X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FStructureFile.java;h=7fe17c8d3d6c9bf9a096a98615213ec8cea3d593;hb=84724ad7b25f65eb6009f70d9b4cb89fc6796622;hp=b2e5b23de9b81f036b07fbb54b6ef9ecf759265b;hpb=08c202dd3ef0f34bde305c11da9eec03520174dc;p=jalview.git
diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index b2e5b23..7fe17c8 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -1,3 +1,23 @@
+/*
+ * 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 jalview.analysis.AlignSeq;
@@ -8,13 +28,13 @@ import jalview.datamodel.AlignmentI;
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;
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;
@@ -22,10 +42,9 @@ import MCview.PDBChain;
public abstract class StructureFile extends AlignFile
{
-
private String id;
- private String dbRefType;
+ private PDBEntry.Type dbRefType;
/**
* set to true to add derived sequence annotations (temp factor read from
@@ -47,9 +66,12 @@ public abstract class StructureFile extends AlignFile
private Vector chains;
- public StructureFile(String inFile, String type) throws IOException
+ private boolean pdbIdAvailable;
+
+ public StructureFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public StructureFile(FileParse fp) throws IOException
@@ -76,10 +98,10 @@ public abstract class StructureFile extends AlignFile
}
- public StructureFile(boolean parseImmediately, String dataObject, String type)
- throws IOException
+ public StructureFile(boolean parseImmediately, String dataObject,
+ DataSourceType sourceType) throws IOException
{
- super(parseImmediately, dataObject, type);
+ super(parseImmediately, dataObject, sourceType);
}
public StructureFile(boolean a, FileParse fp) throws IOException
@@ -91,18 +113,16 @@ 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.setType(getStructureFileType());
if (chain.id != null)
{
- entry.setChainCode(String.valueOf(chain.id));
+ entry.setChainCode(chain.id);
}
if (inFile != null)
{
@@ -116,7 +136,9 @@ 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;
@@ -134,6 +156,26 @@ 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
@@ -153,7 +195,7 @@ public abstract class StructureFile extends AlignFile
new Object[] {});
AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
new Class[] { FileParse.class }).invoke(annotate3d,
- new Object[] { new FileParse(getDataName(), type) }));
+ new Object[] { new FileParse(getDataName(), dataSourceType) }));
for (SequenceI sq : al.getSequences())
{
if (sq.getDatasetSequence() != null)
@@ -262,11 +304,8 @@ public abstract class StructureFile extends AlignFile
Class cl = Class.forName("jalview.ext.jmol.JmolParser");
if (cl != 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) };
+ final Constructor constructor = cl.getConstructor(new Class[] {FileParse.class });
+ final Object[] args = new Object[] { new FileParse(getDataName(), dataSourceType) };
StructureImportSettings.setShowSeqFeatures(false);
StructureImportSettings.setVisibleChainAnnotation(false);
@@ -399,13 +438,18 @@ public abstract class StructureFile extends AlignFile
this.chains = chains;
}
- public String getDbRefType()
+ public Type getDbRefType()
{
return dbRefType;
}
public void setDbRefType(String dbRefType)
{
+ this.dbRefType = Type.getType(dbRefType);
+ }
+
+ public void setDbRefType(Type dbRefType)
+ {
this.dbRefType = dbRefType;
}
@@ -423,4 +467,19 @@ 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;
+ }
}