String modalCodon = String.valueOf(CodingUtils
.decodeCodon(modalCodonEncoded));
if (sortedCodonCounts.length > 1
- && sortedCodonCounts[codons.length - 2] == modalCodonEncoded)
+ && sortedCodonCounts[codons.length - 2] == sortedCodonCounts[codons.length - 1])
{
+ /*
+ * two or more codons share the modal count
+ */
modalCodon = "+";
}
float pid = sortedCodonCounts[sortedCodonCounts.length - 1] * 100
public void setVersion(String version);
/**
- *
- * @param startRes
- * index of start residue in the source DB
- */
- public void setStartRes(int startRes);
-
- /**
- *
- * @return index of start residue in the source DB
- */
- public int getStartRes();
-
- /**
- *
- * @param endRes
- * index of end residue in the source DB
- */
- public void setEndRes(int endRes);
-
- /**
- *
- * @return index of end residue in the source DB
- */
- public int getEndRes();
-
- /**
* access a mapping, if present that can be used to map positions from the
* associated dataset sequence to the DBRef's sequence frame.
*
*/
package jalview.bin;
+import jalview.datamodel.PDBEntry;
import jalview.structure.StructureImportSettings;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
-
- private final static String DEFAULT_STRUCTURE_FORMAT = StructureImportSettings.MMCIF;
- private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.JMOL_PARSER;
+ /**
+ * Allowed values are PDB or mmCIF
+ */
+ private final static String DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.MMCIF
+ .toString();
+
+ private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString();
/**
* Initialises the Jalview Application Log
public class DBRefEntry implements DBRefEntryI
{
String source = "", version = "", accessionId = "";
-
- private int startRes, endRes;
/**
* maps from associated sequence to the database sequence's coordinate system
*/
{
return getSrcAccString();
}
-
- @Override
- public int getStartRes()
- {
- return startRes;
- }
-
- @Override
- public void setStartRes(int startRes)
- {
- this.startRes = startRes;
- }
-
- @Override
- public int getEndRes()
- {
- return endRes;
- }
-
- @Override
- public void setEndRes(int endRes)
- {
- this.endRes = endRes;
- }
}
prot.add(chainseq);
}
- if (StructureImportSettings.isPredictSecondaryStructure())
+ if (StructureImportSettings.isProcessSecondaryStructure())
{
createAnnotation(chainseq, chain, ms.at);
}
for (AlignedCodonFrame acf : jac)
{
AlcodonFrame alc = new AlcodonFrame();
- vamsasSet.addAlcodonFrame(alc);
if (acf.getProtMappings() != null
&& acf.getProtMappings().length > 0)
{
+ boolean hasMap = false;
SequenceI[] dnas = acf.getdnaSeqs();
jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
for (int m = 0; m < pmaps.length; m++)
alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
false));
alc.addAlcodMap(alcmap);
+ hasMap = true;
+ }
+ if (hasMap)
+ {
+ vamsasSet.addAlcodonFrame(alc);
}
}
// TODO: delete this ? dead code from 2.8.3->2.9 ?
mapping });
}
}
+ al.addCodonFrame(cf);
}
- al.addCodonFrame(cf);
}
}
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
+import jalview.datamodel.PDBEntry.Type;
import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
// TODO obtain config value from preference settings.
