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Merge branch 'develop' into trial_merge/JAL-1950
[jalview.git]
/
src
/
jalview
/
ext
/
jmol
/
JmolParser.java
diff --git
a/src/jalview/ext/jmol/JmolParser.java
b/src/jalview/ext/jmol/JmolParser.java
index
b2ba256
..
dc3d0ee
100644
(file)
--- a/
src/jalview/ext/jmol/JmolParser.java
+++ b/
src/jalview/ext/jmol/JmolParser.java
@@
-24,6
+24,7
@@
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
@@
-38,8
+39,6
@@
import java.util.List;
import java.util.Map;
import java.util.Vector;
import java.util.Map;
import java.util.Vector;
-import javajs.awt.Dimension;
-
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
@@
-61,9
+60,10
@@
public class JmolParser extends StructureFile implements JmolStatusListener
{
Viewer viewer = null;
{
Viewer viewer = null;
- public JmolParser(String inFile, String type) throws IOException
+ public JmolParser(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public JmolParser(FileParse fp) throws IOException
}
public JmolParser(FileParse fp) throws IOException
@@
-105,8
+105,9
@@
public class JmolParser extends StructureFile implements JmolStatusListener
// }
// ;
// instead, we distinguish .cif from non-.cif by filename
// }
// ;
// instead, we distinguish .cif from non-.cif by filename
- setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF
- .toString() : "PDB");
+ setStructureFileType(getDataName().toLowerCase().endsWith(".cif")
+ ? PDBEntry.Type.MMCIF.toString()
+ : "PDB");
transformJmolModelToJalview(jmolModel.ms);
}
transformJmolModelToJalview(jmolModel.ms);
}
@@
-135,7
+136,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
{
throw new Error(MessageManager.formatMessage(
"error.jmol_version_not_compatible_with_jalview_version",
{
throw new Error(MessageManager.formatMessage(
"error.jmol_version_not_compatible_with_jalview_version",
- new String[] { JmolViewer.getJmolVersion() }), x);
+ new String[]
+ { JmolViewer.getJmolVersion() }), x);
}
}
return viewer;
}
}
return viewer;
@@
-205,11
+207,10
@@
public class JmolParser extends StructureFile implements JmolStatusListener
}
} catch (OutOfMemoryError er)
{
}
} catch (OutOfMemoryError er)
{
- System.out
- .println("OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
- throw new IOException(
- MessageManager
- .getString("exception.outofmemory_loading_mmcif_file"));
+ System.out.println(
+ "OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
+ throw new IOException(MessageManager
+ .getString("exception.outofmemory_loading_mmcif_file"));
}
}
}
}
@@
-236,8
+237,9
@@
public class JmolParser extends StructureFile implements JmolStatusListener
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
curAtom.resNumber = atom.getResno();
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
curAtom.resNumber = atom.getResno();
- curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
- .getIndex()] : Float.valueOf(atom.getOccupancy100());
+ curAtom.occupancy = ms.occupancies != null
+ ? ms.occupancies[atom.getIndex()]
+ : Float.valueOf(atom.getOccupancy100());
String fmt = new Format("%4i").form(curAtom.resNumber);
curAtom.resNumIns = (fmt + curAtom.insCode);
curAtom.tfactor = atom.getBfactor100() / 100f;
String fmt = new Format("%4i").form(curAtom.resNumber);
curAtom.resNumIns = (fmt + curAtom.insCode);
curAtom.tfactor = atom.getBfactor100() / 100f;
@@
-259,7
+261,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
HashMap<String, org.jmol.modelset.Atom> chainTerMap)
{
// System.out.println("Atom: " + curAtom.getAtomNumber()
HashMap<String, org.jmol.modelset.Atom> chainTerMap)
{
// System.out.println("Atom: " + curAtom.getAtomNumber()
- // + " Last atom index " + curAtom.group.lastAtomIndex);
+ // + " Last atom index " + curAtom.group.lastAtomIndex);
if (chainTerMap == null || prevAtom == null)
{
return true;
if (chainTerMap == null || prevAtom == null)
{
return true;
@@
-282,7
+284,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
{
return false;
}
{
return false;
}
- if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+ if ((curAtom.getResno()
+ - chainTerMap.get(curAtomChId).getResno()) < 5)
{
chainTerMap.put(curAtomChId, curAtom);
return true;
{
chainTerMap.put(curAtomChId, curAtom);
return true;
@@
-297,7
+300,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
{
return false;
}
{
return false;
}
- if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+ if ((curAtom.getResno()
+ - chainTerMap.get(curAtomChId).getResno()) < 5)
{
chainTerMap.put(curAtomChId, curAtom);
return true;
{
chainTerMap.put(curAtomChId, curAtom);
return true;
@@
-305,8
+309,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
return false;
}
// HETATM with resNum jump > 2
return false;
}
// HETATM with resNum jump > 2
- return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
- .getResno()) > 2));
+ return !(curAtom.isHetero()
+ && ((curAtom.getResno() - prevAtom.getResno()) > 2));
}
private void createAnnotation(SequenceI sequence, PDBChain chain,
}
private void createAnnotation(SequenceI sequence, PDBChain chain,
@@
-351,10
+355,10
@@
public class JmolParser extends StructureFile implements JmolStatusListener
SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
int firstResNum)
{
SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
int firstResNum)
{
- char[] seq = sq.getSequence();
+ int length = sq.getLength();
boolean ssFound = false;
boolean ssFound = false;
- Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
- for (int p = 0; p < seq.length; p++)
+ Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+ for (int p = 0; p < length; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
{
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
{
@@
-411,8
+415,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
* @param secstr
* @param secstrcode
*/
* @param secstr
* @param secstrcode
*/
- protected void setSecondaryStructure(STR proteinStructureSubType,
- int pos, char[] secstr, char[] secstrcode)
+ protected void setSecondaryStructure(STR proteinStructureSubType, int pos,
+ char[] secstr, char[] secstrcode)
{
switch (proteinStructureSubType)
{
{
switch (proteinStructureSubType)
{
@@
-472,7
+476,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
* Not implemented - returns null
*/
@Override
* Not implemented - returns null
*/
@Override
- public String print()
+ public String print(SequenceI[] seqs, boolean jvSuffix)
{
return null;
}
{
return null;
}
@@
-489,8
+493,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
@Override
public void notifyCallback(CBK cbType, Object[] data)
{
@Override
public void notifyCallback(CBK cbType, Object[] data)
{
- String strInfo = (data == null || data[1] == null ? null : data[1]
- .toString());
+ String strInfo = (data == null || data[1] == null ? null
+ : data[1].toString());
switch (cbType)
{
case ECHO:
switch (cbType)
{
case ECHO:
@@
-590,7
+594,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
* Not implemented - returns null
*/
@Override
* Not implemented - returns null
*/
@Override
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ public float[][][] functionXYZ(String functionName, int nx, int ny,
+ int nz)
{
return null;
}
{
return null;
}
@@
-626,7
+631,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
* Not implemented - returns null
*/
@Override
* Not implemented - returns null
*/
@Override
- public Dimension resizeInnerPanel(String data)
+ public int[] resizeInnerPanel(String data)
{
return null;
}
{
return null;
}
@@
-642,7
+647,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
return predictSecondaryStructure;
}
return predictSecondaryStructure;
}
- public void setPredictSecondaryStructure(boolean predictSecondaryStructure)
+ public void setPredictSecondaryStructure(
+ boolean predictSecondaryStructure)
{
this.predictSecondaryStructure = predictSecondaryStructure;
}
{
this.predictSecondaryStructure = predictSecondaryStructure;
}