X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=df384a630526958cd957053da69efb4ddf5c2c06;hb=c932f0e85a8852824cdd8ce790af68682732c85c;hp=61a9b484da431e40c4d645a82a37a9f4f224a70a;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java index 61a9b48..df384a6 100644 --- a/src/jalview/io/StructureFile.java +++ b/src/jalview/io/StructureFile.java @@ -20,6 +20,13 @@ */ package jalview.io; +import java.awt.Color; +import java.io.IOException; +import java.lang.reflect.Constructor; +import java.net.MalformedURLException; +import java.util.List; +import java.util.Vector; + import jalview.analysis.AlignSeq; import jalview.api.FeatureSettingsModelI; import jalview.datamodel.Alignment; @@ -30,20 +37,13 @@ import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.SequenceI; +import jalview.ext.jmol.JmolParser; import jalview.structure.StructureImportSettings; - -import java.awt.Color; -import java.io.IOException; -import java.lang.reflect.Constructor; -import java.util.Hashtable; -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; @@ -68,14 +68,72 @@ public abstract class StructureFile extends AlignFile private Vector chains; - public StructureFile(String inFile, String type) throws IOException + private boolean pdbIdAvailable; + + private 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(TFType t) + { + this.temperatureFactorType = t; + } + + public TFType getTemperatureFactorType() + { + 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, + TFType tempfacType) throws IOException { - super(inFile, type); + super(false, inFile, sourceType); + this.setTemperatureFactorType(tempfacType); + doParse(); } public StructureFile(FileParse fp) throws IOException { - super(fp); + this(fp, true); + } + + public StructureFile(FileParse fp, boolean doXferSettings) + throws IOException + { + super(fp, doXferSettings); } public void addSettings(boolean addAlignmentAnnotations, @@ -88,19 +146,23 @@ public abstract class StructureFile extends AlignFile public void xferSettings() { - this.visibleChainAnnotation = StructureImportSettings - .isVisibleChainAnnotation(); - this.predictSecondaryStructure = StructureImportSettings - .isProcessSecondaryStructure(); - this.externalSecondaryStructure = StructureImportSettings - .isExternalSecondaryStructure(); - + if (this.getDoXferSettings()) + { + this.visibleChainAnnotation = StructureImportSettings + .isVisibleChainAnnotation(); + this.predictSecondaryStructure = StructureImportSettings + .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 @@ -112,18 +174,17 @@ public abstract class StructureFile extends AlignFile { } - @SuppressWarnings("rawtypes") protected SequenceI postProcessChain(PDBChain chain) { SequenceI pdbSequence = chain.sequence; pdbSequence.setName(getId() + "|" + pdbSequence.getName()); PDBEntry entry = new PDBEntry(); entry.setId(getId()); + entry.setFakedPDBId(!isPPDBIdAvailable()); entry.setType(getStructureFileType()); - entry.setProperty(new Hashtable()); if (chain.id != null) { - entry.setChainCode(String.valueOf(chain.id)); + entry.setChainCode(chain.id); } if (inFile != null) { @@ -181,7 +242,7 @@ public abstract class StructureFile extends AlignFile protected void processPdbFileWithAnnotate3d(List rna) throws Exception { - // System.out.println("this is a PDB format and RNA sequence"); + // jalview.bin.Console.outPrintln("this is a PDB format and RNA sequence"); // note: we use reflection here so that the applet can compile and run // without the HTTPClient bits and pieces needed for accessing Annotate3D // web service @@ -192,11 +253,13 @@ 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) @@ -223,8 +286,8 @@ 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, @@ -273,7 +336,7 @@ public abstract class StructureFile extends AlignFile processPdbFileWithAnnotate3d(rnaSequences); } catch (Exception x) { - System.err.println("Exceptions when dealing with RNA in pdb file"); + jalview.bin.Console.errPrintln("Exceptions when dealing with RNA in pdb file"); x.printStackTrace(); } @@ -286,61 +349,54 @@ public abstract class StructureFile extends AlignFile { try { - processWithJmolParser(proteinSequences); + processWithJmolParser(proteinSequences, true); } catch (Exception x) { - System.err - .println("Exceptions from Jmol when processing data in pdb file"); + jalview.bin.Console.errPrintln( + "Exceptions from Jmol when processing data in pdb file"); x.printStackTrace(); } } } - @SuppressWarnings({ "unchecked", "rawtypes" }) - private void processWithJmolParser(List prot) throws Exception + private void processWithJmolParser(List prot, + boolean doXferSettings) throws MalformedURLException, IOException { - try + FileParse fp = new FileParse(getDataName(), dataSourceType); + + StructureImportSettings.setShowSeqFeatures(false); + StructureImportSettings.setVisibleChainAnnotation(false); + StructureImportSettings + .setProcessSecondaryStructure(predictSecondaryStructure); + StructureImportSettings + .setExternalSecondaryStructure(externalSecondaryStructure); + StructureImportSettings.setTemperatureFactorType(temperatureFactorType); + JmolParser jmf = new JmolParser(fp, doXferSettings); + AlignmentI al = new Alignment((SequenceI[]) jmf.getSeqsAsArray()); + jmf.addAnnotations(al); + for (SequenceI sq : al.getSequences()) { - - Class cl = Class.forName("jalview.ext.jmol.JmolParser"); - if (cl != null) + if (sq.getDatasetSequence() != null) { - final Constructor constructor = cl - .getConstructor(new Class[] { FileParse.class }); - final Object[] args = new Object[] { new FileParse(getDataName(), - type) }; - - StructureImportSettings.setShowSeqFeatures(false); - StructureImportSettings.setVisibleChainAnnotation(false); - StructureImportSettings - .setProcessSecondaryStructure(predictSecondaryStructure); - StructureImportSettings - .setExternalSecondaryStructure(externalSecondaryStructure); - Object jmf = constructor.newInstance(args); - 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()) - { - if (sq.getDatasetSequence() != null) - { - sq.getDatasetSequence().getAllPDBEntries().clear(); - } - else - { - sq.getAllPDBEntries().clear(); - } - } - replaceAndUpdateChains(prot, al, AlignSeq.PEP, false); + sq.getDatasetSequence().getAllPDBEntries().clear(); + } + else + { + sq.getAllPDBEntries().clear(); } - } catch (ClassNotFoundException q) - { } + replaceAndUpdateChains(prot, al, AlignSeq.PEP, false); 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()) { @@ -349,7 +405,7 @@ public abstract class StructureFile extends AlignFile return chain; } } - throw new Exception("PDB chain not Found!"); + return null; } public void makeResidueList() @@ -395,8 +451,10 @@ 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; @@ -409,7 +467,8 @@ 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) { @@ -418,6 +477,10 @@ public abstract class StructureFile extends AlignFile { dataName = dataName.substring(p + 1); } + if (dataName.indexOf(".") > -1) + { + dataName = dataName.substring(0, dataName.lastIndexOf(".")); + } return dataName; } @@ -470,4 +533,19 @@ 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; + } }