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Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_...
[jalview.git]
/
src
/
MCview
/
PDBfile.java
diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
6da867d
..
ebc52aa
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-23,10
+23,9
@@
package MCview;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
import jalview.io.DataSourceType;
import jalview.io.DataSourceType;
+import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.io.StructureFile;
-import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
import java.io.IOException;
import jalview.util.MessageManager;
import java.io.IOException;
@@
-49,8
+48,7
@@
public class PDBfile extends StructureFile
public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
boolean externalSecStr, String dataObject,
public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
boolean externalSecStr, String dataObject,
- DataSourceType sourceType)
- throws IOException
+ DataSourceType sourceType) throws IOException
{
super(false, dataObject, sourceType);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
{
super(false, dataObject, sourceType);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
@@
-58,8
+56,7
@@
public class PDBfile extends StructureFile
}
public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
}
public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr,
- FileParse source) throws IOException
+ boolean externalSecStr, FileParse source) throws IOException
{
super(false, source);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
{
super(false, source);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
@@
-67,7
+64,7
@@
public class PDBfile extends StructureFile
}
@Override
}
@Override
- public String print()
+ public String print(SequenceI[] seqs, boolean jvSuffix)
{
return null;
}
{
return null;
}
@@
-134,8
+131,7
@@
public class PDBfile extends StructureFile
break;
}
if (line.indexOf("ATOM") == 0
break;
}
if (line.indexOf("ATOM") == 0
- || (StructureImportSettings.isProcessHETATMs()
- && line.indexOf("HETATM") == 0 && !terFlag))
+ || (line.indexOf("HETATM") == 0 && !terFlag))
{
terFlag = false;
{
terFlag = false;
@@
-149,7
+145,7
@@
public class PDBfile extends StructureFile
Atom tmpatom = new Atom(line);
try
{
Atom tmpatom = new Atom(line);
try
{
- tmpchain = findChain(tmpatom.chain);
+ tmpchain = findChain(tmpatom.chain);
if (tmpatom.resNumIns.trim().equals(lastID))
{
// phosphorylated protein - seen both CA and P..
if (tmpatom.resNumIns.trim().equals(lastID))
{
// phosphorylated protein - seen both CA and P..
@@
-193,9
+189,8
@@
public class PDBfile extends StructureFile
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
- throw new IOException(
- MessageManager
- .getString("exception.outofmemory_loading_pdb_file"));
+ throw new IOException(MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
} catch (NumberFormatException ex)
{
if (line != null)
} catch (NumberFormatException ex)
{
if (line != null)
@@
-207,8
+202,6
@@
public class PDBfile extends StructureFile
markCalcIds();
}
markCalcIds();
}
-
-
/**
* Process a parsed chain to construct and return a Sequence, and add it to
* the list of sequences parsed.
/**
* Process a parsed chain to construct and return a Sequence, and add it to
* the list of sequences parsed.
@@
-233,8
+226,8
@@
public class PDBfile extends StructureFile
public static String relocateCalcId(String calcId,
Hashtable<String, String> alreadyLoadedPDB) throws Exception
{
public static String relocateCalcId(String calcId,
Hashtable<String, String> alreadyLoadedPDB) throws Exception
{
- int s = CALC_ID_PREFIX.length(), end = calcId
- .indexOf(CALC_ID_PREFIX, s);
+ int s = CALC_ID_PREFIX.length(),
+ end = calcId.indexOf(CALC_ID_PREFIX, s);
String between = calcId.substring(s, end - 1);
return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
+ calcId.substring(end);
String between = calcId.substring(s, end - 1);
return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
+ calcId.substring(end);