// Set value to 'true' to test PDB processing with Jmol: JAL-1213
boolean isParseWithJMOL = StructureImportSettings
- .getDefaultPDBFileParser().equalsIgnoreCase(
- StructureImportSettings.JMOL_PARSER);
+ .getDefaultPDBFileParser()
+ .equals(StructureImportSettings.StructureParser.JMOL_PARSER);
if (isParseWithJMOL)
{
StructureImportSettings.addSettings(annotFromStructure,
alignFile = new MCview.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);
}
- ((StructureFile) alignFile)
- .setDbRefType(StructureImportSettings.PDB);
+ ((StructureFile) alignFile).setDbRefType(Type.PDB);
}
else if (format.equals("mmCIF"))
{
localSecondaryStruct, serviceSecondaryStruct);
alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);
- ((StructureFile) alignFile)
- .setDbRefType(StructureImportSettings.MMCIF);
+ ((StructureFile) alignFile).setDbRefType(Type.MMCIF);
}
else if (format.equals("STH"))
{
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureImportSettings;
private String id;
- private String dbRefType;
+ private PDBEntry.Type dbRefType;
/**
* set to true to add derived sequence annotations (temp factor read from
this.visibleChainAnnotation = StructureImportSettings
.isVisibleChainAnnotation();
this.predictSecondaryStructure = StructureImportSettings
- .isPredictSecondaryStructure();
+ .isProcessSecondaryStructure();
this.externalSecondaryStructure = StructureImportSettings
.isExternalSecondaryStructure();
DBRefEntry sourceDBRef = new DBRefEntry();
sourceDBRef.setAccessionId(getId());
sourceDBRef.setSource(DBRefSource.PDB);
- sourceDBRef.setStartRes(pdbSequence.getStart());
- sourceDBRef.setEndRes(pdbSequence.getEnd());
pdbSequence.setSourceDBRef(sourceDBRef);
pdbSequence.addPDBId(entry);
pdbSequence.addDBRef(sourceDBRef);
StructureImportSettings.setShowSeqFeatures(false);
StructureImportSettings.setVisibleChainAnnotation(false);
StructureImportSettings
- .setPredictSecondaryStructure(predictSecondaryStructure);
+ .setProcessSecondaryStructure(predictSecondaryStructure);
StructureImportSettings
.setExternalSecondaryStructure(externalSecondaryStructure);
Object jmf = constructor.newInstance(args);
this.chains = chains;
}
- public String getDbRefType()
+ public Type getDbRefType()
{
return dbRefType;
}
public void setDbRefType(String dbRefType)
{
+ this.dbRefType = Type.valueOf(dbRefType);
+ }
+
+ public void setDbRefType(Type dbRefType)
+ {
this.dbRefType = dbRefType;
}
package jalview.structure;
-import jalview.datamodel.DBRefSource;
-
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+
+/**
+ * bean holding settings for structure IO. TODO: tests for validation of values
+ *
+ * @author tcofoegbu
+ *
+ */
public class StructureImportSettings
{
/**
* Set true to predict secondary structure (using JMol for protein, Annotate3D
* for RNA)
*/
- private static boolean predictSecStr = false;
+ private static boolean processSecStr = false;
/**
* Set true (with predictSecondaryStructure=true) to predict secondary
private static boolean showSeqFeatures = true;
- public static final String JMOL_PARSER = "JMolParser";
-
- public static final String JALVIEW_PARSER = "JalViewParser";
-
- public static final String MMCIF = "mmCIF";
+ public enum StructureParser
+ {
+ JMOL_PARSER, JALVIEW_PARSER
+ }
- public static final String PDB = "PDB";
/**
* Determines the default file format for structure files to be downloaded
* from the PDB sequence fetcher. Possible options include: PDB|mmCIF
*/
- private static String defaultStructureFileFormat = DBRefSource.PDB;
+ private static PDBEntry.Type defaultStructureFileFormat = Type.PDB;
/**
* Determines the parser used for parsing PDB format file. Possible options
* are : JMolParser|JalveiwParser
*/
- private static String defaultPDBFileParser = JMOL_PARSER;
+ private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
public static void addSettings(boolean addAlignmentAnnotations,
- boolean predictSecStr, boolean externalSecStr)
+ boolean processSecStr, boolean externalSecStr)
{
StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
- StructureImportSettings.predictSecStr = predictSecStr;
+ StructureImportSettings.processSecStr = processSecStr;
StructureImportSettings.externalSecondaryStructure = externalSecStr;
StructureImportSettings.showSeqFeatures = true;
}
StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
