X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=f498c1ee5c13b5915cabec4a1e56a8a7da55e466;hb=80b889f0cca49103e1b20ed806755a0719789906;hp=2fe386b2d8ceb0071fa5e20c161522c724bb2c8f;hpb=8546ee20c998cd48567d324027d1885a771e688f;p=jalview.git diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java index 2fe386b..f498c1e 100644 --- a/src/jalview/io/StructureFile.java +++ b/src/jalview/io/StructureFile.java @@ -20,6 +20,12 @@ */ package jalview.io; +import java.awt.Color; +import java.io.IOException; +import java.lang.reflect.Constructor; +import java.util.List; +import java.util.Vector; + import jalview.analysis.AlignSeq; import jalview.api.FeatureSettingsModelI; import jalview.datamodel.Alignment; @@ -31,18 +37,11 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.SequenceI; import jalview.structure.StructureImportSettings; - -import java.awt.Color; -import java.io.IOException; -import java.lang.reflect.Constructor; -import java.util.List; -import java.util.Vector; - -import MCview.PDBChain; +import jalview.structure.StructureImportSettings.TFType; +import mc_view.PDBChain; public abstract class StructureFile extends AlignFile { - private String id; private PDBEntry.Type dbRefType; @@ -67,9 +66,61 @@ public abstract class StructureFile extends AlignFile private Vector chains; - public StructureFile(String inFile, String type) throws IOException + private boolean pdbIdAvailable; + + private StructureImportSettings.TFType temperatureFactorType = TFType.DEFAULT; + + private String paeMatrix = null; + + private boolean alphaFoldModel; + + public void setPAEMatrix(String paeFilename) + { + paeMatrix = paeFilename; + } + + public String getPAEMatrix() + { + return paeMatrix; + } + + public boolean hasPAEMatrix() + { + return paeMatrix != null; + } + + public void setTemperatureFactorType(StructureImportSettings.TFType t) + { + this.temperatureFactorType = t; + } + + public StructureImportSettings.TFType getTemperatureFactorType() { - super(inFile, type); + return temperatureFactorType; + } + + public void setAlphafoldModel(boolean afm) + { + alphaFoldModel = afm; + } + + public boolean isAlphafoldModel() + { + return alphaFoldModel; + } + + public StructureFile(Object inFile, DataSourceType sourceType) + throws IOException + { + this(inFile, sourceType, null); + } + + public StructureFile(Object inFile, DataSourceType sourceType, + StructureImportSettings.TFType tempfacType) throws IOException + { + super(false, inFile, sourceType); + this.setTemperatureFactorType(tempfacType); + doParse(); } public StructureFile(FileParse fp) throws IOException @@ -93,13 +144,14 @@ public abstract class StructureFile extends AlignFile .isProcessSecondaryStructure(); this.externalSecondaryStructure = StructureImportSettings .isExternalSecondaryStructure(); - + this.temperatureFactorType = StructureImportSettings + .getTemperatureFactorType(); } - public StructureFile(boolean parseImmediately, String dataObject, - String type) throws IOException + public StructureFile(boolean parseImmediately, Object dataObject, + DataSourceType sourceType) throws IOException { - super(parseImmediately, dataObject, type); + super(parseImmediately, dataObject, sourceType); } public StructureFile(boolean a, FileParse fp) throws IOException @@ -117,6 +169,7 @@ public abstract class StructureFile extends AlignFile pdbSequence.setName(getId() + "|" + pdbSequence.getName()); PDBEntry entry = new PDBEntry(); entry.setId(getId()); + entry.setFakedPDBId(!isPPDBIdAvailable()); entry.setType(getStructureFileType()); if (chain.id != null) { @@ -189,11 +242,13 @@ public abstract class StructureFile extends AlignFile { // TODO: use the PDB ID of the structure if one is available, to save // bandwidth and avoid uploading the whole structure to the service - Object annotate3d = cl.getConstructor(new Class[] {}).newInstance( - new Object[] {}); - AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", - new Class[] { FileParse.class }).invoke(annotate3d, - new Object[] { new FileParse(getDataName(), type) })); + Object annotate3d = cl.getConstructor(new Class[] {}) + .newInstance(new Object[] {}); + AlignmentI al = ((AlignmentI) cl + .getMethod("getRNAMLFor", new Class[] + { FileParse.class }) + .invoke(annotate3d, new Object[] + { new FileParse(getDataName(), dataSourceType) })); for (SequenceI sq : al.getSequences()) { if (sq.getDatasetSequence() != null) @@ -220,8 +275,8 @@ public abstract class StructureFile extends AlignFile } @SuppressWarnings("unchecked") - protected void replaceAndUpdateChains(List prot, - AlignmentI al, String pep, boolean b) + protected void replaceAndUpdateChains(List prot, AlignmentI al, + String pep, boolean b) { List> replaced = AlignSeq .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep, @@ -286,8 +341,8 @@ public abstract class StructureFile extends AlignFile processWithJmolParser(proteinSequences); } catch (Exception x) { - System.err - .println("Exceptions from Jmol when processing data in pdb file"); + System.err.println( + "Exceptions from Jmol when processing data in pdb file"); x.printStackTrace(); } } @@ -303,9 +358,10 @@ public abstract class StructureFile extends AlignFile if (cl != null) { final Constructor constructor = cl - .getConstructor(new Class[] { FileParse.class }); - final Object[] args = new Object[] { new FileParse(getDataName(), - type) }; + .getConstructor(new Class[] + { FileParse.class }); + final Object[] args = new Object[] { + new FileParse(getDataName(), dataSourceType) }; StructureImportSettings.setShowSeqFeatures(false); StructureImportSettings.setVisibleChainAnnotation(false); @@ -313,9 +369,11 @@ public abstract class StructureFile extends AlignFile .setProcessSecondaryStructure(predictSecondaryStructure); StructureImportSettings .setExternalSecondaryStructure(externalSecondaryStructure); + StructureImportSettings + .setTemperatureFactorType(temperatureFactorType); Object jmf = constructor.newInstance(args); - AlignmentI al = new Alignment((SequenceI[]) cl.getMethod( - "getSeqsAsArray", new Class[] {}).invoke(jmf)); + AlignmentI al = new Alignment((SequenceI[]) cl + .getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf)); cl.getMethod("addAnnotations", new Class[] { AlignmentI.class }) .invoke(jmf, al); for (SequenceI sq : al.getSequences()) @@ -337,7 +395,14 @@ public abstract class StructureFile extends AlignFile StructureImportSettings.setShowSeqFeatures(true); } - public PDBChain findChain(String id) throws Exception + /** + * Answers the first PDBChain found matching the given id, or null if none is + * found + * + * @param id + * @return + */ + public PDBChain findChain(String id) { for (PDBChain chain : getChains()) { @@ -346,7 +411,7 @@ public abstract class StructureFile extends AlignFile return chain; } } - throw new Exception("PDB chain not Found!"); + return null; } public void makeResidueList() @@ -392,8 +457,10 @@ public abstract class StructureFile extends AlignFile public static boolean isRNA(SequenceI seq) { - for (char c : seq.getSequence()) + int length = seq.getLength(); + for (int i = 0; i < length; i++) { + char c = seq.getCharAt(i); if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U')) { return false; @@ -406,7 +473,8 @@ public abstract class StructureFile extends AlignFile * make a friendly ID string. * * @param dataName - * @return truncated dataName to after last '/' + * @return truncated dataName to after last '/' and pruned .extension if + * present */ protected String safeName(String dataName) { @@ -415,6 +483,10 @@ public abstract class StructureFile extends AlignFile { dataName = dataName.substring(p + 1); } + if (dataName.indexOf(".") > -1) + { + dataName = dataName.substring(0, dataName.lastIndexOf(".")); + } return dataName; } @@ -467,4 +539,19 @@ public abstract class StructureFile extends AlignFile { return new PDBFeatureSettings(); } + + /** + * Answers true if the structure file has a PDBId + * + * @return + */ + public boolean isPPDBIdAvailable() + { + return pdbIdAvailable; + } + + public void setPDBIdAvailable(boolean pdbIdAvailable) + { + this.pdbIdAvailable = pdbIdAvailable; + } }