X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=df384a630526958cd957053da69efb4ddf5c2c06;hb=b19880049cdb11882e68c75d7960465be4aa8665;hp=fc0e207c7c302648c9e29d2f318532ba73c9d205;hpb=82a6c8e2e25b7534168b68b2c89b9cf195f815a5;p=jalview.git
diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index fc0e207..df384a6 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -1,5 +1,32 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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;
@@ -10,20 +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;
@@ -48,14 +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()
{
- super(inFile, type);
+ 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(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,
@@ -68,19 +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
@@ -92,18 +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.setType(this.dbRefType);
- entry.setProperty(new Hashtable());
+ entry.setFakedPDBId(!isPPDBIdAvailable());
+ entry.setType(getStructureFileType());
if (chain.id != null)
{
- entry.setChainCode(String.valueOf(chain.id));
+ entry.setChainCode(chain.id);
}
if (inFile != null)
{
@@ -117,7 +198,9 @@ public abstract class StructureFile extends AlignFile
DBRefEntry sourceDBRef = new DBRefEntry();
sourceDBRef.setAccessionId(getId());
sourceDBRef.setSource(DBRefSource.PDB);
- pdbSequence.setSourceDBRef(sourceDBRef);
+ // TODO: specify version for 'PDB' database ref if it is read from a file.
+ // TODO: decide if jalview.io should be creating primary refs!
+ sourceDBRef.setVersion("");
pdbSequence.addPDBId(entry);
pdbSequence.addDBRef(sourceDBRef);
SequenceI chainseq = pdbSequence;
@@ -135,11 +218,31 @@ public abstract class StructureFile extends AlignFile
return chainseq;
}
+ /**
+ * filetype of structure file - default is PDB
+ */
+ String structureFileType = PDBEntry.Type.PDB.toString();
+
+ protected void setStructureFileType(String structureFileType)
+ {
+ this.structureFileType = structureFileType;
+ }
+
+ /**
+ * filetype of last file processed
+ *
+ * @return
+ */
+ public String getStructureFileType()
+ {
+ return structureFileType;
+ }
+
@SuppressWarnings({ "unchecked", "rawtypes" })
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
@@ -150,11 +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)
@@ -181,8 +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,
@@ -231,7 +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();
}
@@ -244,62 +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[] {
- boolean.class, boolean.class, boolean.class, FileParse.class });
- final Object[] args = new Object[] { visibleChainAnnotation,
- predictSecondaryStructure, externalSecondaryStructure,
- 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())
{
@@ -308,7 +405,7 @@ public abstract class StructureFile extends AlignFile
return chain;
}
}
- throw new Exception("PDB chain not Found!");
+ return null;
}
public void makeResidueList()
@@ -354,8 +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;
@@ -368,7 +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)
{
@@ -377,6 +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;
}
@@ -407,7 +511,7 @@ public abstract class StructureFile extends AlignFile
public void setDbRefType(String dbRefType)
{
- this.dbRefType = Type.valueOf(dbRefType);
+ this.dbRefType = Type.getType(dbRefType);
}
public void setDbRefType(Type dbRefType)
@@ -429,4 +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;
+ }
}