}
- public static boolean isPredictSecondaryStructure()
+ public static boolean isProcessSecondaryStructure()
{
- return predictSecStr;
+ return processSecStr;
}
- public static void setPredictSecondaryStructure(
- boolean predictSecondaryStructure)
+ public static void setProcessSecondaryStructure(
+ boolean processSecondaryStructure)
{
- StructureImportSettings.predictSecStr = predictSecondaryStructure;
+ StructureImportSettings.processSecStr = processSecondaryStructure;
}
public static boolean isExternalSecondaryStructure()
public static String getDefaultStructureFileFormat()
{
- return defaultStructureFileFormat;
+ return defaultStructureFileFormat.toString();
}
public static void setDefaultStructureFileFormat(
String defaultStructureFileFormat)
{
- StructureImportSettings.defaultStructureFileFormat = defaultStructureFileFormat;
+ StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
+ .valueOf(defaultStructureFileFormat);
}
public static String getDefaultPDBFileParser()
{
- return defaultPDBFileParser;
+ return defaultPDBFileParser.toString();
}
- public static void setDefaultPDBFileParser(String defaultPDBFileParser)
+ public static void setDefaultPDBFileParser(
+ StructureParser defaultPDBFileParser)
{
StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
}
+ public static void setDefaultPDBFileParser(String defaultPDBFileParser)
+ {
+ StructureImportSettings.defaultPDBFileParser = StructureParser
+ .valueOf(defaultPDBFileParser);
+ }
+
}
&& !al.getCodonFrames().isEmpty())
{
/*
- * fudge - check first mapping is protein-to-nucleotide
+ * fudge - check first for protein-to-nucleotide mappings
* (we don't want to do this for protein-to-protein)
*/
- AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
- // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
- MapList[] mapLists = mapping.getdnaToProt();
- // mapLists can be empty if project load has not finished resolving seqs
- if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+ boolean doConsensus = false;
+ for (AlignedCodonFrame mapping : al.getCodonFrames())
+ {
+ // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+ MapList[] mapLists = mapping.getdnaToProt();
+ // mapLists can be empty if project load has not finished resolving seqs
+ if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+ {
+ doConsensus = true;
+ break;
+ }
+ }
+ if (doConsensus)
{
if (calculator
.getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
.getCodonFrames();
if (codonMappings != null && !codonMappings.isEmpty())
{
- // fudge: check mappings are not protein-to-protein
- // TODO: nicer
- AlignedCodonFrame mapping = codonMappings.iterator().next();
- MapList[] mapLists = mapping.getdnaToProt();
- // mapLists can be empty if project load has not finished resolving seqs
- if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+ boolean doConsensus = false;
+ for (AlignedCodonFrame mapping : codonMappings)
+ {
+ // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+ MapList[] mapLists = mapping.getdnaToProt();
+ // mapLists can be empty if project load has not finished resolving
+ // seqs
+ if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+ {
+ doConsensus = true;
+ break;
+ }
+ }
+ if (doConsensus)
{
complementConsensus = new AlignmentAnnotation("cDNA Consensus",
"PID for cDNA", new Annotation[1], 0f, 100f,
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
import java.util.List;
return false;
}
+ /**
+ * Calculate min and max values of annotations and set as graphMin, graphMax
+ * on the AlignmentAnnotation. This is needed because otherwise, well, bad
+ * things happen.
+ *
+ * @param ann
+ * @param anns
+ */
+ protected void setGraphMinMax(AlignmentAnnotation ann, Annotation[] anns)
+ {
+ // TODO feels like this belongs inside AlignmentAnnotation!
+ float max = Float.MIN_VALUE;
+ float min = Float.MAX_VALUE;
+ boolean set = false;
+ for (Annotation a : anns) {
+ if (a != null) {
+ set = true;
+ float val = a.value;
+ max = Math.max(max, val);
+ min = Math.min(min, val);
+ }
+ }
+ if (set)
+ {
+ ann.graphMin = min;
+ ann.graphMax = max;
+ }
+ }
+
}
return;
}
- removeAnnotations();
+ // removeAnnotation();
AlignmentI alignment = alignViewport.getAlignment();
if (alignment != null)
{
alignment, new FeatureRenderer(alignViewport));
for (AlignmentAnnotation ann : anns)
