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Merge branch 'develop' into features/JAL-250_hideredundantseqs
[jalview.git]
/
src
/
MCview
/
PDBfile.java
diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
6d3d342
..
ebc52aa
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-48,8
+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);
@@
-190,9
+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)
@@
-228,8
+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);