codes ASX, GLX, XAA
+ */
+ residues = ResidueProperties.getResidues(false, true);
+ Collections.sort(residues);
+ assertEquals(
+ "[ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLX, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, XAA]",
+ residues.toString());
+ }
}
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
import org.junit.Test;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
public class ComparisonTest
{
SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
assertFalse(Comparison.isNucleotide(new SequenceI[]
{ seq }));
+ assertFalse(Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[]
+ { seq } }));
seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
assertFalse(Comparison.isNucleotide(new SequenceI[]
seq = new Sequence("DNA", "ACTugGCCAG");
SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
+ /*
+ * 90% DNA:
+ */
assertTrue(Comparison.isNucleotide(new SequenceI[]
- { seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 })); // 90% DNA
+ { seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 }));
+ assertTrue(Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[]
+ { seq }, new SequenceI[]
+ { seq, seq, seq }, new SequenceI[]
+ { seq, seq, seq, seq, seq, seq2 } }));
+ /*
+ * 80% DNA:
+ */
assertFalse(Comparison.isNucleotide(new SequenceI[]
- { seq, seq, seq, seq, seq, seq, seq, seq, seq2, seq2 })); // 80% DNA
+ { seq, seq, seq, seq, seq, seq, seq, seq, seq2, seq2 }));
+ assertFalse(Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[]
+ { seq }, new SequenceI[]
+ { seq, seq, seq }, new SequenceI[]
+ { seq, seq, seq, seq, seq2, seq2, null } }));
seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
// 12/14 = 85.7%
assertTrue(Comparison.isNucleotide(new SequenceI[]
{ seq }));
- assertFalse(Comparison.isNucleotide(null));
+ assertFalse(Comparison.isNucleotide((SequenceI[]) null));
+ assertFalse(Comparison.isNucleotide((SequenceI[][]) null));
}
/**
git://source.jalview.org / jalview.git / commitdiff