{
- ann.showAllColLabels = true;
- ann.graph = AlignmentAnnotation.BAR_GRAPH;
- ourAnnots.add(ann);
- alignment.addAnnotation(ann);
+ AlignmentAnnotation theAnn = alignment.findOrCreateAnnotation(
+ ann.label, ann.description, false, null, null);
+ theAnn.showAllColLabels = true;
+ theAnn.graph = AlignmentAnnotation.BAR_GRAPH;
+ theAnn.scaleColLabel = true;
+ theAnn.annotations = ann.annotations;
+ setGraphMinMax(theAnn, theAnn.annotations);
+ theAnn.validateRangeAndDisplay();
+ if (!ourAnnots.contains(theAnn))
+ {
+ ourAnnots.add(theAnn);
+ }
+ // alignment.addAnnotation(ann);
}
} catch (IndexOutOfBoundsException x)
{
ap.adjustAnnotationHeight();
ap.paintAlignment(true);
}
-
- }
-
- /**
- * Remove all our annotations before re-calculating them
- */
- void removeAnnotations()
- {
- for (AlignmentAnnotation ann : ourAnnots)
- {
- alignViewport.getAlignment().deleteAnnotation(ann);
- }
- ourAnnots.clear();
}
@Override
return;
}
- removeAnnotation();
if (alignViewport.getAlignment() != null)
{
try
{
Color color = ColorUtils.getGraduatedColour(count, 0, Color.cyan,
max, Color.blue);
- anns[i] = new Annotation(String.valueOf(count),
- String.valueOf(count), '0', count, color);
+ String str = String.valueOf(count);
+ anns[i] = new Annotation(str, str, '0', count, color);
}
}
/*
- * construct the annotation, save it and add it to the displayed alignment
+ * construct or update the annotation
*/
- AlignmentAnnotation ann = new AlignmentAnnotation(counter.getName(),
- counter.getDescription(), anns);
+ AlignmentAnnotation ann = alignViewport.getAlignment()
+ .findOrCreateAnnotation(counter.getName(),
+ counter.getDescription(), false, null,
+ null);
+ ann.description = counter.getDescription();
ann.showAllColLabels = true;
ann.scaleColLabel = true;
ann.graph = AlignmentAnnotation.BAR_GRAPH;
- ourAnnots.add(ann);
- alignViewport.getAlignment().addAnnotation(ann);
+ ann.annotations = anns;
+ setGraphMinMax(ann, anns);
+ ann.validateRangeAndDisplay();
+ if (!ourAnnots.contains(ann))
+ {
+ ourAnnots.add(ann);
+ }
}
/**
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
return null;
}
String ext = StructureImportSettings.getDefaultStructureFileFormat()
- .equalsIgnoreCase("mmcif") ? ".cif"
- : ".xml";
+ .equals(Type.MMCIF) ? ".cif" : ".xml";
EBIFetchClient ebi = new EBIFetchClient();
file = ebi.fetchDataAsFile("pdb:" + id,
StructureImportSettings.getDefaultStructureFileFormat().toLowerCase(),
import jalview.io.AppletFormatAdapter;
import jalview.io.FileLoader;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import java.util.Vector;
Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("PDB");
StructureImportSettings
- .setDefaultPDBFileParser(StructureImportSettings.JALVIEW_PARSER);
+ .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
@Test(groups = { "Functional" })
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import java.io.File;
.get(0).getId();
StructureImportSettings.setDefaultStructureFileFormat("PDB");
StructureImportSettings
- .setDefaultPDBFileParser(StructureImportSettings.JALVIEW_PARSER);
+ .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
@Test(groups = { "Functional" })
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.List;
Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("PDB");
StructureImportSettings
- .setDefaultPDBFileParser(StructureImportSettings.JALVIEW_PARSER);
+ .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
testRetrieveProteinSeqFromPDB();
}
// TODO delete when auto-fetching of DBRefEntry is implemented
DBRefEntry dbRef = new DBRefEntry("uniprot", "", "P00221");
- dbRef.setStartRes(1);
- dbRef.setEndRes(147);
testSeq.addDBRef(dbRef);
// testSeq.setSourceDBRef(dbRef);
DBRefEntryI expectedDBRef = new DBRefEntry();
expectedDBRef.setSource(DBRefSource.UNIPROT);
expectedDBRef.setAccessionId("P00221");
- expectedDBRef.setStartRes(1);
- expectedDBRef.setEndRes(147);
expectedDBRef.setVersion("");
Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
} catch (Exception e)
DBRefEntryI validDBRef = new DBRefEntry();
validDBRef.setSource(DBRefSource.UNIPROT);
validDBRef.setAccessionId("P00221");
- validDBRef.setStartRes(1);
- validDBRef.setEndRes(147);
validDBRef.setVersion("");
Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
}
git://source.jalview.org / jalview.git / commitdiff